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).
PhD, University of Queensland, 2009
BSc (First Class Honours), University of Queensland, 2004
- Mobile DNA journal: http://mobilednajournal.biomedcentral.com
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Jansz, Natasha; Faulkner, Geoffrey J
Endogenous retroviruses in the origins and treatment of cancer (Journal Article)
In: Genome Biology, 22 (1), pp. 147, 2021, ISSN: 1474-760X.
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Endogenous retroviruses (ERVs) are emerging as promising therapeutic targets in cancer. As remnants of ancient retroviral infections, ERV-derived regulatory elements coordinate expression from gene networks, including those underpinning embryogenesis and immune cell function. ERV activation can promote an interferon response, a phenomenon termed viral mimicry. Although ERV expression is associated with cancer, and provisionally with autoimmune and neurodegenerative diseases, ERV-mediated inflammation is being explored as a way to sensitize tumors to immunotherapy. Here we review ERV co-option in development and innate immunity, the aberrant contribution of ERVs to tumorigenesis, and the wider biomedical potential of therapies directed at ERVs.
Ewing, Adam D; Smits, Nathan; Sanchez-Luque, Francisco J; Faivre, Jamila; Brennan, Paul M; Richardson, Sandra R; Cheetham, Seth W; Faulkner, Geoffrey J
In: Molecular Cell, 2020, ISSN: 1097-2765.
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Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.
Cheetham, Seth W; Faulkner, Geoffrey J; Dinger, Marcel E
In: Nature Reviews Genetics, 21 (3), pp. 191–201, 2020, ISSN: 1471-0064, (Number: 3 Publisher: Nature Publishing Group).
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Pseudogenes are defined as regions of the genome that contain defective copies of genes. They exist across almost all forms of life, and in mammalian genomes are annotated in similar numbers to recognized protein-coding genes. Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution.
Salvador-Palomeque, Carmen; Sanchez-Luque, Francisco J; Fortuna, Patrick R J; Ewing, Adam D; Wolvetang, Ernst J; Richardson, Sandra R; Faulkner, Geoffrey J
In: Mol Cell Biol, 39 (7), 2019, ISSN: 0270-7306.
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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)
In: Molecular Cell, 0 (0), 2019, ISSN: 1097-2765.
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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
Bodea, Gabriela O; McKelvey, Eleanor G Z; Faulkner, Geoffrey J
Retrotransposon-induced mosaicism in the neural genome (Journal Article)
In: Open Biology, 8 (7), pp. 180074, 2018, ISSN: 2046-2441.
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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
In: BioEssays, 40 (6), pp. 1700189, 2018, ISSN: 1521-1878.
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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)
In: Cell Reports, 23 (13), pp. 3730–3740, 2018, ISSN: 2211-1247.
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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)
In: Mobile DNA, 9 (1), pp. 22, 2018, ISSN: 1759-8753.
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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, M Joan; Faulkner, Geoffrey J; Goodier, John L; Lehmann, Ruth; Levin, Henry L
Meeting report: mobile genetic elements and genome plasticity 2018 (Journal Article)
In: Mobile DNA, 9 (1), pp. 21, 2018, ISSN: 1759-8753.
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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
In: PLOS Computational Biology, 14 (3), pp. e1005934, 2018, ISSN: 1553-7358.
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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
In: Genome Research, 2018, ISSN: 1088-9051, 1549-5469.
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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.
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, J. Kenneth; 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)
In: Scientific Data, 4 , pp. 170112, 2017, ISSN: 2052-4463.
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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; noz-Lopez, Martin Mu; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Carreira, Patricia E; Jeddeloh, Jeffrey A; Garcia-Perez, Jose L; Jr, Haig H Kazazian; Ewing, Adam D; Faulkner, Geoffrey J
In: Genome Res., 27 (8), pp. 1395–1405, 2017.
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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
In: Hepatology, 65 (5), pp. 1708–1719, 2017.
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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.
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
In: PLoS Genet., 13 (3), pp. e1006641, 2017.
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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)
In: Nature, 548 (7665), pp. E1–E3, 2017.
Kempen, Marie-Jeanne H C; Bodea, Gabriela O; Faulkner, Geoffrey J
In: Human Retrotransposons in Health and Disease, pp. 107–125, Springer, Cham, 2017.
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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)
In: Trends Genet., 33 (11), pp. 802–816, 2017.
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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)
In: 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).
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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.
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
In: Am. J. Hum. Genet., 98 (5), pp. 830–842, 2016.
(| | )
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
In: Genome Biol., 17 , pp. 100, 2016.
(| | )
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
In: Genome Biol., 17 (1), pp. 259, 2016.
(| | )
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:
Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J
In: Methods Mol. Biol., 1400 , pp. 47–77, 2016.
(| | )
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; noz-Lopez, Martin Mu; Shukla, Ruchi; Wang, Jichang; nadas, 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
In: Nat. Commun., 7 , pp. 10286, 2016.
(| | )
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
Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J
In: Methods in Molecular Biology (Clifton, N.J.), 1400 , pp. 47–77, 2016, ISSN: 1940-6029.
(| | | )
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
In: Mob. DNA, 7 (1), pp. 21, 2016.
(| | )
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.
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)
In: Cell, 161 (2), pp. 228–239, 2015.
(| | )
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; Drabløs, Finn; 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
In: Science, 347 (6225), pp. 1010–1014, 2015.
(| | )
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
Upton, Kyle R; Faulkner, Geoffrey J
In: Mob. DNA, 5 , pp. 15, 2014.
(| | )
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
Richardson, Sandra R; Salvador-Palomeque, Carmen; Faulkner, Geoffrey J
In: Bioessays, 36 (5), pp. 475–481, 2014.
(| | )
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)
In: Nature, 507 (7493), pp. 462-470, 2014.
(| | | )
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
In: Front. Cell. Neurosci., 8 , pp. 41, 2014.
(| | )
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
Richardson, Sandra R; Morell, Santiago; Faulkner, Geoffrey J
L1 retrotransposons and somatic mosaicism in the brain (Journal Article)
In: Annu. Rev. Genet., 48 , pp. 1–27, 2014.
(| | )
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
Carreira, Patricia E; Richardson, Sandra R; Faulkner, Geoffrey J
L1 retrotransposons, cancer stem cells and oncogenesis (Journal Article)
In: FEBS J., 281 (1), pp. 63–73, 2014.
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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.
Faulkner, Geoffrey J
Retrotransposon silencing during embryogenesis: dicer cuts in LINE (Journal Article)
In: PLoS Genet., 9 (11), pp. e1003944, 2013.
Reilly, Matthew T; Faulkner, Geoffrey J; Dubnau, Joshua; Ponomarev, Igor; Gage, Fred H
In: J. Neurosci., 33 (45), pp. 17577–17586, 2013.
(| | )
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
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
In: Sci. Rep., 3 , pp. 2962, 2013.
(| | )
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
Shukla, Ruchi; Upton, Kyle R; noz-Lopez, 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
In: Cell, 153 (1), pp. 101–111, 2013.
(| | )
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.
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 H Kazazian
Extensive somatic L1 retrotransposition in colorectal tumors (Journal Article)
In: Genome Res., 22 (12), pp. 2328–2338, 2012.
(| | )
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
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; ao Fadista, 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; Hornshøj, Henrik; 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
In: Nature, 491 (7424), pp. 393–398, 2012.
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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
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)
In: Genome Res., 22 (3), pp. 486–497, 2012.
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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
In: Proc. Natl. Acad. Sci. U. S. A., 109 (16), pp. E944–53, 2012.
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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.
Upton, Kyle R; Baillie, Kenneth J; Faulkner, Geoffrey J
Is somatic retrotransposition a parasitic or symbiotic phenomenon? (Journal Article)
In: Mob. Genet. Elements, 1 (4), pp. 279–282, 2011.
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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
In: Nature, 479 (7374), pp. 534–537, 2011.
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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)
In: FEBS Lett., 585 (11), pp. 1589–1594, 2011.
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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.
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
In: Genome Res., 20 (2), pp. 257–264, 2010.
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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
In: Trends Genet., 26 (1), pp. 21–28, 2010.
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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.
Faulkner, Geoffrey J; Grimmond, Sean M
Setting CAGE tags in a genomic context (Book Chapter)
In: 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).
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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
In: Bioinformatics, 25 (19), pp. 2615–2616, 2009.
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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
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