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2009 | |
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. | |
Faulkner, Geoffrey J; Carninci, Piero Altruistic functions for selfish DNA (Journal Article) Cell Cycle, 8 (18), pp. 2895–2900, 2009. @article{Faulkner2009-ez, title = {Altruistic functions for selfish DNA}, author = {Geoffrey J Faulkner and Piero Carninci}, url = {http://dx.doi.org/10.4161/cc.8.18.9536}, year = {2009}, date = {2009-01-01}, journal = {Cell Cycle}, volume = {8}, number = {18}, pages = {2895--2900}, abstract = {Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this ``selfish DNA'' or ``junk DNA'' dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo.}, keywords = {}, pubstate = {}, tppubtype = {article} } Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this ``selfish DNA'' or ``junk DNA'' dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo. | |
Consortium, FANTOM; Suzuki, Harukazu; Forrest, Alistair R R; ..., ; Faulkner, Geoffrey J; ..., ; Takahashi, Yukari; Kawai, Jun; Hayashizaki, Yoshihide The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line (Journal Article) Nat. Genet., 41 (5), pp. 553–562, 2009. (Abstract | Links | BibTeX | Altmetric) @article{FANTOM_Consortium2009-hl, title = {The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line}, author = {FANTOM Consortium and Harukazu Suzuki and Alistair R R Forrest and ... and Geoffrey J Faulkner and ... and Yukari Takahashi and Jun Kawai and Yoshihide Hayashizaki}, url = {https://www.ncbi.nlm.nih.gov/pubmed/19377474}, doi = {10.1038/ng.375}, year = {2009}, date = {2009-01-01}, journal = {Nat. Genet.}, volume = {41}, number = {5}, pages = {553--562}, abstract = {Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process. | |
2008 | |
Cloonan, Nicole; Forrest, Alistair R R; Kolle, Gabriel; Gardiner, Brooke B A; Faulkner, Geoffrey J; Brown, Mellissa K; Taylor, Darrin F; Steptoe, Anita L; Wani, Shivangi; Bethel, Graeme; Robertson, Alan J; Perkins, Andrew C; Bruce, Stephen J; Lee, Clarence C; Ranade, Swati S; Peckham, Heather E; Manning, Jonathan M; McKernan, Kevin J; Grimmond, Sean M Stem cell transcriptome profiling via massive-scale mRNA sequencing (Journal Article) Nat. Methods, 5 (7), pp. 613–619, 2008. @article{Cloonan2008-up, title = {Stem cell transcriptome profiling via massive-scale mRNA sequencing}, author = {Nicole Cloonan and Alistair R R Forrest and Gabriel Kolle and Brooke B A Gardiner and Geoffrey J Faulkner and Mellissa K Brown and Darrin F Taylor and Anita L Steptoe and Shivangi Wani and Graeme Bethel and Alan J Robertson and Andrew C Perkins and Stephen J Bruce and Clarence C Lee and Swati S Ranade and Heather E Peckham and Jonathan M Manning and Kevin J McKernan and Sean M Grimmond}, url = {http://dx.doi.org/10.1038/nmeth.1223}, year = {2008}, date = {2008-07-01}, journal = {Nat. Methods}, volume = {5}, number = {7}, pages = {613--619}, abstract = {We developed a massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, to survey the complexity, dynamics and sequence content of transcriptomes in a near-complete fashion. This method generates directional, random-primed, linear cDNA libraries that are optimized for next-generation short-tag sequencing. We surveyed the poly(A)(+) transcriptomes of undifferentiated mouse embryonic stem cells (ESCs) and embryoid bodies (EBs) at an unprecedented depth (10 Gb), using the Applied Biosystems SOLiD technology. These libraries capture the genomic landscape of expression, state-specific expression, single-nucleotide polymorphisms (SNPs), the transcriptional activity of repeat elements, and both known and new alternative splicing events. We investigated the impact of transcriptional complexity on current models of key signaling pathways controlling ESC pluripotency and differentiation, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that our understanding of transcriptional complexity is far from complete.}, keywords = {}, pubstate = {}, tppubtype = {article} } We developed a massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, to survey the complexity, dynamics and sequence content of transcriptomes in a near-complete fashion. This method generates directional, random-primed, linear cDNA libraries that are optimized for next-generation short-tag sequencing. We surveyed the poly(A)(+) transcriptomes of undifferentiated mouse embryonic stem cells (ESCs) and embryoid bodies (EBs) at an unprecedented depth (10 Gb), using the Applied Biosystems SOLiD technology. These libraries capture the genomic landscape of expression, state-specific expression, single-nucleotide polymorphisms (SNPs), the transcriptional activity of repeat elements, and both known and new alternative splicing events. We investigated the impact of transcriptional complexity on current models of key signaling pathways controlling ESC pluripotency and differentiation, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that our understanding of transcriptional complexity is far from complete. | |
Faulkner, Geoffrey J; Forrest, Alistair R R; Chalk, Alistair M; Schroder, Kate; Hayashizaki, Yoshihide; Carninci, Piero; Hume, David A; Grimmond, Sean M A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE (Journal Article) Genomics, 91 (3), pp. 281–288, 2008. @article{Faulkner2008-cj, title = {A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE}, author = {Geoffrey J Faulkner and Alistair R R Forrest and Alistair M Chalk and Kate Schroder and Yoshihide Hayashizaki and Piero Carninci and David A Hume and Sean M Grimmond}, url = {http://dx.doi.org/10.1016/j.ygeno.2007.11.003}, year = {2008}, date = {2008-03-01}, journal = {Genomics}, volume = {91}, number = {3}, pages = {281--288}, abstract = {Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription start site usage and monitor gene activity in mammals. A drawback of the CAGE approach thus far has been the removal of as many as 40% of CAGE sequence tags due to their mapping to multiple genomic locations. Here, we address the origins of multimap tags and present a novel strategy to assign CAGE tags to their most likely source promoter region. When this approach was applied to the FANTOM3 CAGE libraries, the percentage of protein-coding mouse transcriptional frameworks detected by CAGE improved from 42.9 to 57.8% (an increase of 5516 frameworks) with no reduction in CAGE to microarray correlation. These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone.}, keywords = {}, pubstate = {}, tppubtype = {article} } Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription start site usage and monitor gene activity in mammals. A drawback of the CAGE approach thus far has been the removal of as many as 40% of CAGE sequence tags due to their mapping to multiple genomic locations. Here, we address the origins of multimap tags and present a novel strategy to assign CAGE tags to their most likely source promoter region. When this approach was applied to the FANTOM3 CAGE libraries, the percentage of protein-coding mouse transcriptional frameworks detected by CAGE improved from 42.9 to 57.8% (an increase of 5516 frameworks) with no reduction in CAGE to microarray correlation. These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone. | |
2007 | |
Meadows, Nicholas A; Sharma, Sudarshana M; Faulkner, Geoffrey J; Ostrowski, Michael C; Hume, David A; Cassady, Alan I The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor (Journal Article) J. Biol. Chem., 282 (3), pp. 1891–1904, 2007. @article{Meadows2007-fm, title = {The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor}, author = {Nicholas A Meadows and Sudarshana M Sharma and Geoffrey J Faulkner and Michael C Ostrowski and David A Hume and Alan I Cassady}, url = {http://dx.doi.org/10.1074/jbc.M608572200}, year = {2007}, date = {2007-01-01}, journal = {J. Biol. Chem.}, volume = {282}, number = {3}, pages = {1891--1904}, abstract = {Microphthalmia transcription factor (MITF) regulates osteoclast function by controling the expression of genes, including tartrate-resistant acid phosphatase (TRAP) and cathepsin K in response to receptor activator of nuclear factor-kappaB ligand (RANKL)-induced signaling. To identify novel MITF target genes, we have overexpressed MITF in the murine macrophage cell line RAW264.7 subclone 4 (RAW/C4) and examined the gene expression profile after sRANKL-stimulated osteoclastogenesis. Microarray analysis identified a set of genes superinduced by MITF overexpression, including Clcn7 (chloride channel 7) and Ostm1 (osteopetrosis-associated transmembrane protein 1). Using electrophoretic mobility shift assays, we identified two MITF-binding sites (M-boxes) in the Clcn7 promoter and a single M-box in the Ostm1 promoter. An anti-MITF antibody supershifted DNA-protein complexes for promoter sites in both genes, whereas MITF binding was abolished by mutation of these sites. The Clcn7 promoter was transactivated by coexpression of MITF in reporter gene assays. Mutation of one Clcn7 M-box prevented MITF transactivation, but mutation of the second MITF-binding site only reduced basal activity. Chromatin immunoprecipitation assays confirmed that the two Clcn7 MITF binding and responsive regions in vitro bind MITF in genomic DNA. The expression of Clcn7 is repressed in the dominant negative mutant Mitf mouse, mi/mi, indicating that the dysregulated bone resorption seen in these mice can be attributed in part to transcriptional repression of Clcn7. MITF regulation of the TRAP, cathepsin K, Clcn7, and Ostm1 genes, which are critical for osteoclast resorption, suggests that the role of MITF is more significant than previously perceived and that MITF may be a master regulator of osteoclast function and bone resorption.}, keywords = {}, pubstate = {}, tppubtype = {article} } Microphthalmia transcription factor (MITF) regulates osteoclast function by controling the expression of genes, including tartrate-resistant acid phosphatase (TRAP) and cathepsin K in response to receptor activator of nuclear factor-kappaB ligand (RANKL)-induced signaling. To identify novel MITF target genes, we have overexpressed MITF in the murine macrophage cell line RAW264.7 subclone 4 (RAW/C4) and examined the gene expression profile after sRANKL-stimulated osteoclastogenesis. Microarray analysis identified a set of genes superinduced by MITF overexpression, including Clcn7 (chloride channel 7) and Ostm1 (osteopetrosis-associated transmembrane protein 1). Using electrophoretic mobility shift assays, we identified two MITF-binding sites (M-boxes) in the Clcn7 promoter and a single M-box in the Ostm1 promoter. An anti-MITF antibody supershifted DNA-protein complexes for promoter sites in both genes, whereas MITF binding was abolished by mutation of these sites. The Clcn7 promoter was transactivated by coexpression of MITF in reporter gene assays. Mutation of one Clcn7 M-box prevented MITF transactivation, but mutation of the second MITF-binding site only reduced basal activity. Chromatin immunoprecipitation assays confirmed that the two Clcn7 MITF binding and responsive regions in vitro bind MITF in genomic DNA. The expression of Clcn7 is repressed in the dominant negative mutant Mitf mouse, mi/mi, indicating that the dysregulated bone resorption seen in these mice can be attributed in part to transcriptional repression of Clcn7. MITF regulation of the TRAP, cathepsin K, Clcn7, and Ostm1 genes, which are critical for osteoclast resorption, suggests that the role of MITF is more significant than previously perceived and that MITF may be a master regulator of osteoclast function and bone resorption. | |
2006 | |
Forrest, Alistair R R; Taylor, Darrin F; Crowe, Mark L; Chalk, Alistair M; Waddell, Nic J; Kolle, Gabriel; Faulkner, Geoffrey J; Kodzius, Rimantas; Katayama, Shintaro; Wells, Christine; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Grimmond, Sean M Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases (Journal Article) Genome Biol., 7 (1), pp. R5, 2006. @article{Forrest2006-do, title = {Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases}, author = {Alistair R R Forrest and Darrin F Taylor and Mark L Crowe and Alistair M Chalk and Nic J Waddell and Gabriel Kolle and Geoffrey J Faulkner and Rimantas Kodzius and Shintaro Katayama and Christine Wells and Chikatoshi Kai and Jun Kawai and Piero Carninci and Yoshihide Hayashizaki and Sean M Grimmond}, url = {http://dx.doi.org/10.1186/gb-2006-7-1-r5}, year = {2006}, date = {2006-01-01}, journal = {Genome Biol.}, volume = {7}, number = {1}, pages = {R5}, abstract = {BACKGROUND: Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a systematic study to catalog the variant transcripts of every protein kinase-like and phosphatase-like locus of mouse http://variant.imb.uq.edu.au. RESULTS: By reviewing all available transcript evidence, we found that at least 75% of kinase and phosphatase loci in mouse generate alternative splice forms, and that 44% of these loci have well supported alternative 5' exons. In a further analysis of full-length cDNAs, we identified 69% of loci as generating more than one peptide isoform. The 1,469 peptide isoforms generated from these loci correspond to 1,080 unique Interpro domain combinations, many of which lack catalytic or interaction domains. We also report on the existence of likely dominant negative forms for many of the receptor kinases and phosphatases, including some 26 secreted decoys (seven known and 19 novel: Alk, Csf1r, Egfr, Epha1, 3, 5,7 and 10, Ephb1, Flt1, Flt3, Insr, Insrr, Kdr, Met, Ptk7, Ptprc, Ptprd, Ptprg, Ptprl, Ptprn, Ptprn2, Ptpro, Ptprr, Ptprs, and Ptprz1) and 13 transmembrane forms (four known and nine novel: Axl, Bmpr1a, Csf1r, Epha4, 5, 6 and 7, Ntrk2, Ntrk3, Pdgfra, Ptprk, Ptprm, Ptpru). Finally, by mining public gene expression data (MPSS and microarrays), we confirmed tissue-specific expression of ten of the novel isoforms. CONCLUSION: These findings suggest that alternative transcripts of protein kinases and phosphatases are produced that encode different domain structures, and that these variants are likely to play important roles in phosphorylation-dependent signaling pathways.}, keywords = {}, pubstate = {}, tppubtype = {article} } BACKGROUND: Alternative transcripts of protein kinases and protein phosphatases are known to encode peptides with altered substrate affinities, subcellular localizations, and activities. We undertook a systematic study to catalog the variant transcripts of every protein kinase-like and phosphatase-like locus of mouse http://variant.imb.uq.edu.au. RESULTS: By reviewing all available transcript evidence, we found that at least 75% of kinase and phosphatase loci in mouse generate alternative splice forms, and that 44% of these loci have well supported alternative 5' exons. In a further analysis of full-length cDNAs, we identified 69% of loci as generating more than one peptide isoform. The 1,469 peptide isoforms generated from these loci correspond to 1,080 unique Interpro domain combinations, many of which lack catalytic or interaction domains. We also report on the existence of likely dominant negative forms for many of the receptor kinases and phosphatases, including some 26 secreted decoys (seven known and 19 novel: Alk, Csf1r, Egfr, Epha1, 3, 5,7 and 10, Ephb1, Flt1, Flt3, Insr, Insrr, Kdr, Met, Ptk7, Ptprc, Ptprd, Ptprg, Ptprl, Ptprn, Ptprn2, Ptpro, Ptprr, Ptprs, and Ptprz1) and 13 transmembrane forms (four known and nine novel: Axl, Bmpr1a, Csf1r, Epha4, 5, 6 and 7, Ntrk2, Ntrk3, Pdgfra, Ptprk, Ptprm, Ptpru). Finally, by mining public gene expression data (MPSS and microarrays), we confirmed tissue-specific expression of ten of the novel isoforms. CONCLUSION: These findings suggest that alternative transcripts of protein kinases and phosphatases are produced that encode different domain structures, and that these variants are likely to play important roles in phosphorylation-dependent signaling pathways. | |
Wells, Christine A; Chalk, Alistair M; Forrest, Alistair; Taylor, Darrin; Waddell, Nic; Schroder, Kate; Himes, Roy S; Faulkner, Geoffrey; Lo, Sandra; Kasukawa, Takeya; Kawaji, Hideya; Kai, Chikatoshi; Kawai, Jun; Katayama, Shintaro; Carninci, Piero; Hayashizaki, Yoshihide; Hume, David A; Grimmond, Sean M Alternate transcription of the Toll-like receptor signaling cascade (Journal Article) Genome Biology, 7 (2), pp. R10, 2006, ISSN: 1474-760X. (Abstract | Links | BibTeX | Altmetric) @article{wells_alternate_2006, title = {Alternate transcription of the Toll-like receptor signaling cascade}, author = {Christine A Wells and Alistair M Chalk and Alistair Forrest and Darrin Taylor and Nic Waddell and Kate Schroder and Roy S Himes and Geoffrey Faulkner and Sandra Lo and Takeya Kasukawa and Hideya Kawaji and Chikatoshi Kai and Jun Kawai and Shintaro Katayama and Piero Carninci and Yoshihide Hayashizaki and David A Hume and Sean M Grimmond}, doi = {10.1186/gb-2006-7-2-r10}, issn = {1474-760X}, year = {2006}, date = {2006-01-01}, journal = {Genome Biology}, volume = {7}, number = {2}, pages = {R10}, abstract = {BACKGROUND: Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway, derived from a systematic analysis of the FANTOM3 mouse data set. Functional annotation of variant proteins was assessed in light of inflammatory signaling in mouse primary macrophages, and the expression of each variant transcript was assessed by splicing arrays. RESULTS: A total of 256 variant transcripts were identified, including novel variants of Tlr4, Ticam1, Tollip, Rac1, Irak1, 2 and 4, Mapk14/p38, Atf2 and Stat1. The expression of variant transcripts was assessed using custom-designed splicing arrays. We functionally tested the expression of Tlr4 transcripts under a range of cytokine conditions via northern and quantitative real-time polymerase chain reaction. The effects of variant Mapk14/p38 protein expression on macrophage survival were demonstrated. CONCLUSION: Members of the Toll-like receptor signaling pathway are highly alternatively spliced, producing a large number of novel proteins with the potential to functionally alter inflammatory outcomes. These variants are expressed in primary mouse macrophages in response to inflammatory mediators such as interferon-gamma and lipopolysaccharide. Our data suggest a surprisingly common role for variant proteins in diversification/repression of inflammatory signaling.}, keywords = {}, pubstate = {published}, tppubtype = {article} } BACKGROUND: Alternate splicing of key signaling molecules in the Toll-like receptor (Tlr) cascade has been shown to dramatically alter the signaling capacity of inflammatory cells, but it is not known how common this mechanism is. We provide transcriptional evidence of widespread alternate splicing in the Toll-like receptor signaling pathway, derived from a systematic analysis of the FANTOM3 mouse data set. Functional annotation of variant proteins was assessed in light of inflammatory signaling in mouse primary macrophages, and the expression of each variant transcript was assessed by splicing arrays. RESULTS: A total of 256 variant transcripts were identified, including novel variants of Tlr4, Ticam1, Tollip, Rac1, Irak1, 2 and 4, Mapk14/p38, Atf2 and Stat1. The expression of variant transcripts was assessed using custom-designed splicing arrays. We functionally tested the expression of Tlr4 transcripts under a range of cytokine conditions via northern and quantitative real-time polymerase chain reaction. The effects of variant Mapk14/p38 protein expression on macrophage survival were demonstrated. CONCLUSION: Members of the Toll-like receptor signaling pathway are highly alternatively spliced, producing a large number of novel proteins with the potential to functionally alter inflammatory outcomes. These variants are expressed in primary mouse macrophages in response to inflammatory mediators such as interferon-gamma and lipopolysaccharide. Our data suggest a surprisingly common role for variant proteins in diversification/repression of inflammatory signaling. | |
2005 | |
Carninci, P; Kasukawa, T; Katayama, S; Gough, J; Frith, M C; Maeda, N; Oyama, R; Ravasi, T; Lenhard, B; Wells, C; Kodzius, R; Shimokawa, K; Bajic, V B; Brenner, S E; Batalov, S; Forrest, A R R; Zavolan, M; Davis, M J; Wilming, L G; Aidinis, V; Allen, J E; Ambesi-Impiombato, A; Apweiler, R; Aturaliya, R N; Bailey, T L; Bansal, M; Baxter, L; Beisel, K W; Bersano, T; Bono, H; Chalk, A M; Chiu, K P; Choudhary, V; Christoffels, A; Clutterbuck, D R; Crowe, M L; Dalla, E; Dalrymple, B P; de Bono, B; Gatta, Della G; di Bernardo, D; Down, T; Engstrom, P; Fagiolini, M; Faulkner, G; Fletcher, C F; Fukushima, T; Furuno, M; Futaki, S; Gariboldi, M; Georgii-Hemming, P; Gingeras, T R; Gojobori, T; Green, R E; Gustincich, S; Harbers, M; Hayashi, Y; Hensch, T K; Hirokawa, N; Hill, D; Huminiecki, L; Iacono, M; Ikeo, K; Iwama, A; Ishikawa, T; Jakt, M; Kanapin, A; Katoh, M; Kawasawa, Y; Kelso, J; Kitamura, H; Kitano, H; Kollias, G; Krishnan, S P T; Kruger, A; Kummerfeld, S K; Kurochkin, I V; Lareau, L F; Lazarevic, D; Lipovich, L; Liu, J; Liuni, S; McWilliam, S; Babu, Madan M; Madera, M; Marchionni, L; Matsuda, H; Matsuzawa, S; Miki, H; Mignone, F; Miyake, S; Morris, K; Mottagui-Tabar, S; Mulder, N; Nakano, N; Nakauchi, H; Ng, P; Nilsson, R; Nishiguchi, S; Nishikawa, S; Nori, F; Ohara, O; Okazaki, Y; Orlando, V; Pang, K C; Pavan, W J; Pavesi, G; Pesole, G; Petrovsky, N; Piazza, S; Reed, J; Reid, J F; Ring, B Z; Ringwald, M; Rost, B; Ruan, Y; Salzberg, S L; Sandelin, A; Schneider, C; Schönbach, C; Sekiguchi, K; a. Semple, C M; Seno, S; Sessa, L; Sheng, Y; Shibata, Y; Shimada, H; Shimada, K; Silva, D; Sinclair, B; Sperling, S; Stupka, E; Sugiura, K; Sultana, R; Takenaka, Y; Taki, K; Tammoja, K; Tan, S L; Tang, S; Taylor, M S; Tegner, J; Teichmann, S A; Ueda, H R; van Nimwegen, E; Verardo, R; Wei, C L; Yagi, K; Yamanishi, H; Zabarovsky, E; Zhu, S; Zimmer, A; Hide, W; Bult, C; Grimmond, S M; Teasdale, R D; Liu, E T; Brusic, V; Quackenbush, J; Wahlestedt, C; Mattick, J S; Hume, D A; Kai, C; Sasaki, D; Tomaru, Y; Fukuda, S; Kanamori-Katayama, M; Suzuki, M; Aoki, J; Arakawa, T; Iida, J; Imamura, K; Itoh, M; Kato, T; Kawaji, H; Kawagashira, N; Kawashima, T; Kojima, M; Kondo, S; Konno, H; Nakano, K; Ninomiya, N; Nishio, T; Okada, M; Plessy, C; Shibata, K; Shiraki, T; Suzuki, S; Tagami, M; Waki, K; Watahiki, A; Okamura-Oho, Y; Suzuki, H; Kawai, J; Hayashizaki, Y; Consortium, FANTOM; Group, {RIKEN Genome Exploration Research; Group)}, Genome Science Group (Genome Network Project Core The transcriptional landscape of the mammalian genome (Journal Article) Science (New York, N.Y.), 309 (5740), pp. 1559–1563, 2005, ISSN: 1095-9203. (Abstract | Links | BibTeX | Altmetric) @article{carninci_transcriptional_2005, title = {The transcriptional landscape of the mammalian genome}, author = {P Carninci and T Kasukawa and S Katayama and J Gough and M C Frith and N Maeda and R Oyama and T Ravasi and B Lenhard and C Wells and R Kodzius and K Shimokawa and V B Bajic and S E Brenner and S Batalov and A R R Forrest and M Zavolan and M J Davis and L G Wilming and V Aidinis and J E Allen and A Ambesi-Impiombato and R Apweiler and R N Aturaliya and T L Bailey and M Bansal and L Baxter and K W Beisel and T Bersano and H Bono and A M Chalk and K P Chiu and V Choudhary and A Christoffels and D R Clutterbuck and M L Crowe and E Dalla and B P Dalrymple and B de Bono and G Della Gatta and D di Bernardo and T Down and P Engstrom and M Fagiolini and G Faulkner and C F Fletcher and T Fukushima and M Furuno and S Futaki and M Gariboldi and P Georgii-Hemming and T R Gingeras and T Gojobori and R E Green and S Gustincich and M Harbers and Y Hayashi and T K Hensch and N Hirokawa and D Hill and L Huminiecki and M Iacono and K Ikeo and A Iwama and T Ishikawa and M Jakt and A Kanapin and M Katoh and Y Kawasawa and J Kelso and H Kitamura and H Kitano and G Kollias and S P T Krishnan and A Kruger and S K Kummerfeld and I V Kurochkin and L F Lareau and D Lazarevic and L Lipovich and J Liu and S Liuni and S McWilliam and M Madan Babu and M Madera and L Marchionni and H Matsuda and S Matsuzawa and H Miki and F Mignone and S Miyake and K Morris and S Mottagui-Tabar and N Mulder and N Nakano and H Nakauchi and P Ng and R Nilsson and S Nishiguchi and S Nishikawa and F Nori and O Ohara and Y Okazaki and V Orlando and K C Pang and W J Pavan and G Pavesi and G Pesole and N Petrovsky and S Piazza and J Reed and J F Reid and B Z Ring and M Ringwald and B Rost and Y Ruan and S L Salzberg and A Sandelin and C Schneider and C Sch\"{o}nbach and K Sekiguchi and C M a. Semple and S Seno and L Sessa and Y Sheng and Y Shibata and H Shimada and K Shimada and D Silva and B Sinclair and S Sperling and E Stupka and K Sugiura and R Sultana and Y Takenaka and K Taki and K Tammoja and S L Tan and S Tang and M S Taylor and J Tegner and S A Teichmann and H R Ueda and E van Nimwegen and R Verardo and C L Wei and K Yagi and H Yamanishi and E Zabarovsky and S Zhu and A Zimmer and W Hide and C Bult and S M Grimmond and R D Teasdale and E T Liu and V Brusic and J Quackenbush and C Wahlestedt and J S Mattick and D A Hume and C Kai and D Sasaki and Y Tomaru and S Fukuda and M Kanamori-Katayama and M Suzuki and J Aoki and T Arakawa and J Iida and K Imamura and M Itoh and T Kato and H Kawaji and N Kawagashira and T Kawashima and M Kojima and S Kondo and H Konno and K Nakano and N Ninomiya and T Nishio and M Okada and C Plessy and K Shibata and T Shiraki and S Suzuki and M Tagami and K Waki and A Watahiki and Y Okamura-Oho and H Suzuki and J Kawai and Y Hayashizaki and FANTOM Consortium and {RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)}}, doi = {10.1126/science.1112014}, issn = {1095-9203}, year = {2005}, date = {2005-01-01}, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5740}, pages = {1559--1563}, abstract = {This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. | |
2004 | |
Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip Bellerophon: a program to detect chimeric sequences in multiple sequence alignments (Journal Article) Bioinformatics (Oxford, England), 20 (14), pp. 2317–2319, 2004, ISSN: 1367-4803. (Abstract | Links | BibTeX | Altmetric) @article{huber_bellerophon:_2004, title = {Bellerophon: a program to detect chimeric sequences in multiple sequence alignments}, author = {Thomas Huber and Geoffrey Faulkner and Philip Hugenholtz}, doi = {10.1093/bioinformatics/bth226}, issn = {1367-4803}, year = {2004}, date = {2004-09-01}, journal = {Bioinformatics (Oxford, England)}, volume = {20}, number = {14}, pages = {2317--2319}, abstract = {SUMMARY: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. AVAILABILITY: Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/textasciitildehuber/bellerophon.pl}, keywords = {}, pubstate = {published}, tppubtype = {article} } SUMMARY: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. AVAILABILITY: Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/textasciitildehuber/bellerophon.pl | |
Meadows, Nicholas A; Faulkner, Geoffrey J; Wells, Christine A; Ravasi, Timothy; Hume, David A; Sankar, U; Hu, R; Ostrowski, Michael C; Cassady, Alan I Novel genes regulated by microphthalmia transcription factor in macrophages and osteoclasts (Journal Article) Journal of Bone and Mineral Research, 19 (S1), pp. S413–S413, 2004, ISSN: 1523-4681. @article{noauthor_asbmr_2004, title = {Novel genes regulated by microphthalmia transcription factor in macrophages and osteoclasts}, author = {Nicholas A Meadows and Geoffrey J Faulkner and Christine A Wells and Timothy Ravasi and David A Hume and U Sankar and R Hu and Michael C Ostrowski and Alan I Cassady}, url = {http://onlinelibrary.wiley.com/doi/10.1002/jbmr.5650191306/abstract}, doi = {10.1002/jbmr.5650191306}, issn = {1523-4681}, year = {2004}, date = {2004-01-01}, urldate = {2018-01-16}, journal = {Journal of Bone and Mineral Research}, volume = {19}, number = {S1}, pages = {S413--S413}, keywords = {}, pubstate = {published}, tppubtype = {article} } | |
2003 | |
Wells, Christine A; Ravasi, Timothy; Faulkner, Geoffrey J; Carninci, Piero; Okazaki, Yasushi; Hayashizaki, Yoshihide; Sweet, Matthew; Wainwright, Brandon J; Hume, David A Genetic control of the innate immune response (Journal Article) BMC Immunol., 4 , pp. 5, 2003. @article{Wells2003-gh, title = {Genetic control of the innate immune response}, author = {Christine A Wells and Timothy Ravasi and Geoffrey J Faulkner and Piero Carninci and Yasushi Okazaki and Yoshihide Hayashizaki and Matthew Sweet and Brandon J Wainwright and David A Hume}, url = {http://dx.doi.org/10.1186/1471-2172-4-5}, year = {2003}, date = {2003-06-01}, journal = {BMC Immunol.}, volume = {4}, pages = {5}, abstract = {BACKGROUND: Susceptibility to infectious diseases is directed, in part, by the interaction between the invading pathogen and host macrophages. This study examines the influence of genetic background on host-pathogen interactions, by assessing the transcriptional responses of macrophages from five inbred mouse strains to lipopolysaccharide (LPS), a major determinant of responses to gram-negative microorganisms. RESULTS: The mouse strains examined varied greatly in the number, amplitude and rate of induction of genes expressed in response to LPS. The response was attenuated in the C3H/HeJlpsd strain, which has a mutation in the LPS receptor Toll-like receptor 4 (TLR4). Variation between mouse strains allowed clustering into early (C57Bl/6J and DBA/2J) and delayed (BALB/c and C3H/ARC) transcriptional phenotypes. There was no clear correlation between gene induction patterns and variation at the Bcg locus (Slc11A1) or propensity to bias Th1 versus Th2 T cell activation responses. CONCLUSION: Macrophages from each strain responded to LPS with unique gene expression profiles. The variation apparent between genetic backgrounds provides insights into the breadth of possible inflammatory responses, and paradoxically, this divergence was used to identify a common transcriptional program that responds to TLR4 signalling, irrespective of genetic background. Our data indicates that many additional genetic loci control the nature and the extent of transcriptional responses promoted by a single pathogen-associated molecular pattern (PAMP), such as LPS.}, keywords = {}, pubstate = {}, tppubtype = {article} } BACKGROUND: Susceptibility to infectious diseases is directed, in part, by the interaction between the invading pathogen and host macrophages. This study examines the influence of genetic background on host-pathogen interactions, by assessing the transcriptional responses of macrophages from five inbred mouse strains to lipopolysaccharide (LPS), a major determinant of responses to gram-negative microorganisms. RESULTS: The mouse strains examined varied greatly in the number, amplitude and rate of induction of genes expressed in response to LPS. The response was attenuated in the C3H/HeJlpsd strain, which has a mutation in the LPS receptor Toll-like receptor 4 (TLR4). Variation between mouse strains allowed clustering into early (C57Bl/6J and DBA/2J) and delayed (BALB/c and C3H/ARC) transcriptional phenotypes. There was no clear correlation between gene induction patterns and variation at the Bcg locus (Slc11A1) or propensity to bias Th1 versus Th2 T cell activation responses. CONCLUSION: Macrophages from each strain responded to LPS with unique gene expression profiles. The variation apparent between genetic backgrounds provides insights into the breadth of possible inflammatory responses, and paradoxically, this divergence was used to identify a common transcriptional program that responds to TLR4 signalling, irrespective of genetic background. Our data indicates that many additional genetic loci control the nature and the extent of transcriptional responses promoted by a single pathogen-associated molecular pattern (PAMP), such as LPS. | |
Wells, Christine A; Ravasi, Timothy; Sultana, Razvan; Yagi, Ken; Carninci, Piero; Bono, Hidemasa; Faulkner, Geoffrey; Okazaki, Yasushi; Quackenbush, John; Hume, David A; Group, Riken Ger; Members, G S L; Lyons, Paul A Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage (Journal Article) Genome Research, 13 (6b), pp. 1360–1365, 2003, ISSN: 1088-9051, 1549-5469. (Abstract | Links | BibTeX | Altmetric) @article{wells_continued_2003, title = {Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage}, author = {Christine A Wells and Timothy Ravasi and Razvan Sultana and Ken Yagi and Piero Carninci and Hidemasa Bono and Geoffrey Faulkner and Yasushi Okazaki and John Quackenbush and David A Hume and Riken Ger Group and G S L Members and Paul A Lyons}, url = {http://genome.cshlp.org/content/13/6b/1360}, doi = {10.1101/gr.1056103}, issn = {1088-9051, 1549-5469}, year = {2003}, date = {2003-01-01}, urldate = {2018-01-16}, journal = {Genome Research}, volume = {13}, number = {6b}, pages = {1360--1365}, abstract = {The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the present study we have assessed the complexity of the transcriptome expressed in mouse macrophages before and after treatment with lipopolysaccharide, a global regulator of macrophage gene expression, using existing RIKEN 19K arrays. By comparison to array profiles of other cells and tissues, we identify a large set of macrophage-enriched genes, many of which have obvious functions in endocytosis and phagocytosis. In addition, a significant number of LPS-inducible genes were identified. The data suggest that macrophages are a complex source of mRNA for transcriptome studies. To assess complexity and identify additional macrophage expressed genes, cDNA libraries were created from purified populations of macrophage and dendritic cells, a functionally related cell type. Sequence analysis revealed a high incidence of novel mRNAs within these cDNA libraries. These studies provide insights into the depths of transcriptional complexity still untapped amongst products of inducible genes, and identify macrophage and dendritic cell populations as a starting point for sampling the inducible mammalian transcriptome.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the present study we have assessed the complexity of the transcriptome expressed in mouse macrophages before and after treatment with lipopolysaccharide, a global regulator of macrophage gene expression, using existing RIKEN 19K arrays. By comparison to array profiles of other cells and tissues, we identify a large set of macrophage-enriched genes, many of which have obvious functions in endocytosis and phagocytosis. In addition, a significant number of LPS-inducible genes were identified. The data suggest that macrophages are a complex source of mRNA for transcriptome studies. To assess complexity and identify additional macrophage expressed genes, cDNA libraries were created from purified populations of macrophage and dendritic cells, a functionally related cell type. Sequence analysis revealed a high incidence of novel mRNAs within these cDNA libraries. These studies provide insights into the depths of transcriptional complexity still untapped amongst products of inducible genes, and identify macrophage and dendritic cell populations as a starting point for sampling the inducible mammalian transcriptome. | |
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