Biography
I am a computational and molecular biologist with research interests in transposable elements, single-cell genomics and neuroscience. In 2009, I published a first-author Nature Genetics paper describing the transcriptional activity and domestication of mammalian repetitive elements (>500 citations). In the same year, I finished a PhD at the University of Queensland, and was awarded an NHMRC C.J. Martin Fellowship to undertake postdoctoral work at the University of Edinburgh. Whilst in Edinburgh I published Baillie et al. (Nature, 2011). Fulfilling the terms of the C.J. Martin Fellowship, I established my group to the Mater Research Institute – University of Queensland (MRI-UQ) in 2012. I subsequently obtained grant funding from the NIH and NHMRC, including an NHMRC Career Development Fellowship, and published Shukla et al. (Cell, 2013) and Upton et al. (Cell, 2015). I was awarded an NHMRC Research Fellowship (SRFB) in 2016 and a prestigious CSL Centenary Fellowship in 2017. I was promoted to full Professor (Level E) by the University of Queensland in 2016.
To date, I have published 52 peer-reviewed articles, book chapters and reviews (>11,000 citations, h-index 32). 24 of these are as first or last author, including Faulkner et al. (Nature Genetics, 2009), as well as other work published in Nature, Science, Cell, AJHG, NAR, Nature Communications, PNAS, Nature Genetics, Nature Methods, Genome Biology and Genome Research. I have published 3 landmark papers in Nature and Cell as last and sole corresponding author. These papers significantly advanced the somatic L1 mosaicism field. I have written 11 invited reviews, including works in Genome Biology, The Journal of Neuroscience, Annual Reviews Genetics, PLoS Genetics, Trends in Genetics and BioEssays.
I have enjoyed continuous NHMRC fellowship support since 2009 (C.J. Martin 2009-2013; CDF1 2013-2015; SRFB 2016-2020). Baillie et al. (Nature, 2011) was named by the US National Institute of Mental Health as the “No. 1 research advance of 2011”. Baillie et al. (Nature, 2011), Shukla et al. (Cell, 2013) and Upton et al. (Cell, 2015) were highlighted by Faculty of 1000. I am the recipient of the ASMR Queensland Premier’s Award (2009), the FEBS Anniversary Prize (2011) awarded to “the top molecular geneticist in Europe aged <40yrs”, the Lorne Genome Millennium Science Award (2014) for “outstanding contributions to Australian scientific research”, the Centenary Institute Lawrence Creative Prize (2014) “awarded for creative biomedical research excellence”, the Ruth Stephens Gani Medal by the Australian Academy of Science (2016), the Scopus Eureka Prize for Excellence in International Scientific Collaboration (2016) and a CSL Centenary Fellowship (2017).
Qualifications:
PhD, University of Queensland, 2009
BSc (First Class Honours), University of Queensland, 2004
Research Links:
- Mobile DNA journal: http://mobilednajournal.biomedcentral.com
- LinkedIn:
- ResearchGate:
- TRI link:
Publications:
2019 | |
Salvador-Palomeque, Carmen; Sanchez-Luque, Francisco J; Fortuna, Patrick R J; Ewing, Adam D; Wolvetang, Ernst J; Richardson, Sandra R; Faulkner, Geoffrey J Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation (Journal Article) Mol Cell Biol, 39 (7), 2019, ISSN: 0270-7306. (Abstract | Links | BibTeX | Altmetric) @article{salvador-palomeque_dynamic_2019, title = {Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation}, author = {Carmen Salvador-Palomeque and Francisco J Sanchez-Luque and Patrick R J Fortuna and Adam D Ewing and Ernst J Wolvetang and Sandra R Richardson and Geoffrey J Faulkner}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425141/}, doi = {10.1128/MCB.00499-18}, issn = {0270-7306}, year = {2019}, date = {2019-01-01}, urldate = {2019-06-07}, journal = {Mol Cell Biol}, volume = {39}, number = {7}, abstract = {The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells., The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells. L1 retrotransposition can also occur in the neuronal lineage and cause somatic mosaicism. Although DNA methylation mediates L1 promoter repression, the temporal pattern of methylation applied to individual RC-L1s during neurogenesis is unclear. Here, we identified a de novo L1 insertion in a human induced pluripotent stem cell (hiPSC) line via retrotransposon capture sequencing (RC-seq). The L1 insertion was full-length and carried 5ʹ and 3ʹ transductions. The corresponding donor RC-L1 was part of a large and recently active L1 transduction family and was highly mobile in a cultured-cell L1 retrotransposition reporter assay. Notably, we observed distinct and dynamic DNA methylation profiles for the de novo L1 and members of its extended transduction family during neuronal differentiation. These experiments reveal how a de novo L1 insertion in a pluripotent stem cell is rapidly recognized and repressed, albeit incompletely, by the host genome during neurodifferentiation, while retaining potential for further retrotransposition.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells., The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells. L1 retrotransposition can also occur in the neuronal lineage and cause somatic mosaicism. Although DNA methylation mediates L1 promoter repression, the temporal pattern of methylation applied to individual RC-L1s during neurogenesis is unclear. Here, we identified a de novo L1 insertion in a human induced pluripotent stem cell (hiPSC) line via retrotransposon capture sequencing (RC-seq). The L1 insertion was full-length and carried 5ʹ and 3ʹ transductions. The corresponding donor RC-L1 was part of a large and recently active L1 transduction family and was highly mobile in a cultured-cell L1 retrotransposition reporter assay. Notably, we observed distinct and dynamic DNA methylation profiles for the de novo L1 and members of its extended transduction family during neuronal differentiation. These experiments reveal how a de novo L1 insertion in a pluripotent stem cell is rapidly recognized and repressed, albeit incompletely, by the host genome during neurodifferentiation, while retaining potential for further retrotransposition. | |
Sanchez-Luque, Francisco J; Kempen, Marie-Jeanne H C; Gerdes, Patricia; Vargas-Landin, Dulce B; Richardson, Sandra R; Troskie, Robin-Lee; Jesuadian, Samuel J; Cheetham, Seth W; Carreira, Patricia E; Salvador-Palomeque, Carmen; García-Cañadas, Marta; Muñoz-Lopez, Martin; Sanchez, Laura; Lundberg, Mischa; Macia, Angela; Heras, Sara R; Brennan, Paul M; Lister, Ryan; Garcia-Perez, Jose L; Ewing, Adam D; Faulkner, Geoffrey J LINE-1 Evasion of Epigenetic Repression in Humans (Journal Article) Molecular Cell, 0 (0), 2019, ISSN: 1097-2765. (Abstract | Links | BibTeX | Altmetric) @article{sanchez-luque_line-1_2019, title = {LINE-1 Evasion of Epigenetic Repression in Humans}, author = {Francisco J Sanchez-Luque and Marie-Jeanne H C Kempen and Patricia Gerdes and Dulce B Vargas-Landin and Sandra R Richardson and Robin-Lee Troskie and Samuel J Jesuadian and Seth W Cheetham and Patricia E Carreira and Carmen Salvador-Palomeque and Marta Garc\'{i}a-Ca\~{n}adas and Martin Mu\~{n}oz-Lopez and Laura Sanchez and Mischa Lundberg and Angela Macia and Sara R Heras and Paul M Brennan and Ryan Lister and Jose L Garcia-Perez and Adam D Ewing and Geoffrey J Faulkner}, url = {https://www.cell.com/molecular-cell/abstract/S1097-2765(19)30396-X}, doi = {10.1016/j.molcel.2019.05.024}, issn = {1097-2765}, year = {2019}, date = {2019-01-01}, urldate = {2019-06-24}, journal = {Molecular Cell}, volume = {0}, number = {0}, abstract = {textlessh2textgreaterSummarytextless/h2textgreatertextlessptextgreaterEpigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3ʹ transduction. The source (donor) L1 for this insertion was slightly 5ʹ truncated, lacked the YY1 binding site, and was highly mobile when tested textitin vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.textless/ptextgreater}, keywords = {}, pubstate = {published}, tppubtype = {article} } textlessh2textgreaterSummarytextless/h2textgreatertextlessptextgreaterEpigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3ʹ transduction. The source (donor) L1 for this insertion was slightly 5ʹ truncated, lacked the YY1 binding site, and was highly mobile when tested textitin vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.textless/ptextgreater | |
2018 | |
Bodea, Gabriela O; McKelvey, Eleanor G Z; Faulkner, Geoffrey J Retrotransposon-induced mosaicism in the neural genome (Journal Article) Open Biology, 8 (7), pp. 180074, 2018, ISSN: 2046-2441. (Abstract | Links | BibTeX | Altmetric) @article{bodea_retrotransposon-induced_2018, title = {Retrotransposon-induced mosaicism in the neural genome}, author = {Gabriela O Bodea and Eleanor G Z McKelvey and Geoffrey J Faulkner}, url = {http://rsob.royalsocietypublishing.org/content/8/7/180074}, doi = {10.1098/rsob.180074}, issn = {2046-2441}, year = {2018}, date = {2018-07-01}, urldate = {2018-08-28}, journal = {Open Biology}, volume = {8}, number = {7}, pages = {180074}, abstract = {Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions. | |
Richardson, Sandra R; Faulkner, Geoffrey J Heritable L1 Retrotransposition Events During Development: Understanding Their Origins (Journal Article) BioEssays, 40 (6), pp. 1700189, 2018, ISSN: 1521-1878. (Abstract | Links | BibTeX | Altmetric) @article{richardson_heritable_2018, title = {Heritable L1 Retrotransposition Events During Development: Understanding Their Origins}, author = {Sandra R Richardson and Geoffrey J Faulkner}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201700189}, doi = {10.1002/bies.201700189}, issn = {1521-1878}, year = {2018}, date = {2018-06-01}, urldate = {2018-08-28}, journal = {BioEssays}, volume = {40}, number = {6}, pages = {1700189}, abstract = {The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, “Heritable L1 retrotransposition in the mouse primordial germline and early embryo,” we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes. In parallel, we outline outstanding questions regarding the stage-specificity, regulation, and functional impact of embryonic and germline L1 retrotransposition, and propose avenues for future research in this field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, “Heritable L1 retrotransposition in the mouse primordial germline and early embryo,” we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes. In parallel, we outline outstanding questions regarding the stage-specificity, regulation, and functional impact of embryonic and germline L1 retrotransposition, and propose avenues for future research in this field. | |
Nguyen, Thu H M; Carreira, Patricia E; Sanchez-Luque, Francisco J; Schauer, Stephanie N; Fagg, Allister C; Richardson, Sandra R; Davies, Claire M; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Troskie, Robin-Lee; James, Cini; Beaven, Elizabeth A; Wallis, Tristan P; Coward, Jermaine I G; Chetty, Naven P; Crandon, Alexander J; Venter, Deon J; Armes, Jane E; Perrin, Lewis C; Hooper, John D; Ewing, Adam D; Upton, Kyle R; Faulkner, Geoffrey J L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution (Journal Article) Cell Reports, 23 (13), pp. 3730–3740, 2018, ISSN: 2211-1247. (Abstract | Links | BibTeX | Altmetric) @article{nguyen_l1_2018, title = {L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution}, author = {Thu H M Nguyen and Patricia E Carreira and Francisco J Sanchez-Luque and Stephanie N Schauer and Allister C Fagg and Sandra R Richardson and Claire M Davies and Samuel J Jesuadian and Marie-Jeanne H C Kempen and Robin-Lee Troskie and Cini James and Elizabeth A Beaven and Tristan P Wallis and Jermaine I G Coward and Naven P Chetty and Alexander J Crandon and Deon J Venter and Jane E Armes and Lewis C Perrin and John D Hooper and Adam D Ewing and Kyle R Upton and Geoffrey J Faulkner}, url = {http://www.sciencedirect.com/science/article/pii/S2211124718308714}, doi = {10.1016/j.celrep.2018.05.090}, issn = {2211-1247}, year = {2018}, date = {2018-06-01}, urldate = {2018-08-28}, journal = {Cell Reports}, volume = {23}, number = {13}, pages = {3730--3740}, abstract = {Summary LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Summary LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity. | |
Faulkner, Geoffrey J; Billon, Victor L1 retrotransposition in the soma: a field jumping ahead (Journal Article) Mobile DNA, 9 (1), pp. 22, 2018, ISSN: 1759-8753. (Abstract | Links | BibTeX | Altmetric) @article{faulkner_l1_2018, title = {L1 retrotransposition in the soma: a field jumping ahead}, author = {Geoffrey J Faulkner and Victor Billon}, url = {https://doi.org/10.1186/s13100-018-0128-1}, doi = {10.1186/s13100-018-0128-1}, issn = {1759-8753}, year = {2018}, date = {2018-01-01}, urldate = {2018-08-28}, journal = {Mobile DNA}, volume = {9}, number = {1}, pages = {22}, abstract = {Retrotransposons are transposable elements (TEs) capable of “jumping” in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Retrotransposons are transposable elements (TEs) capable of “jumping” in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition. | |
Abrams, John M; Arkhipova, Irina R; Belfort, Marlene; Boeke, Jef D; Curcio, Joan M; Faulkner, Geoffrey J; Goodier, John L; Lehmann, Ruth; Levin, Henry L Meeting report: mobile genetic elements and genome plasticity 2018 (Journal Article) Mobile DNA, 9 (1), pp. 21, 2018, ISSN: 1759-8753. (Abstract | Links | BibTeX | Altmetric) @article{abrams_meeting_2018, title = {Meeting report: mobile genetic elements and genome plasticity 2018}, author = {John M Abrams and Irina R Arkhipova and Marlene Belfort and Jef D Boeke and M Joan Curcio and Geoffrey J Faulkner and John L Goodier and Ruth Lehmann and Henry L Levin}, url = {https://doi.org/10.1186/s13100-018-0126-3}, doi = {10.1186/s13100-018-0126-3}, issn = {1759-8753}, year = {2018}, date = {2018-01-01}, urldate = {2018-08-28}, journal = {Mobile DNA}, volume = {9}, number = {1}, pages = {21}, abstract = {The Mobile Genetic Elements and Genome Plasticity conference was hosted by Keystone Symposia in Santa Fe, NM USA, February 11\textendash15, 2018. The organizers were Marlene Belfort, Evan Eichler, Henry Levin and Lynn Maquat. The goal of this conference was to bring together scientists from around the world to discuss the function of transposable elements and their impact on host species. Central themes of the meeting included recent innovations in genome analysis and the role of mobile DNA in disease and evolution. The conference included 200 scientists who participated in poster presentations, short talks selected from abstracts, and invited talks. A total of 58 talks were organized into eight sessions and two workshops. The topics varied from mechanisms of mobilization, to the structure of genomes and their defense strategies to protect against transposable elements.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mobile Genetic Elements and Genome Plasticity conference was hosted by Keystone Symposia in Santa Fe, NM USA, February 11–15, 2018. The organizers were Marlene Belfort, Evan Eichler, Henry Levin and Lynn Maquat. The goal of this conference was to bring together scientists from around the world to discuss the function of transposable elements and their impact on host species. Central themes of the meeting included recent innovations in genome analysis and the role of mobile DNA in disease and evolution. The conference included 200 scientists who participated in poster presentations, short talks selected from abstracts, and invited talks. A total of 58 talks were organized into eight sessions and two workshops. The topics varied from mechanisms of mobilization, to the structure of genomes and their defense strategies to protect against transposable elements. | |
Baillie, Kenneth J; Bretherick, Andrew; Haley, Christopher S; Clohisey, Sara; Gray, Alan; Neyton, Lucile P A; Barrett, Jeffrey; Stahl, Eli A; Tenesa, Albert; Andersson, Robin; Brown, Ben J; Faulkner, Geoffrey J; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Itoh, Masayoshi; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Consortium, Iibdgc; Mole, Damian; Bajic, Vladimir B; Heutink, Peter; Rehli, Michael; Kawaji, Hideya; Sandelin, Albin; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A; Hacohen, Nir; Freeman, Thomas C; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Hume, David A Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease (Journal Article) PLOS Computational Biology, 14 (3), pp. e1005934, 2018, ISSN: 1553-7358. (Abstract | Links | BibTeX | Altmetric) @article{baillie_shared_2018, title = {Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease}, author = {Kenneth J Baillie and Andrew Bretherick and Christopher S Haley and Sara Clohisey and Alan Gray and Lucile P A Neyton and Jeffrey Barrett and Eli A Stahl and Albert Tenesa and Robin Andersson and Ben J Brown and Geoffrey J Faulkner and Marina Lizio and Ulf Schaefer and Carsten Daub and Masayoshi Itoh and Naoto Kondo and Timo Lassmann and Jun Kawai and Iibdgc Consortium and Damian Mole and Vladimir B Bajic and Peter Heutink and Michael Rehli and Hideya Kawaji and Albin Sandelin and Harukazu Suzuki and Jack Satsangi and Christine A Wells and Nir Hacohen and Thomas C Freeman and Yoshihide Hayashizaki and Piero Carninci and Alistair R R Forrest and David A Hume}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005934}, doi = {10.1371/journal.pcbi.1005934}, issn = {1553-7358}, year = {2018}, date = {2018-01-01}, urldate = {2018-08-28}, journal = {PLOS Computational Biology}, volume = {14}, number = {3}, pages = {e1005934}, abstract = {Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn’s disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn’s disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits. | |
Schauer, Stephanie N; Carreira, Patricia E; Shukla, Ruchi; Gerhardt, Daniel J; Gerdes, Patricia; Sanchez-Luque, Francisco J; Nicoli, Paola; Kindlova, Michaela; Ghisletti, Serena; Santos, Alexandre Dos; Rapoud, Delphine; Samuel, Didier; Faivre, Jamila; Ewing, Adam D; Richardson, Sandra R; Faulkner, Geoffrey J L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis (Journal Article) Genome Research, 2018, ISSN: 1088-9051, 1549-5469. (Abstract | Links | BibTeX | Altmetric) @article{schauer_l1_2018, title = {L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis}, author = {Stephanie N Schauer and Patricia E Carreira and Ruchi Shukla and Daniel J Gerhardt and Patricia Gerdes and Francisco J Sanchez-Luque and Paola Nicoli and Michaela Kindlova and Serena Ghisletti and Alexandre Dos Santos and Delphine Rapoud and Didier Samuel and Jamila Faivre and Adam D Ewing and Sandra R Richardson and Geoffrey J Faulkner}, url = {http://genome.cshlp.org/content/early/2018/04/11/gr.226993.117}, doi = {10.1101/gr.226993.117}, issn = {1088-9051, 1549-5469}, year = {2018}, date = {2018-01-01}, urldate = {2018-08-28}, journal = {Genome Research}, abstract = {The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole-genome sequencing (WGS) to an Abcb4 (Mdr2)−/− mouse model of hepatic carcinogenesis and demonstrated for the first time that L1 mobilization occurs in murine tumors. In 12 HCC nodules obtained from 10 animals, we validated four somatic L1 insertions by PCR and capillary sequencing, including TF subfamily elements, and one GF subfamily example. One of the TF insertions carried a 3′ transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from 25 HCC patients with a history of alcohol abuse. Finally, we used RC-seq and WGS to identify three tumor-specific L1 insertions among 10 intra-hepatic cholangiocarcinoma (ICC) patients, including one insertion traced to a donor L1 on Chromosome 22 known to be highly active in other cancers. This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole-genome sequencing (WGS) to an Abcb4 (Mdr2)−/− mouse model of hepatic carcinogenesis and demonstrated for the first time that L1 mobilization occurs in murine tumors. In 12 HCC nodules obtained from 10 animals, we validated four somatic L1 insertions by PCR and capillary sequencing, including TF subfamily elements, and one GF subfamily example. One of the TF insertions carried a 3′ transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from 25 HCC patients with a history of alcohol abuse. Finally, we used RC-seq and WGS to identify three tumor-specific L1 insertions among 10 intra-hepatic cholangiocarcinoma (ICC) patients, including one insertion traced to a donor L1 on Chromosome 22 known to be highly active in other cancers. This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors. | |
2017 | |
Noguchi, Shuhei ; Arakawa, Takahiro ; Fukuda, Shiro ; Furuno, Masaaki ; Hasegawa, Akira ; Hori, Fumi ; Ishikawa-Kato, Sachi ; Kaida, Kaoru ; Kaiho, Ai ; Kanamori-Katayama, Mutsumi ; Kawashima, Tsugumi ; Kojima, Miki ; Kubosaki, Atsutaka ; Manabe, Ri-ichiroh ; Murata, Mitsuyoshi ; Nagao-Sato, Sayaka ; Nakazato, Kenichi ; Ninomiya, Noriko ; Nishiyori-Sueki, Hiromi ; Noma, Shohei ; Saijyo, Eri ; Saka, Akiko ; Sakai, Mizuho ; Simon, Christophe ; Suzuki, Naoko ; Tagami, Michihira ; Watanabe, Shoko ; Yoshida, Shigehiro ; Arner, Peter ; Axton, Richard A; Babina, Magda ; Baillie, Kenneth J; Barnett, Timothy C; Beckhouse, Anthony G; Blumenthal, Antje ; Bodega, Beatrice ; Bonetti, Alessandro ; Briggs, James ; Brombacher, Frank ; Carlisle, Ailsa J; Clevers, Hans C; Davis, Carrie A; Detmar, Michael ; Dohi, Taeko ; Edge, Albert S B; Edinger, Matthias ; Ehrlund, Anna ; Ekwall, Karl ; Endoh, Mitsuhiro ; Enomoto, Hideki ; Eslami, Afsaneh ; Fagiolini, Michela ; Fairbairn, Lynsey ; Farach-Carson, Mary C; Faulkner, Geoffrey J FANTOM5 CAGE profiles of human and mouse samples (Journal Article) Scientific Data, 4 , pp. 170112, 2017, ISSN: 2052-4463. (Abstract | Links | BibTeX | Altmetric) @article{noguchi_fantom5_2017, title = {FANTOM5 CAGE profiles of human and mouse samples}, author = {Noguchi, Shuhei and Arakawa, Takahiro and Fukuda, Shiro and Furuno, Masaaki and Hasegawa, Akira and Hori, Fumi and Ishikawa-Kato, Sachi and Kaida, Kaoru and Kaiho, Ai and Kanamori-Katayama, Mutsumi and Kawashima, Tsugumi and Kojima, Miki and Kubosaki, Atsutaka and Manabe, Ri-ichiroh and Murata, Mitsuyoshi and Nagao-Sato, Sayaka and Nakazato, Kenichi and Ninomiya, Noriko and Nishiyori-Sueki, Hiromi and Noma, Shohei and Saijyo, Eri and Saka, Akiko and Sakai, Mizuho and Simon, Christophe and Suzuki, Naoko and Tagami, Michihira and Watanabe, Shoko and Yoshida, Shigehiro and Arner, Peter and Axton, Richard A. and Babina, Magda and Baillie, J. Kenneth and Barnett, Timothy C. and Beckhouse, Anthony G. and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessandro and Briggs, James and Brombacher, Frank and Carlisle, Ailsa J. and Clevers, Hans C. and Davis, Carrie A. and Detmar, Michael and Dohi, Taeko and Edge, Albert S. B. and Edinger, Matthias and Ehrlund, Anna and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and Eslami, Afsaneh and Fagiolini, Michela and Fairbairn, Lynsey and Farach-Carson, Mary C. and Faulkner, Geoffrey J.}, doi = {10.1038/sdata.2017.112}, issn = {2052-4463}, year = {2017}, date = {2017-08-29}, journal = {Scientific Data}, volume = {4}, pages = {170112}, abstract = {In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities. | |
Richardson, Sandra R; Gerdes, Patricia; Gerhardt, Daniel J; Sanchez-Luque, Francisco J; Bodea, Gabriela-Oana; ~n, Martin Mu; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Carreira, Patricia E; Jeddeloh, Jeffrey A; Garcia-Perez, Jose L; Jr, Haig Kazazian H; Ewing, Adam D; Faulkner, Geoffrey J Heritable L1 retrotransposition in the mouse primordial germline and early embryo (Journal Article) Genome Res., 27 (8), pp. 1395–1405, 2017. @article{Richardson2017-hr, title = {Heritable L1 retrotransposition in the mouse primordial germline and early embryo}, author = {Sandra R Richardson and Patricia Gerdes and Daniel J Gerhardt and Francisco J Sanchez-Luque and Gabriela-Oana Bodea and Martin Mu{~n}oz-Lopez and Samuel J Jesuadian and Marie-Jeanne H C Kempen and Patricia E Carreira and Jeffrey A Jeddeloh and Jose L Garcia-Perez and Haig H Kazazian Jr and Adam D Ewing and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1101/gr.219022.116}, year = {2017}, date = {2017-08-01}, journal = {Genome Res.}, volume = {27}, number = {8}, pages = {1395--1405}, abstract = {LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of $geq$1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo.}, keywords = {}, pubstate = {published}, tppubtype = {article} } LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of $geq$1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo. | |
Ravà, Micol; D'Andrea, Aleco; Doni, Mirko; Kress, Theresia R; Ostuni, Renato; Bianchi, Valerio; Morelli, Marco J; Collino, Agnese; Ghisletti, Serena; Nicoli, Paola; Recordati, Camilla; Iascone, Maria; Sonzogni, Aurelio; D'Antiga, Lorenzo; Shukla, Ruchi; Faulkner, Geoffrey J; Natoli, Gioacchino; Campaner, Stefano; Amati, Bruno Mutual epithelium-macrophage dependency in liver carcinogenesis mediated by ST18 (Journal Article) Hepatology, 65 (5), pp. 1708–1719, 2017. @article{Rava2017-wf, title = {Mutual epithelium-macrophage dependency in liver carcinogenesis mediated by ST18}, author = {Micol Rav\`{a} and Aleco D'Andrea and Mirko Doni and Theresia R Kress and Renato Ostuni and Valerio Bianchi and Marco J Morelli and Agnese Collino and Serena Ghisletti and Paola Nicoli and Camilla Recordati and Maria Iascone and Aurelio Sonzogni and Lorenzo D'Antiga and Ruchi Shukla and Geoffrey J Faulkner and Gioacchino Natoli and Stefano Campaner and Bruno Amati}, url = {http://dx.doi.org/10.1002/hep.28942}, year = {2017}, date = {2017-05-01}, journal = {Hepatology}, volume = {65}, number = {5}, pages = {1708--1719}, abstract = {The ST18 gene has been proposed to act either as a tumor suppressor or as an oncogene in different human cancers, but direct evidence for its role in tumorigenesis has been lacking thus far. Here, we demonstrate that ST18 is critical for tumor progression and maintenance in a mouse model of liver cancer, based on oncogenic transformation and adoptive transfer of primary precursor cells (hepatoblasts). ST18 messenger RNA (mRNA) and protein were detectable neither in normal liver nor in cultured hepatoblasts, but were readily expressed after subcutaneous engraftment and tumor growth. ST18 expression in liver cells was induced by inflammatory cues, including acute or chronic inflammation in vivo, as well as coculture with macrophages in vitro. Knocking down the ST18 mRNA in transplanted hepatoblasts delayed tumor progression. Induction of ST18 knockdown in pre-established tumors caused rapid tumor involution associated with pervasive morphological changes, proliferative arrest, and apoptosis in tumor cells, as well as depletion of tumor-associated macrophages, vascular ectasia, and hemorrhage. Reciprocally, systemic depletion of macrophages in recipient animals had very similar phenotypic consequences, impairing either tumor development or maintenance, and suppressing ST18 expression in hepatoblasts. Finally, RNA sequencing of ST18-depleted tumors before involution revealed down-regulation of inflammatory response genes, pointing to the suppression of nuclear factor kappa B-dependent transcription. CONCLUSION: ST18 expression in epithelial cells is induced by tumor-associated macrophages, contributing to the reciprocal feed-forward loop between both cell types in liver tumorigenesis. Our findings warrant the exploration of means to interfere with ST18-dependent epithelium-macrophage interactions in a therapeutic setting. (Hepatology 2017;65:1708-1719).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The ST18 gene has been proposed to act either as a tumor suppressor or as an oncogene in different human cancers, but direct evidence for its role in tumorigenesis has been lacking thus far. Here, we demonstrate that ST18 is critical for tumor progression and maintenance in a mouse model of liver cancer, based on oncogenic transformation and adoptive transfer of primary precursor cells (hepatoblasts). ST18 messenger RNA (mRNA) and protein were detectable neither in normal liver nor in cultured hepatoblasts, but were readily expressed after subcutaneous engraftment and tumor growth. ST18 expression in liver cells was induced by inflammatory cues, including acute or chronic inflammation in vivo, as well as coculture with macrophages in vitro. Knocking down the ST18 mRNA in transplanted hepatoblasts delayed tumor progression. Induction of ST18 knockdown in pre-established tumors caused rapid tumor involution associated with pervasive morphological changes, proliferative arrest, and apoptosis in tumor cells, as well as depletion of tumor-associated macrophages, vascular ectasia, and hemorrhage. Reciprocally, systemic depletion of macrophages in recipient animals had very similar phenotypic consequences, impairing either tumor development or maintenance, and suppressing ST18 expression in hepatoblasts. Finally, RNA sequencing of ST18-depleted tumors before involution revealed down-regulation of inflammatory response genes, pointing to the suppression of nuclear factor kappa B-dependent transcription. CONCLUSION: ST18 expression in epithelial cells is induced by tumor-associated macrophages, contributing to the reciprocal feed-forward loop between both cell types in liver tumorigenesis. Our findings warrant the exploration of means to interfere with ST18-dependent epithelium-macrophage interactions in a therapeutic setting. (Hepatology 2017;65:1708-1719). | |
Baillie, Kenneth J; Arner, Erik; Daub, Carsten; Hoon, Michiel De; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Carninci, Piero; Forrest, Alistair R R; Hayashizaki, Yoshihide; Consortium, FANTOM; Faulkner, Geoffrey J; Wells, Christine A; Rehli, Michael; Pavli, Paul; Summers, Kim M; Hume, David A PLoS Genet., 13 (3), pp. e1006641, 2017. @article{Baillie2017-es, title = {Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease}, author = {Kenneth J Baillie and Erik Arner and Carsten Daub and Michiel De Hoon and Masayoshi Itoh and Hideya Kawaji and Timo Lassmann and Piero Carninci and Alistair R R Forrest and Yoshihide Hayashizaki and FANTOM Consortium and Geoffrey J Faulkner and Christine A Wells and Michael Rehli and Paul Pavli and Kim M Summers and David A Hume}, url = {http://dx.doi.org/10.1371/journal.pgen.1006641}, year = {2017}, date = {2017-03-01}, journal = {PLoS Genet.}, volume = {13}, number = {3}, pages = {e1006641}, abstract = {The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease.}, keywords = {}, pubstate = {}, tppubtype = {article} } The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease. | |
Wolf, Gernot; Rebollo, Rita; Karimi, Mohammad M; Ewing, Adam D; Kamada, Rui; Wu, Warren; Wu, Brenda; Bachu, Mahesh; Ozato, Keiko; Faulkner, Geoffrey J; Mager, Dixie L; Lorincz, Matthew C; Macfarlan, Todd S On the role of H3.3 in retroviral silencing (Journal Article) Nature, 548 (7665), pp. E1–E3, 2017. @article{Wolf2017-iq, title = {On the role of H3.3 in retroviral silencing}, author = {Gernot Wolf and Rita Rebollo and Mohammad M Karimi and Adam D Ewing and Rui Kamada and Warren Wu and Brenda Wu and Mahesh Bachu and Keiko Ozato and Geoffrey J Faulkner and Dixie L Mager and Matthew C Lorincz and Todd S Macfarlan}, url = {http://dx.doi.org/10.1038/nature23277}, year = {2017}, date = {2017-01-01}, journal = {Nature}, volume = {548}, number = {7665}, pages = {E1--E3}, keywords = {}, pubstate = {}, tppubtype = {article} } | |
Kempen, Marie-Jeanne H C; Bodea, Gabriela O; Faulkner, Geoffrey J Neuronal Genome Plasticity: Retrotransposons, Environment and Disease (Incollection) Human Retrotransposons in Health and Disease, pp. 107–125, Springer, Cham, 2017. @incollection{Kempen2017-eq, title = {Neuronal Genome Plasticity: Retrotransposons, Environment and Disease}, author = {Marie-Jeanne H C Kempen and Gabriela O Bodea and Geoffrey J Faulkner}, url = {https://link.springer.com/chapter/10.1007/978-3-319-48344-3_5}, year = {2017}, date = {2017-01-01}, booktitle = {Human Retrotransposons in Health and Disease}, pages = {107--125}, publisher = {Springer, Cham}, abstract = {The neuronal genome has long been considered as a stably persisting entity interpreted as the foundation of neurobiology. Over the past decade, it has become increasingly clear that mobile genetic elements, such as the retrotransposon LINE-1 (L1), are actively transcribed and transpose in the healthy brain. L1 activity therefore provides a route to somatic genome diversity and dynamism in neuronal populations. Here, we discuss the discovery of L1 retrotransposition during neurogenesis, and consider how neuronal cells regulate retrotransposition in response to endogenous and environmental stimuli. We also bring forward hypotheses relating to how L1 impacts normal brain development and function, as well as how abnormal L1 mobilisation could contribute to neurological disease susceptibility and pathophysiology.}, keywords = {}, pubstate = {}, tppubtype = {incollection} } The neuronal genome has long been considered as a stably persisting entity interpreted as the foundation of neurobiology. Over the past decade, it has become increasingly clear that mobile genetic elements, such as the retrotransposon LINE-1 (L1), are actively transcribed and transpose in the healthy brain. L1 activity therefore provides a route to somatic genome diversity and dynamism in neuronal populations. Here, we discuss the discovery of L1 retrotransposition during neurogenesis, and consider how neuronal cells regulate retrotransposition in response to endogenous and environmental stimuli. We also bring forward hypotheses relating to how L1 impacts normal brain development and function, as well as how abnormal L1 mobilisation could contribute to neurological disease susceptibility and pathophysiology. | |
Faulkner, Geoffrey J; Garcia-Perez, Jose L L1 Mosaicism in Mammals: Extent, Effects, and Evolution (Journal Article) Trends Genet., 33 (11), pp. 802–816, 2017. @article{Faulkner2017-cs, title = {L1 Mosaicism in Mammals: Extent, Effects, and Evolution}, author = {Geoffrey J Faulkner and Jose L Garcia-Perez}, url = {http://dx.doi.org/10.1016/j.tig.2017.07.004}, year = {2017}, date = {2017-01-01}, journal = {Trends Genet.}, volume = {33}, number = {11}, pages = {802--816}, abstract = {The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism. | |
Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J Analysis of Somatic LINE-1 Insertions in Neurons (Incollection) Genomic Mosaicism in Neurons and Other Cell Types, pp. 219–251, Humana Press, New York, NY, 2017, ISBN: 978-1-4939-7279-1 978-1-4939-7280-7, (DOI: 10.1007/978-1-4939-7280-7_12). @incollection{sanchez-luque_analysis_2017, title = {Analysis of Somatic LINE-1 Insertions in Neurons}, author = {Francisco J Sanchez-Luque and Sandra R Richardson and Geoffrey J Faulkner}, url = {https://link.springer.com/protocol/10.1007/978-1-4939-7280-7_12}, isbn = {978-1-4939-7279-1 978-1-4939-7280-7}, year = {2017}, date = {2017-01-01}, urldate = {2018-01-16}, booktitle = {Genomic Mosaicism in Neurons and Other Cell Types}, pages = {219--251}, publisher = {Humana Press, New York, NY}, series = {Neuromethods}, abstract = {The method described here is designed to detect and localize somatic genome variation caused by the human retrotransposon LINE-1 (L1) in the genome of neuronal cells. This method combines single-cell manipulation and whole genome amplification technology with a hybridization-based, high-throughput sequencing method called Retrotransposon Capture sequencing (RC-seq) for the precise analysis of the L1 insertion content of single cell genomes. The method is divided into four major sections: extraction of neuronal nuclei and single nuclei isolation; whole genome amplification; RC-seq; and experimental validation of putative insertions.}, note = {DOI: 10.1007/978-1-4939-7280-7_12}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } The method described here is designed to detect and localize somatic genome variation caused by the human retrotransposon LINE-1 (L1) in the genome of neuronal cells. This method combines single-cell manipulation and whole genome amplification technology with a hybridization-based, high-throughput sequencing method called Retrotransposon Capture sequencing (RC-seq) for the precise analysis of the L1 insertion content of single cell genomes. The method is divided into four major sections: extraction of neuronal nuclei and single nuclei isolation; whole genome amplification; RC-seq; and experimental validation of putative insertions. | |
2016 | |
Li, Jun; Woods, Susan L; Healey, Sue; Beesley, Jonathan; Chen, Xiaoqing; Lee, Jason S; Sivakumaran, Haran; Wayte, Nicci; Nones, Katia; Waterfall, Joshua J; Pearson, John; Patch, Anne-Marie; Senz, Janine; Ferreira, Manuel A; Kaurah, Pardeep; Mackenzie, Robertson; Heravi-Moussavi, Alireza; Hansford, Samantha; Lannagan, Tamsin R M; Spurdle, Amanda B; Simpson, Peter T; da Silva, Leonard; Lakhani, Sunil R; Clouston, Andrew D; Bettington, Mark; Grimpen, Florian; Busuttil, Rita A; Costanzo, Natasha Di; Boussioutas, Alex; Jeanjean, Marie; Chong, George; Fabre, Aurélie; Olschwang, Sylviane; Faulkner, Geoffrey J; Bellos, Evangelos; Coin, Lachlan; Rioux, Kevin; Bathe, Oliver F; Wen, Xiaogang; Martin, Hilary C; Neklason, Deborah W; Davis, Sean R; Walker, Robert L; Calzone, Kathleen A; Avital, Itzhak; Heller, Theo; Koh, Christopher; Pineda, Marbin; Rudloff, Udo; Quezado, Martha; Pichurin, Pavel N; Hulick, Peter J; Weissman, Scott M; Newlin, Anna; Rubinstein, Wendy S; Sampson, Jone E; Hamman, Kelly; Goldgar, David; Poplawski, Nicola; Phillips, Kerry; Schofield, Lyn; Armstrong, Jacqueline; Kiraly-Borri, Cathy; Suthers, Graeme K; Huntsman, David G; Foulkes, William D; Carneiro, Fatima; Lindor, Noralane M; Edwards, Stacey L; French, Juliet D; Waddell, Nicola; Meltzer, Paul S; Worthley, Daniel L; Schrader, Kasmintan A; Chenevix-Trench, Georgia Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant (Journal Article) Am. J. Hum. Genet., 98 (5), pp. 830–842, 2016. @article{Li2016-ug, title = {Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant}, author = {Jun Li and Susan L Woods and Sue Healey and Jonathan Beesley and Xiaoqing Chen and Jason S Lee and Haran Sivakumaran and Nicci Wayte and Katia Nones and Joshua J Waterfall and John Pearson and Anne-Marie Patch and Janine Senz and Manuel A Ferreira and Pardeep Kaurah and Robertson Mackenzie and Alireza Heravi-Moussavi and Samantha Hansford and Tamsin R M Lannagan and Amanda B Spurdle and Peter T Simpson and Leonard da Silva and Sunil R Lakhani and Andrew D Clouston and Mark Bettington and Florian Grimpen and Rita A Busuttil and Natasha Di Costanzo and Alex Boussioutas and Marie Jeanjean and George Chong and Aur\'{e}lie Fabre and Sylviane Olschwang and Geoffrey J Faulkner and Evangelos Bellos and Lachlan Coin and Kevin Rioux and Oliver F Bathe and Xiaogang Wen and Hilary C Martin and Deborah W Neklason and Sean R Davis and Robert L Walker and Kathleen A Calzone and Itzhak Avital and Theo Heller and Christopher Koh and Marbin Pineda and Udo Rudloff and Martha Quezado and Pavel N Pichurin and Peter J Hulick and Scott M Weissman and Anna Newlin and Wendy S Rubinstein and Jone E Sampson and Kelly Hamman and David Goldgar and Nicola Poplawski and Kerry Phillips and Lyn Schofield and Jacqueline Armstrong and Cathy Kiraly-Borri and Graeme K Suthers and David G Huntsman and William D Foulkes and Fatima Carneiro and Noralane M Lindor and Stacey L Edwards and Juliet D French and Nicola Waddell and Paul S Meltzer and Daniel L Worthley and Kasmintan A Schrader and Georgia Chenevix-Trench}, url = {http://dx.doi.org/10.1016/j.ajhg.2016.03.001}, year = {2016}, date = {2016-05-01}, journal = {Am. J. Hum. Genet.}, volume = {98}, number = {5}, pages = {830--842}, abstract = {Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal-dominant cancer-predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. We mapped the gene to 5q22 and found loss of the wild-type allele on 5q in fundic gland polyps from affected individuals. Whole-exome and -genome sequencing failed to find causal mutations but, through Sanger sequencing, we identified point mutations in APC promoter 1B that co-segregated with disease in all six families. The mutations reduced binding of the YY1 transcription factor and impaired activity of the APC promoter 1B in luciferase assays. Analysis of blood and saliva from carriers showed allelic imbalance of APC, suggesting that these mutations lead to decreased allele-specific expression in vivo. Similar mutations in APC promoter 1B occur in rare families with familial adenomatous polyposis (FAP). Promoter 1A is methylated in GAPPS and sporadic FGPs and in normal stomach, which suggests that 1B transcripts are more important than 1A in gastric mucosa. This might explain why all known GAPPS-affected families carry promoter 1B point mutations but only rare FAP-affected families carry similar mutations, the colonic cells usually being protected by the expression of the 1A isoform. Gastric polyposis and cancer have been previously described in some FAP-affected individuals with large deletions around promoter 1B. Our finding that GAPPS is caused by point mutations in the same promoter suggests that families with mutations affecting the promoter 1B are at risk of gastric adenocarcinoma, regardless of whether or not colorectal polyps are present.}, keywords = {}, pubstate = {}, tppubtype = {article} } Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal-dominant cancer-predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. We mapped the gene to 5q22 and found loss of the wild-type allele on 5q in fundic gland polyps from affected individuals. Whole-exome and -genome sequencing failed to find causal mutations but, through Sanger sequencing, we identified point mutations in APC promoter 1B that co-segregated with disease in all six families. The mutations reduced binding of the YY1 transcription factor and impaired activity of the APC promoter 1B in luciferase assays. Analysis of blood and saliva from carriers showed allelic imbalance of APC, suggesting that these mutations lead to decreased allele-specific expression in vivo. Similar mutations in APC promoter 1B occur in rare families with familial adenomatous polyposis (FAP). Promoter 1A is methylated in GAPPS and sporadic FGPs and in normal stomach, which suggests that 1B transcripts are more important than 1A in gastric mucosa. This might explain why all known GAPPS-affected families carry promoter 1B point mutations but only rare FAP-affected families carry similar mutations, the colonic cells usually being protected by the expression of the 1A isoform. Gastric polyposis and cancer have been previously described in some FAP-affected individuals with large deletions around promoter 1B. Our finding that GAPPS is caused by point mutations in the same promoter suggests that families with mutations affecting the promoter 1B are at risk of gastric adenocarcinoma, regardless of whether or not colorectal polyps are present. | |
Gerdes, Patricia; Richardson, Sandra R; Mager, Dixie L; Faulkner, Geoffrey J Transposable elements in the mammalian embryo: pioneers surviving through stealth and service (Journal Article) Genome Biol., 17 , pp. 100, 2016. @article{Gerdes2016-yk, title = {Transposable elements in the mammalian embryo: pioneers surviving through stealth and service}, author = {Patricia Gerdes and Sandra R Richardson and Dixie L Mager and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1186/s13059-016-0965-5}, year = {2016}, date = {2016-05-01}, journal = {Genome Biol.}, volume = {17}, pages = {100}, abstract = {Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomologous recombination, and other potentially deleterious processes can cause sporadic disease by disrupting genome integrity or inducing abrupt gene expression changes. Here, we discuss recent evidence suggesting that TEs may contribute regulatory innovation to mammalian embryonic and pluripotent states as a means to ward off complete repression by their host genome.}, keywords = {}, pubstate = {}, tppubtype = {article} } Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomologous recombination, and other potentially deleterious processes can cause sporadic disease by disrupting genome integrity or inducing abrupt gene expression changes. Here, we discuss recent evidence suggesting that TEs may contribute regulatory innovation to mammalian embryonic and pluripotent states as a means to ward off complete repression by their host genome. | |
Gerdes, Patricia; Richardson, Sandra R; Faulkner, Geoffrey J TET enzymes: double agents in the transposable element-host genome conflict (Journal Article) Genome Biol., 17 (1), pp. 259, 2016. @article{Gerdes2016-ga, title = {TET enzymes: double agents in the transposable element-host genome conflict}, author = {Patricia Gerdes and Sandra R Richardson and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1186/s13059-016-1124-8}, year = {2016}, date = {2016-01-01}, journal = {Genome Biol.}, volume = {17}, number = {1}, pages = {259}, abstract = {The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticated over evolutionary time to benefit the host genome. In an exciting new study, de la Rica and colleagues have uncovered a complex relationship between ten-eleven translocation (TET) proteins and retrotransposons in mouse embryonic stem cells (ESCs), implicating TETs as enhancers in the exaptation and function of retroelement sequences. Furthermore, they have demonstrated that active demethylation of retrotransposons does not correlate with their increased expression in ESCs, calling into question long-held assumptions regarding the importance of DNA demethylation for retrotransposon expression, and revealing novel epigenetic players in retrotransposon control.Please see related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1096-8.}, keywords = {}, pubstate = {}, tppubtype = {article} } The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticated over evolutionary time to benefit the host genome. In an exciting new study, de la Rica and colleagues have uncovered a complex relationship between ten-eleven translocation (TET) proteins and retrotransposons in mouse embryonic stem cells (ESCs), implicating TETs as enhancers in the exaptation and function of retroelement sequences. Furthermore, they have demonstrated that active demethylation of retrotransposons does not correlate with their increased expression in ESCs, calling into question long-held assumptions regarding the importance of DNA demethylation for retrotransposon expression, and revealing novel epigenetic players in retrotransposon control.Please see related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1096-8. | |
Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans (Journal Article) Methods Mol. Biol., 1400 , pp. 47–77, 2016. @article{Sanchez-Luque2016-vi, title = {Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans}, author = {Francisco J Sanchez-Luque and Sandra R Richardson and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1007/978-1-4939-3372-3_4}, year = {2016}, date = {2016-01-01}, journal = {Methods Mol. Biol.}, volume = {1400}, pages = {47--77}, abstract = {Mobile genetic elements (MGEs) are of critical importance in genomics and developmental biology. Polymorphic and somatic MGE insertions have the potential to impact the phenotype of an individual, depending on their genomic locations and functional consequences. However, the identification of polymorphic and somatic insertions among the plethora of copies residing in the genome presents a formidable technical challenge. Whole genome sequencing has the potential to address this problem; however, its efficacy depends on the abundance of cells carrying the new insertion. Robust detection of somatic insertions present in only a subset of cells within a given sample can also be prohibitively expensive due to a requirement for high sequencing depth. Here, we describe retrotransposon capture sequencing (RC-seq), a sequence capture approach in which Illumina libraries are enriched for fragments containing the 5' and 3' termini of specific MGEs. RC-seq allows the detection of known polymorphic insertions present in an individual, as well as the identification of rare or private germline insertions not previously described. Furthermore, RC-seq can be used to detect and characterize somatic insertions, providing a valuable tool to elucidate the extent and characteristics of MGE activity in healthy tissues and in various disease states.}, keywords = {}, pubstate = {}, tppubtype = {article} } Mobile genetic elements (MGEs) are of critical importance in genomics and developmental biology. Polymorphic and somatic MGE insertions have the potential to impact the phenotype of an individual, depending on their genomic locations and functional consequences. However, the identification of polymorphic and somatic insertions among the plethora of copies residing in the genome presents a formidable technical challenge. Whole genome sequencing has the potential to address this problem; however, its efficacy depends on the abundance of cells carrying the new insertion. Robust detection of somatic insertions present in only a subset of cells within a given sample can also be prohibitively expensive due to a requirement for high sequencing depth. Here, we describe retrotransposon capture sequencing (RC-seq), a sequence capture approach in which Illumina libraries are enriched for fragments containing the 5' and 3' termini of specific MGEs. RC-seq allows the detection of known polymorphic insertions present in an individual, as well as the identification of rare or private germline insertions not previously described. Furthermore, RC-seq can be used to detect and characterize somatic insertions, providing a valuable tool to elucidate the extent and characteristics of MGE activity in healthy tissues and in various disease states. | |
Klawitter, Sabine; Fuchs, Nina V; Upton, Kyle R; ~n, Martin Mu; Shukla, Ruchi; Wang, Jichang; ~n, Marta Garcia-Ca; Lopez-Ruiz, Cesar; Gerhardt, Daniel J; Sebe, Attila; Grabundzija, Ivana; Merkert, Sylvia; Gerdes, Patricia; Pulgarin, Andres J; Bock, Anja; Held, Ulrike; Witthuhn, Anett; Haase, Alexandra; Sarkadi, Balázs; Löwer, Johannes; Wolvetang, Ernst J; Martin, Ulrich; Ivics, Zoltán; Izsvák, Zsuzsanna; Garcia-Perez, Jose L; Faulkner, Geoffrey J; Schumann, Gerald G Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells (Journal Article) Nat. Commun., 7 , pp. 10286, 2016. @article{Klawitter2016-ur, title = {Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells}, author = {Sabine Klawitter and Nina V Fuchs and Kyle R Upton and Martin Mu{~n}oz-Lopez and Ruchi Shukla and Jichang Wang and Marta Garcia-Ca{~n}adas and Cesar Lopez-Ruiz and Daniel J Gerhardt and Attila Sebe and Ivana Grabundzija and Sylvia Merkert and Patricia Gerdes and Andres J Pulgarin and Anja Bock and Ulrike Held and Anett Witthuhn and Alexandra Haase and Bal\'{a}zs Sarkadi and Johannes L\"{o}wer and Ernst J Wolvetang and Ulrich Martin and Zolt\'{a}n Ivics and Zsuzsanna Izsv\'{a}k and Jose L Garcia-Perez and Geoffrey J Faulkner and Gerald G Schumann}, url = {http://dx.doi.org/10.1038/ncomms10286}, year = {2016}, date = {2016-01-01}, journal = {Nat. Commun.}, volume = {7}, pages = {10286}, abstract = {Human induced pluripotent stem cells (hiPSCs) are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. Genetic and epigenetic abnormalities have been reported by Wissing and colleagues to occur during hiPSC derivation, including mobilization of engineered LINE-1 (L1) retrotransposons. However, incidence and functional impact of endogenous retrotransposition in hiPSCs are yet to be established. Here we apply retrotransposon capture sequencing to eight hiPSC lines and three human embryonic stem cell (hESC) lines, revealing endogenous L1, Alu and SINE-VNTR-Alu (SVA) mobilization during reprogramming and pluripotent stem cell cultivation. Surprisingly, 4/7 de novo L1 insertions are full length and 6/11 retrotransposition events occurred in protein-coding genes expressed in pluripotent stem cells. We further demonstrate that an intronic L1 insertion in the CADPS2 gene is acquired during hiPSC cultivation and disrupts CADPS2 expression. These experiments elucidate endogenous retrotransposition, and its potential consequences, in hiPSCs and hESCs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Human induced pluripotent stem cells (hiPSCs) are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. Genetic and epigenetic abnormalities have been reported by Wissing and colleagues to occur during hiPSC derivation, including mobilization of engineered LINE-1 (L1) retrotransposons. However, incidence and functional impact of endogenous retrotransposition in hiPSCs are yet to be established. Here we apply retrotransposon capture sequencing to eight hiPSC lines and three human embryonic stem cell (hESC) lines, revealing endogenous L1, Alu and SINE-VNTR-Alu (SVA) mobilization during reprogramming and pluripotent stem cell cultivation. Surprisingly, 4/7 de novo L1 insertions are full length and 6/11 retrotransposition events occurred in protein-coding genes expressed in pluripotent stem cells. We further demonstrate that an intronic L1 insertion in the CADPS2 gene is acquired during hiPSC cultivation and disrupts CADPS2 expression. These experiments elucidate endogenous retrotransposition, and its potential consequences, in hiPSCs and hESCs. | |
Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans (Journal Article) Methods in Molecular Biology (Clifton, N.J.), 1400 , pp. 47–77, 2016, ISSN: 1940-6029. (Abstract | Links | BibTeX | Altmetric) @article{sanchez-luque_retrotransposon_2016, title = {Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans}, author = {Francisco J Sanchez-Luque and Sandra R Richardson and Geoffrey J Faulkner}, doi = {10.1007/978-1-4939-3372-3_4}, issn = {1940-6029}, year = {2016}, date = {2016-01-01}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1400}, pages = {47--77}, abstract = {Mobile genetic elements (MGEs) are of critical importance in genomics and developmental biology. Polymorphic and somatic MGE insertions have the potential to impact the phenotype of an individual, depending on their genomic locations and functional consequences. However, the identification of polymorphic and somatic insertions among the plethora of copies residing in the genome presents a formidable technical challenge. Whole genome sequencing has the potential to address this problem; however, its efficacy depends on the abundance of cells carrying the new insertion. Robust detection of somatic insertions present in only a subset of cells within a given sample can also be prohibitively expensive due to a requirement for high sequencing depth. Here, we describe retrotransposon capture sequencing (RC-seq), a sequence capture approach in which Illumina libraries are enriched for fragments containing the 5' and 3' termini of specific MGEs. RC-seq allows the detection of known polymorphic insertions present in an individual, as well as the identification of rare or private germline insertions not previously described. Furthermore, RC-seq can be used to detect and characterize somatic insertions, providing a valuable tool to elucidate the extent and characteristics of MGE activity in healthy tissues and in various disease states.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mobile genetic elements (MGEs) are of critical importance in genomics and developmental biology. Polymorphic and somatic MGE insertions have the potential to impact the phenotype of an individual, depending on their genomic locations and functional consequences. However, the identification of polymorphic and somatic insertions among the plethora of copies residing in the genome presents a formidable technical challenge. Whole genome sequencing has the potential to address this problem; however, its efficacy depends on the abundance of cells carrying the new insertion. Robust detection of somatic insertions present in only a subset of cells within a given sample can also be prohibitively expensive due to a requirement for high sequencing depth. Here, we describe retrotransposon capture sequencing (RC-seq), a sequence capture approach in which Illumina libraries are enriched for fragments containing the 5' and 3' termini of specific MGEs. RC-seq allows the detection of known polymorphic insertions present in an individual, as well as the identification of rare or private germline insertions not previously described. Furthermore, RC-seq can be used to detect and characterize somatic insertions, providing a valuable tool to elucidate the extent and characteristics of MGE activity in healthy tissues and in various disease states. | |
Carreira, Patricia E; Ewing, Adam D; Li, Guibo; Schauer, Stephanie N; Upton, Kyle R; Fagg, Allister C; Morell, Santiago; Kindlova, Michaela; Gerdes, Patricia; Richardson, Sandra R; Li, Bo; Gerhardt, Daniel J; Wang, Jun; Brennan, Paul M; Faulkner, Geoffrey J Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme (Journal Article) Mob. DNA, 7 (1), pp. 21, 2016. @article{Carreira2016-vr, title = {Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme}, author = {Patricia E Carreira and Adam D Ewing and Guibo Li and Stephanie N Schauer and Kyle R Upton and Allister C Fagg and Santiago Morell and Michaela Kindlova and Patricia Gerdes and Sandra R Richardson and Bo Li and Daniel J Gerhardt and Jun Wang and Paul M Brennan and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1186/s13100-016-0076-6}, year = {2016}, date = {2016-01-01}, journal = {Mob. DNA}, volume = {7}, number = {1}, pages = {21}, abstract = {LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers.}, keywords = {}, pubstate = {published}, tppubtype = {article} } LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. | |
2015 | |
Upton, Kyle R; Gerhardt, Daniel J; Jesuadian, Samuel J; Richardson, Sandra R; Sánchez-Luque, Francisco J; Bodea, Gabriela O; Ewing, Adam D; Salvador-Palomeque, Carmen; van der Knaap, Marjo S; Brennan, Paul M; Vanderver, Adeline; Faulkner, Geoffrey J Ubiquitous L1 mosaicism in hippocampal neurons (Journal Article) Cell, 161 (2), pp. 228–239, 2015. @article{Upton2015-qu, title = {Ubiquitous L1 mosaicism in hippocampal neurons}, author = {Kyle R Upton and Daniel J Gerhardt and Samuel J Jesuadian and Sandra R Richardson and Francisco J S\'{a}nchez-Luque and Gabriela O Bodea and Adam D Ewing and Carmen Salvador-Palomeque and Marjo S van der Knaap and Paul M Brennan and Adeline Vanderver and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1016/j.cell.2015.03.026}, year = {2015}, date = {2015-04-01}, journal = {Cell}, volume = {161}, number = {2}, pages = {228--239}, abstract = {Somatic LINE-1 (L1) retrotransposition during neurogenesis is a potential source of genotypic variation among neurons. As a neurogenic niche, the hippocampus supports pronounced L1 activity. However, the basal parameters and biological impact of L1-driven mosaicism remain unclear. Here, we performed single-cell retrotransposon capture sequencing (RC-seq) on individual human hippocampal neurons and glia, as well as cortical neurons. An estimated 13.7 somatic L1 insertions occurred per hippocampal neuron and carried the sequence hallmarks of target-primed reverse transcription. Notably, hippocampal neuron L1 insertions were specifically enriched in transcribed neuronal stem cell enhancers and hippocampus genes, increasing their probability of functional relevance. In addition, bias against intronic L1 insertions sense oriented relative to their host gene was observed, perhaps indicating moderate selection against this configuration in vivo. These experiments demonstrate pervasive L1 mosaicism at genomic loci expressed in hippocampal neurons.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Somatic LINE-1 (L1) retrotransposition during neurogenesis is a potential source of genotypic variation among neurons. As a neurogenic niche, the hippocampus supports pronounced L1 activity. However, the basal parameters and biological impact of L1-driven mosaicism remain unclear. Here, we performed single-cell retrotransposon capture sequencing (RC-seq) on individual human hippocampal neurons and glia, as well as cortical neurons. An estimated 13.7 somatic L1 insertions occurred per hippocampal neuron and carried the sequence hallmarks of target-primed reverse transcription. Notably, hippocampal neuron L1 insertions were specifically enriched in transcribed neuronal stem cell enhancers and hippocampus genes, increasing their probability of functional relevance. In addition, bias against intronic L1 insertions sense oriented relative to their host gene was observed, perhaps indicating moderate selection against this configuration in vivo. These experiments demonstrate pervasive L1 mosaicism at genomic loci expressed in hippocampal neurons. | |
Arner, Erik; Daub, Carsten O; Vitting-Seerup, Kristoffer; Andersson, Robin; Lilje, Berit; ø, Finn Drabl; Lennartsson, Andreas; Rönnerblad, Michelle; Hrydziuszko, Olga; Vitezic, Morana; Freeman, Tom C; Alhendi, Ahmad M N; Arner, Peter; Axton, Richard; Baillie, Kenneth J; Beckhouse, Anthony; Bodega, Beatrice; Briggs, James; Brombacher, Frank; Davis, Margaret; Detmar, Michael; Ehrlund, Anna; Endoh, Mitsuhiro; Eslami, Afsaneh; Fagiolini, Michela; Fairbairn, Lynsey; Faulkner, Geoffrey J; Ferrai, Carmelo; Fisher, Malcolm E; Forrester, Lesley; Goldowitz, Daniel; Guler, Reto; Ha, Thomas; Hara, Mitsuko; Herlyn, Meenhard; Ikawa, Tomokatsu; Kai, Chieko; Kawamoto, Hiroshi; Khachigian, Levon M; Klinken, Peter S; Kojima, Soichi; Koseki, Haruhiko; Klein, Sarah; Mejhert, Niklas; Miyaguchi, Ken; Mizuno, Yosuke; Morimoto, Mitsuru; Morris, Kelly J; Mummery, Christine; Nakachi, Yutaka; Ogishima, Soichi; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Qin, Xian-Yang; Roy, Sugata; Sato, Hiroki; Savvi, Suzana; Saxena, Alka; Schwegmann, Anita; Sugiyama, Daisuke; Swoboda, Rolf; Tanaka, Hiroshi; Tomoiu, Andru; Winteringham, Louise N; Wolvetang, Ernst; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Zabierowski, Susan; Zhang, Peter; Abugessaisa, Imad; Bertin, Nicolas; Diehl, Alexander D; Fukuda, Shiro; Furuno, Masaaki; Harshbarger, Jayson; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Ishizu, Yuri; Itoh, Masayoshi; Kawashima, Tsugumi; Kojima, Miki; Kondo, Naoto; Lizio, Marina; Meehan, Terrence F; Mungall, Christopher J; Murata, Mitsuyoshi; Nishiyori-Sueki, Hiromi; Sahin, Serkan; Nagao-Sato, Sayaka; Severin, Jessica; de Hoon, Michiel J L; Kawai, Jun; Kasukawa, Takeya; Lassmann, Timo; Suzuki, Harukazu; Kawaji, Hideya; Summers, Kim M; Wells, Christine; Consortium, FANTOM; Hume, David A; Forrest, Alistair R R; Sandelin, Albin; Carninci, Piero; Hayashizaki, Yoshihide Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells (Journal Article) Science, 347 (6225), pp. 1010–1014, 2015. @article{Arner2015-de, title = {Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells}, author = {Erik Arner and Carsten O Daub and Kristoffer Vitting-Seerup and Robin Andersson and Berit Lilje and Finn Drabl{\o}s and Andreas Lennartsson and Michelle R\"{o}nnerblad and Olga Hrydziuszko and Morana Vitezic and Tom C Freeman and Ahmad M N Alhendi and Peter Arner and Richard Axton and Kenneth J Baillie and Anthony Beckhouse and Beatrice Bodega and James Briggs and Frank Brombacher and Margaret Davis and Michael Detmar and Anna Ehrlund and Mitsuhiro Endoh and Afsaneh Eslami and Michela Fagiolini and Lynsey Fairbairn and Geoffrey J Faulkner and Carmelo Ferrai and Malcolm E Fisher and Lesley Forrester and Daniel Goldowitz and Reto Guler and Thomas Ha and Mitsuko Hara and Meenhard Herlyn and Tomokatsu Ikawa and Chieko Kai and Hiroshi Kawamoto and Levon M Khachigian and Peter S Klinken and Soichi Kojima and Haruhiko Koseki and Sarah Klein and Niklas Mejhert and Ken Miyaguchi and Yosuke Mizuno and Mitsuru Morimoto and Kelly J Morris and Christine Mummery and Yutaka Nakachi and Soichi Ogishima and Mariko Okada-Hatakeyama and Yasushi Okazaki and Valerio Orlando and Dmitry Ovchinnikov and Robert Passier and Margaret Patrikakis and Ana Pombo and Xian-Yang Qin and Sugata Roy and Hiroki Sato and Suzana Savvi and Alka Saxena and Anita Schwegmann and Daisuke Sugiyama and Rolf Swoboda and Hiroshi Tanaka and Andru Tomoiu and Louise N Winteringham and Ernst Wolvetang and Chiyo Yanagi-Mizuochi and Misako Yoneda and Susan Zabierowski and Peter Zhang and Imad Abugessaisa and Nicolas Bertin and Alexander D Diehl and Shiro Fukuda and Masaaki Furuno and Jayson Harshbarger and Akira Hasegawa and Fumi Hori and Sachi Ishikawa-Kato and Yuri Ishizu and Masayoshi Itoh and Tsugumi Kawashima and Miki Kojima and Naoto Kondo and Marina Lizio and Terrence F Meehan and Christopher J Mungall and Mitsuyoshi Murata and Hiromi Nishiyori-Sueki and Serkan Sahin and Sayaka Nagao-Sato and Jessica Severin and Michiel J L de Hoon and Jun Kawai and Takeya Kasukawa and Timo Lassmann and Harukazu Suzuki and Hideya Kawaji and Kim M Summers and Christine Wells and FANTOM Consortium and David A Hume and Alistair R R Forrest and Albin Sandelin and Piero Carninci and Yoshihide Hayashizaki}, url = {http://dx.doi.org/10.1126/science.1259418}, year = {2015}, date = {2015-01-01}, journal = {Science}, volume = {347}, number = {6225}, pages = {1010--1014}, abstract = {Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.}, keywords = {}, pubstate = {}, tppubtype = {article} } Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation. | |
2014 | |
Upton, Kyle R; Faulkner, Geoffrey J Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis (Journal Article) Mob. DNA, 5 , pp. 15, 2014. @article{Upton2014-zu, title = {Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis}, author = {Kyle R Upton and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1186/1759-8753-5-15}, year = {2014}, date = {2014-05-01}, journal = {Mob. DNA}, volume = {5}, pages = {15}, abstract = {Transposable elements (TEs) are a prominent feature of most eukaryotic genomes. Despite rapidly accumulating evidence for the role of TE-driven insertional mutagenesis and structural variation in genome evolution, few clear examples of individual TEs impacting biology via perturbed gene regulation are available. A recent report describes the discovery of an alternative promoter for the murine erythroid transcription factor Pu.1. This promoter is located in an ORR1A0 long terminal repeat (LTR) retrotransposon intronic to Pu.1 and is regulated by the Kr\"{u}ppel-like factors KLF1 and KLF3. Expression of the resultant chimeric transcript, called Pu.2, spontaneously induces erythroid differentiation in vitro. These experiments illustrate how transcription factor binding sites spread by retrotransposition have the potential to impact networks encoding key biological processes in the host genome.}, keywords = {}, pubstate = {}, tppubtype = {article} } Transposable elements (TEs) are a prominent feature of most eukaryotic genomes. Despite rapidly accumulating evidence for the role of TE-driven insertional mutagenesis and structural variation in genome evolution, few clear examples of individual TEs impacting biology via perturbed gene regulation are available. A recent report describes the discovery of an alternative promoter for the murine erythroid transcription factor Pu.1. This promoter is located in an ORR1A0 long terminal repeat (LTR) retrotransposon intronic to Pu.1 and is regulated by the Krüppel-like factors KLF1 and KLF3. Expression of the resultant chimeric transcript, called Pu.2, spontaneously induces erythroid differentiation in vitro. These experiments illustrate how transcription factor binding sites spread by retrotransposition have the potential to impact networks encoding key biological processes in the host genome. | |
Richardson, Sandra R; Salvador-Palomeque, Carmen; Faulkner, Geoffrey J Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population (Journal Article) Bioessays, 36 (5), pp. 475–481, 2014. @article{Richardson2014-yj, title = {Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population}, author = {Sandra R Richardson and Carmen Salvador-Palomeque and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1002/bies.201300181}, year = {2014}, date = {2014-05-01}, journal = {Bioessays}, volume = {36}, number = {5}, pages = {475--481}, abstract = {Gene retrocopies are generated by reverse transcription and genomic integration of mRNA. As such, retrocopies present an important exception to the central dogma of molecular biology, and have substantially impacted the functional landscape of the metazoan genome. While an estimated 8,000-17,000 retrocopies exist in the human genome reference sequence, the extent of variation between individuals in terms of retrocopy content has remained largely unexplored. Three recent studies by Abyzov et al., Ewing et al. and Schrider et al. have exploited 1,000 Genomes Project Consortium data, as well as other sources of whole-genome sequencing data, to uncover novel gene retrocopies. Here, we compare the methods and results of these three studies, highlight the impact of retrocopies in human diversity and genome evolution, and speculate on the potential for somatic gene retrocopies to impact cancer etiology and genetic diversity among individual neurons in the mammalian brain.}, keywords = {}, pubstate = {}, tppubtype = {article} } Gene retrocopies are generated by reverse transcription and genomic integration of mRNA. As such, retrocopies present an important exception to the central dogma of molecular biology, and have substantially impacted the functional landscape of the metazoan genome. While an estimated 8,000-17,000 retrocopies exist in the human genome reference sequence, the extent of variation between individuals in terms of retrocopy content has remained largely unexplored. Three recent studies by Abyzov et al., Ewing et al. and Schrider et al. have exploited 1,000 Genomes Project Consortium data, as well as other sources of whole-genome sequencing data, to uncover novel gene retrocopies. Here, we compare the methods and results of these three studies, highlight the impact of retrocopies in human diversity and genome evolution, and speculate on the potential for somatic gene retrocopies to impact cancer etiology and genetic diversity among individual neurons in the mammalian brain. | |
Consortium, {FANTOM; the PMI, RIKEN; (DGT)}, CLST; Forrest, Alistair R R; Kawaji, Hideya; ..., ; Faulkner, Geoffrey J; ..., ; Hume, David A; Carninci, Piero; Hayashizaki, Yoshihide A promoter-level mammalian expression atlas (Journal Article) Nature, 507 (7493), pp. 462-470, 2014. (Abstract | Links | BibTeX | Altmetric) @article{Consortium2014, title = {A promoter-level mammalian expression atlas}, author = {{FANTOM Consortium and RIKEN the PMI and CLST (DGT)} and Alistair R R Forrest and Hideya Kawaji and ... and Geoffrey J Faulkner and ... and David A Hume and Piero Carninci and Yoshihide Hayashizaki}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24670764}, doi = {10.1038/nature13182}, year = {2014}, date = {2014-03-26}, journal = {Nature}, volume = {507}, number = {7493}, pages = {462-470}, abstract = {Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research. | |
Pascarella, Giovanni; Lazarevic, Dejan; Plessy, Charles; Bertin, Nicolas; Akalin, Altuna; Vlachouli, Christina; Simone, Roberto; Faulkner, Geoffrey J; Zucchelli, Silvia; Kawai, Jun; Daub, Carsten O; Hayashizaki, Yoshihide; Lenhard, Boris; Carninci, Piero; Gustincich, Stefano NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements (Journal Article) Front. Cell. Neurosci., 8 , pp. 41, 2014. @article{Pascarella2014-oq, title = {NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements}, author = {Giovanni Pascarella and Dejan Lazarevic and Charles Plessy and Nicolas Bertin and Altuna Akalin and Christina Vlachouli and Roberto Simone and Geoffrey J Faulkner and Silvia Zucchelli and Jun Kawai and Carsten O Daub and Yoshihide Hayashizaki and Boris Lenhard and Piero Carninci and Stefano Gustincich}, url = {http://dx.doi.org/10.3389/fncel.2014.00041}, year = {2014}, date = {2014-02-01}, journal = {Front. Cell. Neurosci.}, volume = {8}, pages = {41}, abstract = {By coupling laser capture microdissection to nanoCAGE technology and next-generation sequencing we have identified the genome-wide collection of active promoters in the mouse Main Olfactory Epithelium (MOE). Transcription start sites (TSSs) for the large majority of Olfactory Receptors (ORs) have been previously mapped increasing our understanding of their promoter architecture. Here we show that in our nanoCAGE libraries of the mouse MOE we detect a large number of tags mapped in loci hosting Type-1 and Type-2 Vomeronasal Receptors genes (V1Rs and V2Rs). These loci also show a massive expression of Long Interspersed Nuclear Elements (LINEs). We have validated the expression of selected receptors detected by nanoCAGE with in situ hybridization, RT-PCR and qRT-PCR. This work extends the repertory of receptors capable of sensing chemical signals in the MOE, suggesting intriguing interplays between MOE and VNO for pheromone processing and positioning transcribed LINEs as candidate regulatory RNAs for VRs expression.}, keywords = {}, pubstate = {}, tppubtype = {article} } By coupling laser capture microdissection to nanoCAGE technology and next-generation sequencing we have identified the genome-wide collection of active promoters in the mouse Main Olfactory Epithelium (MOE). Transcription start sites (TSSs) for the large majority of Olfactory Receptors (ORs) have been previously mapped increasing our understanding of their promoter architecture. Here we show that in our nanoCAGE libraries of the mouse MOE we detect a large number of tags mapped in loci hosting Type-1 and Type-2 Vomeronasal Receptors genes (V1Rs and V2Rs). These loci also show a massive expression of Long Interspersed Nuclear Elements (LINEs). We have validated the expression of selected receptors detected by nanoCAGE with in situ hybridization, RT-PCR and qRT-PCR. This work extends the repertory of receptors capable of sensing chemical signals in the MOE, suggesting intriguing interplays between MOE and VNO for pheromone processing and positioning transcribed LINEs as candidate regulatory RNAs for VRs expression. | |
Richardson, Sandra R; Morell, Santiago; Faulkner, Geoffrey J L1 retrotransposons and somatic mosaicism in the brain (Journal Article) Annu. Rev. Genet., 48 , pp. 1–27, 2014. @article{Richardson2014-nf, title = {L1 retrotransposons and somatic mosaicism in the brain}, author = {Sandra R Richardson and Santiago Morell and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1146/annurev-genet-120213-092412}, year = {2014}, date = {2014-01-01}, journal = {Annu. Rev. Genet.}, volume = {48}, pages = {1--27}, abstract = {Long interspersed element 1 (LINE-1 or L1) retrotransposons have generated one-third of the human genome, and their ongoing mobility is a source of inter- and intraindividual genetic diversity. Although retrotransposition in metazoans has long been considered a germline phenomenon, recent experiments using cultured cells, animal models, and human tissues have revealed extensive L1 mobilization in rodent and human neurons, as well as mobile element activity in the Drosophila brain. In this review, we evaluate the available evidence for L1 retrotransposition in the brain and discuss mechanisms that may regulate neuronal retrotransposition in vivo. We compare experimental strategies used to map de novo somatic retrotransposition events and present the optimal criteria to identify a somatic L1 insertion. Finally, we discuss the unresolved impact of L1-mediated somatic mosaicism upon normal neurobiology, as well as its potential to drive neurological disease.}, keywords = {}, pubstate = {}, tppubtype = {article} } Long interspersed element 1 (LINE-1 or L1) retrotransposons have generated one-third of the human genome, and their ongoing mobility is a source of inter- and intraindividual genetic diversity. Although retrotransposition in metazoans has long been considered a germline phenomenon, recent experiments using cultured cells, animal models, and human tissues have revealed extensive L1 mobilization in rodent and human neurons, as well as mobile element activity in the Drosophila brain. In this review, we evaluate the available evidence for L1 retrotransposition in the brain and discuss mechanisms that may regulate neuronal retrotransposition in vivo. We compare experimental strategies used to map de novo somatic retrotransposition events and present the optimal criteria to identify a somatic L1 insertion. Finally, we discuss the unresolved impact of L1-mediated somatic mosaicism upon normal neurobiology, as well as its potential to drive neurological disease. | |
Carreira, Patricia E; Richardson, Sandra R; Faulkner, Geoffrey J L1 retrotransposons, cancer stem cells and oncogenesis (Journal Article) FEBS J., 281 (1), pp. 63–73, 2014. @article{Carreira2014-oa, title = {L1 retrotransposons, cancer stem cells and oncogenesis}, author = {Patricia E Carreira and Sandra R Richardson and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1111/febs.12601}, year = {2014}, date = {2014-01-01}, journal = {FEBS J.}, volume = {281}, number = {1}, pages = {63--73}, abstract = {Retrotransposons have played a central role in human genome evolution. The accumulation of heritable L1, Alu and SVA retrotransposon insertions continues to generate structural variation within and between populations, and can result in spontaneous genetic disease. Recent works have reported somatic L1 retrotransposition in tumours, which in some cases may contribute to oncogenesis. Intriguingly, L1 mobilization appears to occur almost exclusively in cancers of epithelial cell origin. In this review, we discuss how L1 retrotransposition could potentially trigger neoplastic transformation, based on the established correlation between L1 activity and cellular plasticity, and the proven capacity of L1-mediated insertional mutagenesis to decisively alter gene expression and functional output.}, keywords = {}, pubstate = {}, tppubtype = {article} } Retrotransposons have played a central role in human genome evolution. The accumulation of heritable L1, Alu and SVA retrotransposon insertions continues to generate structural variation within and between populations, and can result in spontaneous genetic disease. Recent works have reported somatic L1 retrotransposition in tumours, which in some cases may contribute to oncogenesis. Intriguingly, L1 mobilization appears to occur almost exclusively in cancers of epithelial cell origin. In this review, we discuss how L1 retrotransposition could potentially trigger neoplastic transformation, based on the established correlation between L1 activity and cellular plasticity, and the proven capacity of L1-mediated insertional mutagenesis to decisively alter gene expression and functional output. | |
2013 | |
Faulkner, Geoffrey J Retrotransposon silencing during embryogenesis: dicer cuts in LINE (Journal Article) PLoS Genet., 9 (11), pp. e1003944, 2013. @article{Faulkner2013-sf, title = {Retrotransposon silencing during embryogenesis: dicer cuts in LINE}, author = {Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1371/journal.pgen.1003944}, year = {2013}, date = {2013-11-01}, journal = {PLoS Genet.}, volume = {9}, number = {11}, pages = {e1003944}, keywords = {}, pubstate = {}, tppubtype = {article} } | |
Reilly, Matthew T; Faulkner, Geoffrey J; Dubnau, Joshua; Ponomarev, Igor; Gage, Fred H The role of transposable elements in health and diseases of the central nervous system (Journal Article) J. Neurosci., 33 (45), pp. 17577–17586, 2013. @article{Reilly2013-ne, title = {The role of transposable elements in health and diseases of the central nervous system}, author = {Matthew T Reilly and Geoffrey J Faulkner and Joshua Dubnau and Igor Ponomarev and Fred H Gage}, url = {http://dx.doi.org/10.1523/JNEUROSCI.3369-13.2013}, year = {2013}, date = {2013-11-01}, journal = {J. Neurosci.}, volume = {33}, number = {45}, pages = {17577--17586}, abstract = {First discovered in maize by Barbara McClintock in the 1940s, transposable elements (TEs) are DNA sequences that in some cases have the ability to move along chromosomes or ``transpose'' in the genome. This revolutionary finding was initially met with resistance by the scientific community and viewed by some as heretical. A large body of knowledge has accumulated over the last 60 years on the biology of TEs. Indeed, it is now known that TEs can generate genomic instability and reconfigure gene expression networks both in the germline and somatic cells. This review highlights recent findings on the role of TEs in health and diseases of the CNS, which were presented at the 2013 Society for Neuroscience meeting. The work of the speakers in this symposium shows that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings on TE expression and function in the CNS have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in shaping individual behavior and contribute to vulnerability to disease.}, keywords = {}, pubstate = {}, tppubtype = {article} } First discovered in maize by Barbara McClintock in the 1940s, transposable elements (TEs) are DNA sequences that in some cases have the ability to move along chromosomes or ``transpose'' in the genome. This revolutionary finding was initially met with resistance by the scientific community and viewed by some as heretical. A large body of knowledge has accumulated over the last 60 years on the biology of TEs. Indeed, it is now known that TEs can generate genomic instability and reconfigure gene expression networks both in the germline and somatic cells. This review highlights recent findings on the role of TEs in health and diseases of the CNS, which were presented at the 2013 Society for Neuroscience meeting. The work of the speakers in this symposium shows that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings on TE expression and function in the CNS have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in shaping individual behavior and contribute to vulnerability to disease. | |
Li, Jian-Liang; Mazar, Joseph; Zhong, Cuncong; Faulkner, Geoffrey J; Govindarajan, Subramaniam S; Zhang, Zhan; Dinger, Marcel E; Meredith, Gavin; Adams, Christopher; Zhang, Shaojie; Mattick, John S; Ray, Animesh; Perera, Ranjan J Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network (Journal Article) Sci. Rep., 3 , pp. 2962, 2013. @article{Li2013-qx, title = {Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network}, author = {Jian-Liang Li and Joseph Mazar and Cuncong Zhong and Geoffrey J Faulkner and Subramaniam S Govindarajan and Zhan Zhang and Marcel E Dinger and Gavin Meredith and Christopher Adams and Shaojie Zhang and John S Mattick and Animesh Ray and Ranjan J Perera}, url = {http://dx.doi.org/10.1038/srep02962}, year = {2013}, date = {2013-01-01}, journal = {Sci. Rep.}, volume = {3}, pages = {2962}, abstract = {Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity.}, keywords = {}, pubstate = {}, tppubtype = {article} } Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity. | |
Shukla, Ruchi; Upton, Kyle R; ~n, Martin Mu; Gerhardt, Daniel J; Fisher, Malcolm E; Nguyen, Thu; Brennan, Paul M; Baillie, Kenneth J; Collino, Agnese; Ghisletti, Serena; Sinha, Shruti; Iannelli, Fabio; Radaelli, Enrico; Santos, Alexandre Dos; Rapoud, Delphine; Guettier, Catherine; Samuel, Didier; Natoli, Gioacchino; Carninci, Piero; Ciccarelli, Francesca D; Garcia-Perez, Jose Luis; Faivre, Jamila; Faulkner, Geoffrey J Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma (Journal Article) Cell, 153 (1), pp. 101–111, 2013. @article{Shukla2013-dp, title = {Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma}, author = {Ruchi Shukla and Kyle R Upton and Martin Mu{~n}oz-Lopez and Daniel J Gerhardt and Malcolm E Fisher and Thu Nguyen and Paul M Brennan and Kenneth J Baillie and Agnese Collino and Serena Ghisletti and Shruti Sinha and Fabio Iannelli and Enrico Radaelli and Alexandre Dos Santos and Delphine Rapoud and Catherine Guettier and Didier Samuel and Gioacchino Natoli and Piero Carninci and Francesca D Ciccarelli and Jose Luis Garcia-Perez and Jamila Faivre and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1016/j.cell.2013.02.032}, year = {2013}, date = {2013-01-01}, journal = {Cell}, volume = {153}, number = {1}, pages = {101--111}, abstract = {LINE-1 (L1) retrotransposons are mobile genetic elements comprising ~17% of the human genome. New L1 insertions can profoundly alter gene function and cause disease, though their significance in cancer remains unclear. Here, we applied enhanced retrotransposon capture sequencing (RC-seq) to 19 hepatocellular carcinoma (HCC) genomes and elucidated two archetypal L1-mediated mechanisms enabling tumorigenesis. In the first example, 4/19 (21.1%) donors presented germline retrotransposition events in the tumor suppressor mutated in colorectal cancers (MCC). MCC expression was ablated in each case, enabling oncogenic $beta$-catenin/Wnt signaling. In the second example, suppression of tumorigenicity 18 (ST18) was activated by a tumor-specific L1 insertion. Experimental assays confirmed that the L1 interrupted a negative feedback loop by blocking ST18 repression of its enhancer. ST18 was also frequently amplified in HCC nodules from Mdr2(-/-) mice, supporting its assignment as a candidate liver oncogene. These proof-of-principle results substantiate L1-mediated retrotransposition as an important etiological factor in HCC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } LINE-1 (L1) retrotransposons are mobile genetic elements comprising ~17% of the human genome. New L1 insertions can profoundly alter gene function and cause disease, though their significance in cancer remains unclear. Here, we applied enhanced retrotransposon capture sequencing (RC-seq) to 19 hepatocellular carcinoma (HCC) genomes and elucidated two archetypal L1-mediated mechanisms enabling tumorigenesis. In the first example, 4/19 (21.1%) donors presented germline retrotransposition events in the tumor suppressor mutated in colorectal cancers (MCC). MCC expression was ablated in each case, enabling oncogenic $beta$-catenin/Wnt signaling. In the second example, suppression of tumorigenicity 18 (ST18) was activated by a tumor-specific L1 insertion. Experimental assays confirmed that the L1 interrupted a negative feedback loop by blocking ST18 repression of its enhancer. ST18 was also frequently amplified in HCC nodules from Mdr2(-/-) mice, supporting its assignment as a candidate liver oncogene. These proof-of-principle results substantiate L1-mediated retrotransposition as an important etiological factor in HCC. | |
2012 | |
Solyom, Szilvia; Ewing, Adam D; Rahrmann, Eric P; Doucet, Tara; Nelson, Heather H; Burns, Michael B; Harris, Reuben S; Sigmon, David F; Casella, Alex; Erlanger, Bracha; Wheelan, Sarah; Upton, Kyle R; Shukla, Ruchi; Faulkner, Geoffrey J; Largaespada, David A; Jr, Haig Kazazian H Extensive somatic L1 retrotransposition in colorectal tumors (Journal Article) Genome Res., 22 (12), pp. 2328–2338, 2012. @article{Solyom2012-pc, title = {Extensive somatic L1 retrotransposition in colorectal tumors}, author = {Szilvia Solyom and Adam D Ewing and Eric P Rahrmann and Tara Doucet and Heather H Nelson and Michael B Burns and Reuben S Harris and David F Sigmon and Alex Casella and Bracha Erlanger and Sarah Wheelan and Kyle R Upton and Ruchi Shukla and Geoffrey J Faulkner and David A Largaespada and Haig H Kazazian Jr}, url = {http://dx.doi.org/10.1101/gr.145235.112}, year = {2012}, date = {2012-12-01}, journal = {Genome Res.}, volume = {22}, number = {12}, pages = {2328--2338}, abstract = {L1 retrotransposons comprise 17% of the human genome and are its only autonomous mobile elements. Although L1-induced insertional mutagenesis causes Mendelian disease, their mutagenic load in cancer has been elusive. Using L1-targeted resequencing of 16 colorectal tumor and matched normal DNAs, we found that certain cancers were excessively mutagenized by human-specific L1s, while no verifiable insertions were present in normal tissues. We confirmed de novo L1 insertions in malignancy by both validating and sequencing 69/107 tumor-specific insertions and retrieving both 5' and 3' junctions for 35. In contrast to germline polymorphic L1s, all insertions were severely 5' truncated. Validated insertion numbers varied from up to 17 in some tumors to none in three others, and correlated with the age of the patients. Numerous genes with a role in tumorigenesis were targeted, including ODZ3, ROBO2, PTPRM, PCM1, and CDH11. Thus, somatic retrotransposition may play an etiologic role in colorectal cancer.}, keywords = {}, pubstate = {}, tppubtype = {article} } L1 retrotransposons comprise 17% of the human genome and are its only autonomous mobile elements. Although L1-induced insertional mutagenesis causes Mendelian disease, their mutagenic load in cancer has been elusive. Using L1-targeted resequencing of 16 colorectal tumor and matched normal DNAs, we found that certain cancers were excessively mutagenized by human-specific L1s, while no verifiable insertions were present in normal tissues. We confirmed de novo L1 insertions in malignancy by both validating and sequencing 69/107 tumor-specific insertions and retrieving both 5' and 3' junctions for 35. In contrast to germline polymorphic L1s, all insertions were severely 5' truncated. Validated insertion numbers varied from up to 17 in some tumors to none in three others, and correlated with the age of the patients. Numerous genes with a role in tumorigenesis were targeted, including ODZ3, ROBO2, PTPRM, PCM1, and CDH11. Thus, somatic retrotransposition may play an etiologic role in colorectal cancer. | |
Groenen, Martien A M; Archibald, Alan L; Uenishi, Hirohide; Tuggle, Christopher K; Takeuchi, Yasuhiro; Rothschild, Max F; Rogel-Gaillard, Claire; Park, Chankyu; Milan, Denis; Megens, Hendrik-Jan; Li, Shengting; Larkin, Denis M; Kim, Heebal; Frantz, Laurent A F; Caccamo, Mario; Ahn, Hyeonju; Aken, Bronwen L; Anselmo, Anna; Anthon, Christian; Auvil, Loretta; Badaoui, Bouabid; Beattie, Craig W; Bendixen, Christian; Berman, Daniel; Blecha, Frank; Blomberg, Jonas; Bolund, Lars; Bosse, Mirte; Botti, Sara; Bujie, Zhan; Bystrom, Megan; Capitanu, Boris; Carvalho-Silva, Denise; Chardon, Patrick; Chen, Celine; Cheng, Ryan; Choi, Sang-Haeng; Chow, William; Clark, Richard C; Clee, Christopher; Crooijmans, Richard P M A; Dawson, Harry D; Dehais, Patrice; Sapio, Fioravante De; Dibbits, Bert; Drou, Nizar; Du, Zhi-Qiang; Eversole, Kellye; ~a, Jo; Fairley, Susan; Faraut, Thomas; Faulkner, Geoffrey J; Fowler, Katie E; Fredholm, Merete; Fritz, Eric; Gilbert, James G R; Giuffra, Elisabetta; Gorodkin, Jan; Griffin, Darren K; Harrow, Jennifer L; Hayward, Alexander; Howe, Kerstin; Hu, Zhi-Liang; Humphray, Sean J; Hunt, Toby; ø, Henrik Hornsh; Jeon, Jin-Tae; Jern, Patric; Jones, Matthew; Jurka, Jerzy; Kanamori, Hiroyuki; Kapetanovic, Ronan; Kim, Jaebum; Kim, Jae-Hwan; Kim, Kyu-Won; Kim, Tae-Hun; Larson, Greger; Lee, Kyooyeol; Lee, Kyung-Tai; Leggett, Richard; Lewin, Harris A; Li, Yingrui; Liu, Wansheng; Loveland, Jane E; Lu, Yao; Lunney, Joan K; Ma, Jian; Madsen, Ole; Mann, Katherine; Matthews, Lucy; McLaren, Stuart; Morozumi, Takeya; Murtaugh, Michael P; Narayan, Jitendra; Nguyen, Dinh Truong; Ni, Peixiang; Oh, Song-Jung; Onteru, Suneel; Panitz, Frank; Park, Eung-Woo; Park, Hong-Seog; Pascal, Geraldine; Paudel, Yogesh; Perez-Enciso, Miguel; Ramirez-Gonzalez, Ricardo; Reecy, James M; Rodriguez-Zas, Sandra; Rohrer, Gary A; Rund, Lauretta; Sang, Yongming; Schachtschneider, Kyle; Schraiber, Joshua G; Schwartz, John; Scobie, Linda; Scott, Carol; Searle, Stephen; Servin, Bertrand; Southey, Bruce R; Sperber, Goran; Stadler, Peter; Sweedler, Jonathan V; Tafer, Hakim; Thomsen, Bo; Wali, Rashmi; Wang, Jian; Wang, Jun; White, Simon; Xu, Xun; Yerle, Martine; Zhang, Guojie; Zhang, Jianguo; Zhang, Jie; Zhao, Shuhong; Rogers, Jane; Churcher, Carol; Schook, Lawrence B Analyses of pig genomes provide insight into porcine demography and evolution (Journal Article) Nature, 491 (7424), pp. 393–398, 2012. @article{Groenen2012-st, title = {Analyses of pig genomes provide insight into porcine demography and evolution}, author = {Martien A M Groenen and Alan L Archibald and Hirohide Uenishi and Christopher K Tuggle and Yasuhiro Takeuchi and Max F Rothschild and Claire Rogel-Gaillard and Chankyu Park and Denis Milan and Hendrik-Jan Megens and Shengting Li and Denis M Larkin and Heebal Kim and Laurent A F Frantz and Mario Caccamo and Hyeonju Ahn and Bronwen L Aken and Anna Anselmo and Christian Anthon and Loretta Auvil and Bouabid Badaoui and Craig W Beattie and Christian Bendixen and Daniel Berman and Frank Blecha and Jonas Blomberg and Lars Bolund and Mirte Bosse and Sara Botti and Zhan Bujie and Megan Bystrom and Boris Capitanu and Denise Carvalho-Silva and Patrick Chardon and Celine Chen and Ryan Cheng and Sang-Haeng Choi and William Chow and Richard C Clark and Christopher Clee and Richard P M A Crooijmans and Harry D Dawson and Patrice Dehais and Fioravante De Sapio and Bert Dibbits and Nizar Drou and Zhi-Qiang Du and Kellye Eversole and Jo{~a}o Fadista and Susan Fairley and Thomas Faraut and Geoffrey J Faulkner and Katie E Fowler and Merete Fredholm and Eric Fritz and James G R Gilbert and Elisabetta Giuffra and Jan Gorodkin and Darren K Griffin and Jennifer L Harrow and Alexander Hayward and Kerstin Howe and Zhi-Liang Hu and Sean J Humphray and Toby Hunt and Henrik Hornsh{\o}j and Jin-Tae Jeon and Patric Jern and Matthew Jones and Jerzy Jurka and Hiroyuki Kanamori and Ronan Kapetanovic and Jaebum Kim and Jae-Hwan Kim and Kyu-Won Kim and Tae-Hun Kim and Greger Larson and Kyooyeol Lee and Kyung-Tai Lee and Richard Leggett and Harris A Lewin and Yingrui Li and Wansheng Liu and Jane E Loveland and Yao Lu and Joan K Lunney and Jian Ma and Ole Madsen and Katherine Mann and Lucy Matthews and Stuart McLaren and Takeya Morozumi and Michael P Murtaugh and Jitendra Narayan and Dinh Truong Nguyen and Peixiang Ni and Song-Jung Oh and Suneel Onteru and Frank Panitz and Eung-Woo Park and Hong-Seog Park and Geraldine Pascal and Yogesh Paudel and Miguel Perez-Enciso and Ricardo Ramirez-Gonzalez and James M Reecy and Sandra Rodriguez-Zas and Gary A Rohrer and Lauretta Rund and Yongming Sang and Kyle Schachtschneider and Joshua G Schraiber and John Schwartz and Linda Scobie and Carol Scott and Stephen Searle and Bertrand Servin and Bruce R Southey and Goran Sperber and Peter Stadler and Jonathan V Sweedler and Hakim Tafer and Bo Thomsen and Rashmi Wali and Jian Wang and Jun Wang and Simon White and Xun Xu and Martine Yerle and Guojie Zhang and Jianguo Zhang and Jie Zhang and Shuhong Zhao and Jane Rogers and Carol Churcher and Lawrence B Schook}, url = {http://dx.doi.org/10.1038/nature11622}, year = {2012}, date = {2012-11-01}, journal = {Nature}, volume = {491}, number = {7424}, pages = {393--398}, abstract = {For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.}, keywords = {}, pubstate = {}, tppubtype = {article} } For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. | |
Plessy, Charles; Pascarella, Giovanni; Bertin, Nicolas; Akalin, Altuna; Carrieri, Claudia; Vassalli, Anne; Lazarevic, Dejan; Severin, Jessica; Vlachouli, Christina; Simone, Roberto; Faulkner, Geoffrey J; Kawai, Jun; Daub, Carsten O; Zucchelli, Silvia; Hayashizaki, Yoshihide; Mombaerts, Peter; Lenhard, Boris; Gustincich, Stefano; Carninci, Piero Promoter architecture of mouse olfactory receptor genes (Journal Article) Genome Res., 22 (3), pp. 486–497, 2012. @article{Plessy2012-qp, title = {Promoter architecture of mouse olfactory receptor genes}, author = {Charles Plessy and Giovanni Pascarella and Nicolas Bertin and Altuna Akalin and Claudia Carrieri and Anne Vassalli and Dejan Lazarevic and Jessica Severin and Christina Vlachouli and Roberto Simone and Geoffrey J Faulkner and Jun Kawai and Carsten O Daub and Silvia Zucchelli and Yoshihide Hayashizaki and Peter Mombaerts and Boris Lenhard and Stefano Gustincich and Piero Carninci}, url = {http://dx.doi.org/10.1101/gr.126201.111}, year = {2012}, date = {2012-03-01}, journal = {Genome Res.}, volume = {22}, number = {3}, pages = {486--497}, abstract = {Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice.}, keywords = {}, pubstate = {}, tppubtype = {article} } Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice. | |
Schroder, Kate; Irvine, Katharine M; Taylor, Martin S; Bokil, Nilesh J; Cao, Kim-Anh Le; Masterman, Kelly-Anne; Labzin, Larisa I; Semple, Colin A; Kapetanovic, Ronan; Fairbairn, Lynsey; Akalin, Altuna; Faulkner, Geoffrey J; Baillie, John Kenneth; Gongora, Milena; Daub, Carsten O; Kawaji, Hideya; McLachlan, Geoffrey J; Goldman, Nick; Grimmond, Sean M; Carninci, Piero; Suzuki, Harukazu; Hayashizaki, Yoshihide; Lenhard, Boris; Hume, David A; Sweet, Matthew J Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages (Journal Article) Proc. Natl. Acad. Sci. U. S. A., 109 (16), pp. E944–53, 2012. @article{Schroder2012-yr, title = {Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages}, author = {Kate Schroder and Katharine M Irvine and Martin S Taylor and Nilesh J Bokil and Kim-Anh Le Cao and Kelly-Anne Masterman and Larisa I Labzin and Colin A Semple and Ronan Kapetanovic and Lynsey Fairbairn and Altuna Akalin and Geoffrey J Faulkner and John Kenneth Baillie and Milena Gongora and Carsten O Daub and Hideya Kawaji and Geoffrey J McLachlan and Nick Goldman and Sean M Grimmond and Piero Carninci and Harukazu Suzuki and Yoshihide Hayashizaki and Boris Lenhard and David A Hume and Matthew J Sweet}, url = {http://dx.doi.org/10.1073/pnas.1110156109}, year = {2012}, date = {2012-01-01}, journal = {Proc. Natl. Acad. Sci. U. S. A.}, volume = {109}, number = {16}, pages = {E944--53}, abstract = {Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies differences in the transcriptional responses of primary human and mouse macrophages to the Toll-like receptor (TLR)-4 agonist lipopolysaccharide (LPS). By using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5' ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologues were identified as ``divergently regulated''). We further demonstrate concordant regulation of human-specific LPS target genes in primary pig macrophages. Divergently regulated orthologues were enriched for genes encoding cellular ``inputs'' such as cell surface receptors (e.g., TLR6, IL-7R$alpha$) and functional ``outputs'' such as inflammatory cytokines/chemokines (e.g., CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. Functional consequences of divergent gene regulation were confirmed by showing LPS pretreatment boosts subsequent TLR6 responses in mouse but not human macrophages, in keeping with mouse-specific TLR6 induction. Divergently regulated genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced interspecies promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change.}, keywords = {}, pubstate = {}, tppubtype = {article} } Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing interspecies differences in the transcriptional responses of primary human and mouse macrophages to the Toll-like receptor (TLR)-4 agonist lipopolysaccharide (LPS). By using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5' ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologues were identified as ``divergently regulated''). We further demonstrate concordant regulation of human-specific LPS target genes in primary pig macrophages. Divergently regulated orthologues were enriched for genes encoding cellular ``inputs'' such as cell surface receptors (e.g., TLR6, IL-7R$alpha$) and functional ``outputs'' such as inflammatory cytokines/chemokines (e.g., CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. Functional consequences of divergent gene regulation were confirmed by showing LPS pretreatment boosts subsequent TLR6 responses in mouse but not human macrophages, in keeping with mouse-specific TLR6 induction. Divergently regulated genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced interspecies promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change. | |
2011 | |
Upton, Kyle R; Baillie, Kenneth J; Faulkner, Geoffrey J Is somatic retrotransposition a parasitic or symbiotic phenomenon? (Journal Article) Mob. Genet. Elements, 1 (4), pp. 279–282, 2011. @article{Upton2011-cl, title = {Is somatic retrotransposition a parasitic or symbiotic phenomenon?}, author = {Kyle R Upton and Kenneth J Baillie and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.4161/mge.18422}, year = {2011}, date = {2011-11-01}, journal = {Mob. Genet. Elements}, volume = {1}, number = {4}, pages = {279--282}, abstract = {The extraordinary evolutionary success of transposable elements (TEs) invites us to question the nature of the co-evolutionary dynamics between TE and host. Although sometimes assumed to be wholly parasitic, TEs have penetrated and spread throughout eukaryotic genomes at a rate unparalleled by other parasites. This near-ubiquity, occurring despite the potentially deleterious effects of insertional mutagenesis, raises the possibility that a counterbalancing benefit exists for the host. Such a benefit may act at the population level to generate genomic diversity within a species and hence greater adaptability under new selective pressures, or at the level of primary gain for the individual. Recent studies have highlighted the occurrence of retrotransposition events in the germline and discovered a surprisingly high rate of mobilization in somatic cells. Here we examine the available evidence for somatic retrotransposition and discuss how this phenomenon may confer a selective advantage upon an individual or species.}, keywords = {}, pubstate = {}, tppubtype = {article} } The extraordinary evolutionary success of transposable elements (TEs) invites us to question the nature of the co-evolutionary dynamics between TE and host. Although sometimes assumed to be wholly parasitic, TEs have penetrated and spread throughout eukaryotic genomes at a rate unparalleled by other parasites. This near-ubiquity, occurring despite the potentially deleterious effects of insertional mutagenesis, raises the possibility that a counterbalancing benefit exists for the host. Such a benefit may act at the population level to generate genomic diversity within a species and hence greater adaptability under new selective pressures, or at the level of primary gain for the individual. Recent studies have highlighted the occurrence of retrotransposition events in the germline and discovered a surprisingly high rate of mobilization in somatic cells. Here we examine the available evidence for somatic retrotransposition and discuss how this phenomenon may confer a selective advantage upon an individual or species. | |
Baillie, Kenneth J; Barnett, Mark W; Upton, Kyle R; Gerhardt, Daniel J; Richmond, Todd A; Sapio, Fioravante De; Brennan, Paul M; Rizzu, Patrizia; Smith, Sarah; Fell, Mark; Talbot, Richard T; Gustincich, Stefano; Freeman, Thomas C; Mattick, John S; Hume, David A; Heutink, Peter; Carninci, Piero; Jeddeloh, Jeffrey A; Faulkner, Geoffrey J Somatic retrotransposition alters the genetic landscape of the human brain (Journal Article) Nature, 479 (7374), pp. 534–537, 2011. @article{Baillie2011-cw, title = {Somatic retrotransposition alters the genetic landscape of the human brain}, author = {Kenneth J Baillie and Mark W Barnett and Kyle R Upton and Daniel J Gerhardt and Todd A Richmond and Fioravante De Sapio and Paul M Brennan and Patrizia Rizzu and Sarah Smith and Mark Fell and Richard T Talbot and Stefano Gustincich and Thomas C Freeman and John S Mattick and David A Hume and Peter Heutink and Piero Carninci and Jeffrey A Jeddeloh and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1038/nature10531}, year = {2011}, date = {2011-10-01}, journal = {Nature}, volume = {479}, number = {7374}, pages = {534--537}, abstract = {Retrotransposons are mobile genetic elements that use a germline 'copy-and-paste' mechanism to spread throughout metazoan genomes. At least 50 per cent of the human genome is derived from retrotransposons, with three active families (L1, Alu and SVA) associated with insertional mutagenesis and disease. Epigenetic and post-transcriptional suppression block retrotransposition in somatic cells, excluding early embryo development and some malignancies. Recent reports of L1 expression and copy number variation in the human brain suggest that L1 mobilization may also occur during later development. However, the corresponding integration sites have not been mapped. Here we apply a high-throughput method to identify numerous L1, Alu and SVA germline mutations, as well as 7,743 putative somatic L1 insertions, in the hippocampus and caudate nucleus of three individuals. Surprisingly, we also found 13,692 somatic Alu insertions and 1,350 SVA insertions. Our results demonstrate that retrotransposons mobilize to protein-coding genes differentially expressed and active in the brain. Thus, somatic genome mosaicism driven by retrotransposition may reshape the genetic circuitry that underpins normal and abnormal neurobiological processes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Retrotransposons are mobile genetic elements that use a germline 'copy-and-paste' mechanism to spread throughout metazoan genomes. At least 50 per cent of the human genome is derived from retrotransposons, with three active families (L1, Alu and SVA) associated with insertional mutagenesis and disease. Epigenetic and post-transcriptional suppression block retrotransposition in somatic cells, excluding early embryo development and some malignancies. Recent reports of L1 expression and copy number variation in the human brain suggest that L1 mobilization may also occur during later development. However, the corresponding integration sites have not been mapped. Here we apply a high-throughput method to identify numerous L1, Alu and SVA germline mutations, as well as 7,743 putative somatic L1 insertions, in the hippocampus and caudate nucleus of three individuals. Surprisingly, we also found 13,692 somatic Alu insertions and 1,350 SVA insertions. Our results demonstrate that retrotransposons mobilize to protein-coding genes differentially expressed and active in the brain. Thus, somatic genome mosaicism driven by retrotransposition may reshape the genetic circuitry that underpins normal and abnormal neurobiological processes. | |
Faulkner, Geoffrey J Retrotransposons: mobile and mutagenic from conception to death (Journal Article) FEBS Lett., 585 (11), pp. 1589–1594, 2011. @article{Faulkner2011-hs, title = {Retrotransposons: mobile and mutagenic from conception to death}, author = {Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1016/j.febslet.2011.03.061}, year = {2011}, date = {2011-01-01}, journal = {FEBS Lett.}, volume = {585}, number = {11}, pages = {1589--1594}, abstract = {Mobile genetic elements feature prominently in mammalian genome evolution. Several transposition-competent retrotransposon families (L1, Alu, SVA) remain active in the human germ line, leading to pathogenesis as well as genome structural variation across the global population. High-throughput screening approaches have recently been developed to detect retrotransposon insertion polymorphisms. Evidence produced by these and other genome-scale technologies indicates an expanded role for retrotransposition in human biology, including somatic mobilisation in the developing embryo and in neural cells.}, keywords = {}, pubstate = {}, tppubtype = {article} } Mobile genetic elements feature prominently in mammalian genome evolution. Several transposition-competent retrotransposon families (L1, Alu, SVA) remain active in the human germ line, leading to pathogenesis as well as genome structural variation across the global population. High-throughput screening approaches have recently been developed to detect retrotransposon insertion polymorphisms. Evidence produced by these and other genome-scale technologies indicates an expanded role for retrotransposition in human biology, including somatic mobilisation in the developing embryo and in neural cells. | |
2010 | |
de Hoon, Michiel J L; Taft, Ryan J; Hashimoto, Takehiro; Kanamori-Katayama, Mutsumi; Kawaji, Hideya; Kawano, Mitsuoki; Kishima, Mami; Lassmann, Timo; Faulkner, Geoffrey J; Mattick, John S; Daub, Carsten O; Carninci, Piero; Kawai, Jun; Suzuki, Harukazu; Hayashizaki, Yoshihide Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries (Journal Article) Genome Res., 20 (2), pp. 257–264, 2010. @article{De_Hoon2010-nt, title = {Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries}, author = {Michiel J L de Hoon and Ryan J Taft and Takehiro Hashimoto and Mutsumi Kanamori-Katayama and Hideya Kawaji and Mitsuoki Kawano and Mami Kishima and Timo Lassmann and Geoffrey J Faulkner and John S Mattick and Carsten O Daub and Piero Carninci and Jun Kawai and Harukazu Suzuki and Yoshihide Hayashizaki}, url = {http://dx.doi.org/10.1101/gr.095273.109}, year = {2010}, date = {2010-02-01}, journal = {Genome Res.}, volume = {20}, number = {2}, pages = {257--264}, abstract = {MicroRNAs (miRNAs) are short (20-23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals.}, keywords = {}, pubstate = {}, tppubtype = {article} } MicroRNAs (miRNAs) are short (20-23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals. | |
Mattick, John S; Taft, Ryan J; Faulkner, Geoffrey J A global view of genomic information--moving beyond the gene and the master regulator (Journal Article) Trends Genet., 26 (1), pp. 21–28, 2010. @article{Mattick2010-dl, title = {A global view of genomic information--moving beyond the gene and the master regulator}, author = {John S Mattick and Ryan J Taft and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1016/j.tig.2009.11.002}, year = {2010}, date = {2010-01-01}, journal = {Trends Genet.}, volume = {26}, number = {1}, pages = {21--28}, abstract = {The current view of gene regulation in complex organisms holds that gene expression is largely controlled by the combinatoric actions of transcription factors and other regulatory proteins, some of which powerfully influence cell type. Recent large-scale studies have confirmed that cellular differentiation involves many different regulatory factors. However, other studies indicate that the genome is pervasively transcribed to produce a variety of short and long non-protein-coding RNAs, including those derived from retrotransposed sequences, which also play important roles in the epigenetic regulation of gene expression. The evidence suggests that ontogenesis requires interplay between state-specific regulatory proteins, multitasked effector complexes and target-specific RNAs that recruit these complexes to their sites of action. Moreover, the semi-continuous nature of the transcriptome prompts the reassessment of 'genes' as discrete entities and indicates that the mammalian genome might be more accurately viewed as islands of protein-coding information in a sea of cis- and trans-acting regulatory sequences.}, keywords = {}, pubstate = {}, tppubtype = {article} } The current view of gene regulation in complex organisms holds that gene expression is largely controlled by the combinatoric actions of transcription factors and other regulatory proteins, some of which powerfully influence cell type. Recent large-scale studies have confirmed that cellular differentiation involves many different regulatory factors. However, other studies indicate that the genome is pervasively transcribed to produce a variety of short and long non-protein-coding RNAs, including those derived from retrotransposed sequences, which also play important roles in the epigenetic regulation of gene expression. The evidence suggests that ontogenesis requires interplay between state-specific regulatory proteins, multitasked effector complexes and target-specific RNAs that recruit these complexes to their sites of action. Moreover, the semi-continuous nature of the transcriptome prompts the reassessment of 'genes' as discrete entities and indicates that the mammalian genome might be more accurately viewed as islands of protein-coding information in a sea of cis- and trans-acting regulatory sequences. | |
2009 | |
Faulkner, Geoffrey J; Grimmond, Sean M Setting CAGE tags in a genomic context (Book Chapter) Carninci, Piero (Ed.): Cap-Analysis Gene Expression (CAGE) - the Science of Decoding Genes Transcription, Chapter 8, pp. 93-100, 2009, ISBN: 9789814241342, (Accessed: 2017-11-24). (Abstract | Links | BibTeX | Altmetric) @inbook{Faulkner2009c, title = {Setting CAGE tags in a genomic context}, author = {Geoffrey J Faulkner and Sean M Grimmond}, editor = {Piero Carninci}, doi = {10.4032/9789814241359}, isbn = {9789814241342}, year = {2009}, date = {2009-10-31}, booktitle = {Cap-Analysis Gene Expression (CAGE) - the Science of Decoding Genes Transcription}, pages = {93-100}, chapter = {8}, abstract = {The detection and quantification of transcriptional activity on the genome by CAGE requires reliable and high-throughput tag mapping. Here, we discuss the basic considerations of sequence tag mapping and how these apply to CAGE. The current CAGE mapping pipeline is then described in detail, in particular how it has been updated to utilize iterative global exact matching for each tag rather than heuristic algorithm local alignment. Combined with the addition of a novel method to resolve tags that map to multiple genomic locations, the most recent evolution of the CAGE mapping pipeline is faster, more accurate and provides better coverage than the previous approach, as we demonstrate using a sample CAGE library. Finally, the pipeline is easily customized for other sequence tag technologies, suggesting broad utility in the era of next-generation sequencing.}, howpublished = {urlhttp://www.panstanford.com/books/9789814241342.html}, note = {Accessed: 2017-11-24}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } The detection and quantification of transcriptional activity on the genome by CAGE requires reliable and high-throughput tag mapping. Here, we discuss the basic considerations of sequence tag mapping and how these apply to CAGE. The current CAGE mapping pipeline is then described in detail, in particular how it has been updated to utilize iterative global exact matching for each tag rather than heuristic algorithm local alignment. Combined with the addition of a novel method to resolve tags that map to multiple genomic locations, the most recent evolution of the CAGE mapping pipeline is faster, more accurate and provides better coverage than the previous approach, as we demonstrate using a sample CAGE library. Finally, the pipeline is easily customized for other sequence tag technologies, suggesting broad utility in the era of next-generation sequencing. | |
Cloonan, Nicole; Xu, Qinying; Faulkner, Geoffrey J; Taylor, Darrin F; Tang, Dave T P; Kolle, Gabriel; Grimmond, Sean M RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data (Journal Article) Bioinformatics, 25 (19), pp. 2615–2616, 2009. @article{Cloonan2009-qj, title = {RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data}, author = {Nicole Cloonan and Qinying Xu and Geoffrey J Faulkner and Darrin F Taylor and Dave T P Tang and Gabriel Kolle and Sean M Grimmond}, url = {http://dx.doi.org/10.1093/bioinformatics/btp459}, year = {2009}, date = {2009-10-01}, journal = {Bioinformatics}, volume = {25}, number = {19}, pages = {2615--2616}, abstract = {UNLABELLED: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context. AVAILABILITY: Executables, source code, and exon-junction libraries are available from http://grimmond.imb.uq.edu.au/RNA-MATE/}, keywords = {}, pubstate = {}, tppubtype = {article} } UNLABELLED: Mapping of next-generation sequencing data derived from RNA samples (RNAseq) presents different genome mapping challenges than data derived from DNA. For example, tags that cross exon-junction boundaries will often not map to a reference genome, and the strand specificity of the data needs to be retained. Here we present RNA-MATE, a computational pipeline based on a recursive mapping strategy for placing strand specific RNAseq data onto a reference genome. Maximizing the mappable tags can provide significant savings in the cost of sequencing experiments. This pipeline provides an automatic and integrated way to align color-space sequencing data, collate this information and generate files for examining gene-expression data in a genomic context. AVAILABILITY: Executables, source code, and exon-junction libraries are available from http://grimmond.imb.uq.edu.au/RNA-MATE/ | |
Hashimoto, Takehiro; de Hoon, Michiel J L; Grimmond, Sean M; Daub, Carsten O; Hayashizaki, Yoshihide; Faulkner, Geoffrey J Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite (Journal Article) Bioinformatics, 25 (19), pp. 2613–2614, 2009. @article{Hashimoto2009-pm, title = {Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite}, author = {Takehiro Hashimoto and Michiel J L de Hoon and Sean M Grimmond and Carsten O Daub and Yoshihide Hayashizaki and Geoffrey J Faulkner}, url = {http://dx.doi.org/10.1093/bioinformatics/btp438}, year = {2009}, date = {2009-10-01}, journal = {Bioinformatics}, volume = {25}, number = {19}, pages = {2613--2614}, abstract = {UNLABELLED: Multi-mapping sequence tags are a significant impediment to short-read sequencing platforms. These tags are routinely omitted from further analysis, leading to experimental bias and reduced coverage. Here, we present MuMRescueLite, a low-resource requirement version of the MuMRescue software that has been used by several next generation sequencing projects to probabilistically reincorporate multi-mapping tags into mapped short read data. AVAILABILITY AND IMPLEMENTATION: MuMRescueLite is written in Python; executables and documentation are available from http://genome.gsc.riken.jp/osc/english/software/.}, keywords = {}, pubstate = {}, tppubtype = {article} } UNLABELLED: Multi-mapping sequence tags are a significant impediment to short-read sequencing platforms. These tags are routinely omitted from further analysis, leading to experimental bias and reduced coverage. Here, we present MuMRescueLite, a low-resource requirement version of the MuMRescue software that has been used by several next generation sequencing projects to probabilistically reincorporate multi-mapping tags into mapped short read data. AVAILABILITY AND IMPLEMENTATION: MuMRescueLite is written in Python; executables and documentation are available from http://genome.gsc.riken.jp/osc/english/software/. | |
Taft, Ryan J; Glazov, Evgeny A; Cloonan, Nicole; Simons, Cas; Stephen, Stuart; Faulkner, Geoffrey J; Lassmann, Timo; Forrest, Alistair R R; Grimmond, Sean M; Schroder, Kate; Irvine, Katharine; Arakawa, Takahiro; Nakamura, Mari; Kubosaki, Atsutaka; Hayashida, Kengo; Kawazu, Chika; Murata, Mitsuyoshi; Nishiyori, Hiromi; Fukuda, Shiro; Kawai, Jun; Daub, Carsten O; Hume, David A; Suzuki, Harukazu; Orlando, Valerio; Carninci, Piero; Hayashizaki, Yoshihide; Mattick, John S Tiny RNAs associated with transcription start sites in animals (Journal Article) Nat. Genet., 41 (5), pp. 572–578, 2009. @article{Taft2009-ma, title = {Tiny RNAs associated with transcription start sites in animals}, author = {Ryan J Taft and Evgeny A Glazov and Nicole Cloonan and Cas Simons and Stuart Stephen and Geoffrey J Faulkner and Timo Lassmann and Alistair R R Forrest and Sean M Grimmond and Kate Schroder and Katharine Irvine and Takahiro Arakawa and Mari Nakamura and Atsutaka Kubosaki and Kengo Hayashida and Chika Kawazu and Mitsuyoshi Murata and Hiromi Nishiyori and Shiro Fukuda and Jun Kawai and Carsten O Daub and David A Hume and Harukazu Suzuki and Valerio Orlando and Piero Carninci and Yoshihide Hayashizaki and John S Mattick}, url = {http://dx.doi.org/10.1038/ng.312}, year = {2009}, date = {2009-05-01}, journal = {Nat. Genet.}, volume = {41}, number = {5}, pages = {572--578}, abstract = {It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within -60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5' ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes.}, keywords = {}, pubstate = {}, tppubtype = {article} } It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within -60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5' ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes. | |
Faulkner, Geoffrey J; Kimura, Yasumasa; Daub, Carsten O; Wani, Shivangi; Plessy, Charles; Irvine, Katharine M; Schroder, Kate; Cloonan, Nicole; Steptoe, Anita L; Lassmann, Timo; Waki, Kazunori; Hornig, Nadine; Arakawa, Takahiro; Takahashi, Hazuki; Kawai, Jun; Forrest, Alistair R R; Suzuki, Harukazu; Hayashizaki, Yoshihide; Hume, David A; Orlando, Valerio; Grimmond, Sean M; Carninci, Piero The regulated retrotransposon transcriptome of mammalian cells (Journal Article) Nat. Genet., 41 (5), pp. 563–571, 2009. @article{Faulkner2009-vh, title = {The regulated retrotransposon transcriptome of mammalian cells}, author = {Geoffrey J Faulkner and Yasumasa Kimura and Carsten O Daub and Shivangi Wani and Charles Plessy and Katharine M Irvine and Kate Schroder and Nicole Cloonan and Anita L Steptoe and Timo Lassmann and Kazunori Waki and Nadine Hornig and Takahiro Arakawa and Hazuki Takahashi and Jun Kawai and Alistair R R Forrest and Harukazu Suzuki and Yoshihide Hayashizaki and David A Hume and Valerio Orlando and Sean M Grimmond and Piero Carninci}, url = {http://dx.doi.org/10.1038/ng.368}, year = {2009}, date = {2009-05-01}, journal = {Nat. Genet.}, volume = {41}, number = {5}, pages = {563--571}, abstract = {Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6-30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5' of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3' UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6-30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5' of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3' UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome. | |
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