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Comparative analysis of the transcriptome across distant species

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dc.contributor.author Gerstein, Mark B.
dc.contributor.author Djebali, Sarah
dc.contributor.author Lagarde, Julien
dc.contributor.author Pervouchine, Dmitri D.
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Tanzer, Andrea
dc.contributor.author Waterston, Robert
dc.date.accessioned 2015-06-16T08:18:22Z
dc.date.available 2015-06-16T08:18:22Z
dc.date.issued 2014
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/nature13424
dc.identifier.issn 0028-0836
dc.identifier.uri http://hdl.handle.net/10230/23828
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.
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.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Publishing Group
dc.relation.ispartof Nature. 2014; 512: 445-448
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 material
dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/3.0/
dc.subject.other Caenorhabditis elegans -- Embriologia
dc.subject.other Drosòfila -- Genètica
dc.subject.other Regulació genètica
dc.title Comparative analysis of the transcriptome across distant species
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/nature13424
dc.subject.keyword Comparative genomics
dc.subject.keyword Transcriptomics
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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