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

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 lin...

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Autores principales:	Daniel Ramsköld, Eric T Wang, Christopher B Burge, Rickard Sandberg
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0257c368ecd045d7820e2fcbac49a9f5
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spelling	oai:doaj.org-article:0257c368ecd045d7820e2fcbac49a9f52021-11-25T05:42:47ZAn abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.1553-734X1553-735810.1371/journal.pcbi.1000598https://doaj.org/article/0257c368ecd045d7820e2fcbac49a9f52009-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20011106/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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.Daniel RamsköldEric T WangChristopher B BurgeRickard SandbergPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 12, p e1000598 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Daniel Ramsköld Eric T Wang Christopher B Burge Rickard Sandberg An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
description	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.
format	article
author	Daniel Ramsköld Eric T Wang Christopher B Burge Rickard Sandberg
author_facet	Daniel Ramsköld Eric T Wang Christopher B Burge Rickard Sandberg
author_sort	Daniel Ramsköld
title	An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
title_short	An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
title_full	An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
title_fullStr	An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
title_full_unstemmed	An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
title_sort	abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/0257c368ecd045d7820e2fcbac49a9f5
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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.

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