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...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-12-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20011106/?tool=EBI |
| _version_ | 1811173512418689024 |
|---|---|
| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-10T17:48:13Z |
| format | Article |
| id | doaj.art-0257c368ecd045d7820e2fcbac49a9f5 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-10T17:48:13Z |
| publishDate | 2009-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-0257c368ecd045d7820e2fcbac49a9f52023-02-02T22:56:18ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582009-12-01512e100059810.1371/journal.pcbi.1000598An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.Daniel RamsköldEric T WangChristopher B BurgeRickard SandbergThe 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20011106/?tool=EBI |
| spellingShingle | Daniel Ramsköld Eric T Wang Christopher B Burge Rickard Sandberg An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Computational Biology |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20011106/?tool=EBI |
| work_keys_str_mv | AT danielramskold anabundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT erictwang anabundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT christopherbburge anabundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT rickardsandberg anabundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT danielramskold abundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT erictwang abundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT christopherbburge abundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata AT rickardsandberg abundanceofubiquitouslyexpressedgenesrevealedbytissuetranscriptomesequencedata |