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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data

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dc.contributor.author Burge, Christopher B.
dc.contributor.author Wang, Eric T.
dc.contributor.author Ramsköld, Daniel
dc.contributor.author Sandberg, Rickard
dc.date.accessioned 2010-09-15T17:44:41Z
dc.date.available 2010-09-15T17:44:41Z
dc.date.issued 2009-12
dc.date.submitted 2009-07
dc.identifier.issn 1553-7358
dc.identifier.issn 1553-734X
dc.identifier.uri http://hdl.handle.net/1721.1/58548
dc.description.abstract The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out. We characterized the features of mammalian tissue transcriptomes at the gene level through analysis of RNA deep sequencing (RNA-Seq) data across human and mouse tissues and cell lines. We observed that roughly 8,000 protein-coding genes were ubiquitously expressed, contributing to around 75% of all mRNAs by message copy number in most tissues. These mRNAs encoded proteins that were often intracellular, and tended to be involved in metabolism, transcription, RNA processing or translation. In contrast, genes for secreted or plasma membrane proteins were generally expressed in only a subset of tissues. The distribution of expression levels was broad but fairly continuous: no support was found for the concept of distinct expression classes of genes. Expression estimates that included reads mapping to coding exons only correlated better with qRT-PCR data than estimates which also included 3′ untranslated regions (UTRs). Muscle and liver had the least complex transcriptomes, in that they expressed predominantly ubiquitous genes and a large fraction of the transcripts came from a few highly expressed genes, whereas brain, kidney and testis expressed more complex transcriptomes with the vast majority of genes expressed and relatively small contributions from the most expressed genes. mRNAs expressed in brain had unusually long 3′UTRs, and mean 3′UTR length was higher for genes involved in development, morphogenesis and signal transduction, suggesting added complexity of UTR-based regulation for these genes. Our results support a model in which variable exterior components feed into a large, densely connected core composed of ubiquitously expressed intracellular proteins. en_US
dc.description.sponsorship National Institutes of Health (U.S.) en_US
dc.description.sponsorship Knut and Alice Wallenbergs Foundation en_US
dc.description.sponsorship Ake Wibergs Foundation en_US
dc.language.iso en_US
dc.publisher Public Library of Science en_US
dc.relation.isversionof http://dx.doi.org/10.1371/journal.pcbi.1000598 en_US
dc.rights Creative Commons Attribution en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.5/ en_US
dc.source PLoS en_US
dc.title An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data en_US
dc.type Article en_US
dc.identifier.citation Ramsköld, Daniel et al. “An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data.” PLoS Comput Biol 5.12 (2009): e1000598. en_US
dc.contributor.department Massachusetts Institute of Technology. Department of Biology en_US
dc.contributor.department Whitaker College of Health Sciences and Technology en_US
dc.contributor.approver Burge, Christopher B.
dc.contributor.mitauthor Burge, Christopher B.
dc.contributor.mitauthor Wang, Eric T.
dc.relation.journal PLoS Computational Biology en_US
dc.identifier.mitlicense PUBLISHER_CC en_US
dc.eprint.version Final published version en_US
dc.type.uri http://purl.org/eprint/type/JournalArticle en_US
eprint.status http://purl.org/eprint/status/PeerReviewed en_US
dspace.orderedauthors Ramsköld, Daniel; Wang, Eric T.; Burge, Christopher B.; Sandberg, Rickard en


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