Comparative analysis of the transcriptome across distant species

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• dc.contributor.author Gerstein, Mark B.ca
• dc.contributor.author Djebali, Sarahca
• dc.contributor.author Lagarde, Julienca
• dc.contributor.author Pervouchine, Dmitri D.ca
• dc.contributor.author Guigó Serra, Rodericca
• dc.contributor.author Tanzer, Andreaca
• dc.contributor.author Waterston, Robertca
• dc.date.accessioned 2015-06-16T08:18:22Z
• dc.date.available 2015-06-16T08:18:22Z
• dc.date.issued 2014ca
• dc.description.abstract The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features1, 2, 3, 4, 5, 6. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a ‘universal model’ based on a single set of organism-independent parameters.en
• dc.description.sponsorship In particular, this work was funded by a contract from the National Human Genome Research Institute modENCODE Project, contract U01 HG004271 and U54 HG006944, to S.E.C. (principal investigator) and P.C., T.R.G., R.A.H. and B.R.G. (co-principal investigators) with additional support from R01 GM076655 (S.E.C.) both under Department of Energy contract no. DE-AC02-05CH11231, and U54 HG007005 to B.R.G. J.B.B.’s work was supported by NHGRI K99 HG006698 and DOE DE-AC02-05CH11231. Work in P.J.B.’s group was supported by the modENCODE DAC sub award 5710003102, 1U01HG007031-01 and the ENCODE DAC 5U01HG004695-04. Work in M.B.G.’s group was supported by NIH grants HG007000 and HG007355. Work in Bloomington was supported in part by the Indiana METACyt Initiative of Indiana University, funded by an award from the Lilly Endowment, Inc. Work in E.C.L.’s group was supported by U01-HG004261 and RC2-HG005639. P.J.P. acknowledges support from the National Institutes of Health (grant no. U01HG004258). We thank the HAVANA team for providing annotation of the human reference genome, whose work is supported by National Institutes of Health (grant no. 5U54HG004555), the Wellcome Trust (grant no. WT098051). R.G. acknowledges support from the Spanish Ministry of Education (grant BIO2011-26205). We also acknowledge use of the Yale University Biomedical High Performance Computing Center. R.W.'s lab was supported by grant no. U01 HG 004263.en
• dc.format.mimetype application/pdfca
• dc.identifier.citation Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB et al. Comparative analysis of the transcriptome across distant species. Nature. 2014; 512: 445-448. DOI 10.1038/nature13424ca
• dc.identifier.doi http://dx.doi.org/10.1038/nature13424
• dc.identifier.issn 0028-0836ca
• dc.identifier.uri http://hdl.handle.net/10230/23828
• dc.language.iso engca
• dc.publisher Nature Publishing Groupca
• dc.relation.ispartof Nature. 2014; 512: 445-448
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
• dc.rights © Nature Publishing Group. http://dx.doi.org/10.1038/nature13424/nThis work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the materialen
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/
• dc.subject.keyword Comparative genomicsen
• dc.subject.keyword Transcriptomicsen
• dc.subject.other Caenorhabditis elegans -- Embriologiaca
• dc.subject.other Drosòfila -- Genèticaca
• dc.subject.other Regulació genèticaca
• dc.title Comparative analysis of the transcriptome across distant speciesen
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca