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Variation in alternative splicing across human tissues
BACKGROUND: Alternative pre-mRNA splicing (AS) is widely used by higher eukaryotes to generate different protein isoforms in specific cell or tissue types. To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2004
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545594/ https://www.ncbi.nlm.nih.gov/pubmed/15461793 http://dx.doi.org/10.1186/gb-2004-5-10-r74 |
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author | Yeo, Gene Holste, Dirk Kreiman, Gabriel Burge, Christopher B |
author_facet | Yeo, Gene Holste, Dirk Kreiman, Gabriel Burge, Christopher B |
author_sort | Yeo, Gene |
collection | PubMed |
description | BACKGROUND: Alternative pre-mRNA splicing (AS) is widely used by higher eukaryotes to generate different protein isoforms in specific cell or tissue types. To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from libraries of cDNAs from different tissues. RESULTS: Controlling for differences in EST coverage among tissues, we found that the brain and testis had the highest levels of exon skipping. The most pronounced differences between tissues were seen for the frequencies of alternative 3' splice site and alternative 5' splice site usage, which were about 50 to 100% higher in the liver than in any other human tissue studied. Quantifying differences in splice junction usage, the brain, pancreas, liver and the peripheral nervous system had the most distinctive patterns of AS. Analysis of available microarray expression data showed that the liver had the most divergent pattern of expression of serine-arginine protein and heterogeneous ribonucleoprotein genes compared to the other human tissues studied, possibly contributing to the unusually high frequency of alternative splice site usage seen in liver. Sequence motifs enriched in alternative exons in genes expressed in the brain, testis and liver suggest specific splicing factors that may be important in AS regulation in these tissues. CONCLUSIONS: This study distinguishes the human brain, testis and liver as having unusually high levels of AS, highlights differences in the types of AS occurring commonly in different tissues, and identifies candidate cis-regulatory elements and trans-acting factors likely to have important roles in tissue-specific AS in human cells. |
format | Text |
id | pubmed-545594 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2004 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-5455942005-01-26 Variation in alternative splicing across human tissues Yeo, Gene Holste, Dirk Kreiman, Gabriel Burge, Christopher B Genome Biol Research BACKGROUND: Alternative pre-mRNA splicing (AS) is widely used by higher eukaryotes to generate different protein isoforms in specific cell or tissue types. To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from libraries of cDNAs from different tissues. RESULTS: Controlling for differences in EST coverage among tissues, we found that the brain and testis had the highest levels of exon skipping. The most pronounced differences between tissues were seen for the frequencies of alternative 3' splice site and alternative 5' splice site usage, which were about 50 to 100% higher in the liver than in any other human tissue studied. Quantifying differences in splice junction usage, the brain, pancreas, liver and the peripheral nervous system had the most distinctive patterns of AS. Analysis of available microarray expression data showed that the liver had the most divergent pattern of expression of serine-arginine protein and heterogeneous ribonucleoprotein genes compared to the other human tissues studied, possibly contributing to the unusually high frequency of alternative splice site usage seen in liver. Sequence motifs enriched in alternative exons in genes expressed in the brain, testis and liver suggest specific splicing factors that may be important in AS regulation in these tissues. CONCLUSIONS: This study distinguishes the human brain, testis and liver as having unusually high levels of AS, highlights differences in the types of AS occurring commonly in different tissues, and identifies candidate cis-regulatory elements and trans-acting factors likely to have important roles in tissue-specific AS in human cells. BioMed Central 2004 2004-09-13 /pmc/articles/PMC545594/ /pubmed/15461793 http://dx.doi.org/10.1186/gb-2004-5-10-r74 Text en Copyright © 2004 Yeo et al.; licensee BioMed Central Ltd. |
spellingShingle | Research Yeo, Gene Holste, Dirk Kreiman, Gabriel Burge, Christopher B Variation in alternative splicing across human tissues |
title | Variation in alternative splicing across human tissues |
title_full | Variation in alternative splicing across human tissues |
title_fullStr | Variation in alternative splicing across human tissues |
title_full_unstemmed | Variation in alternative splicing across human tissues |
title_short | Variation in alternative splicing across human tissues |
title_sort | variation in alternative splicing across human tissues |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC545594/ https://www.ncbi.nlm.nih.gov/pubmed/15461793 http://dx.doi.org/10.1186/gb-2004-5-10-r74 |
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