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Gene length and expression level shape genomic novelties
Gene duplication and alternative splicing are important mechanisms in the production of genomic novelties. Previous work has shown that a gene’s family size and the number of splice variants it produces are inversely related, although the underlying reason is not well understood. Here, we report tha...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158763/ https://www.ncbi.nlm.nih.gov/pubmed/25015383 http://dx.doi.org/10.1101/gr.169722.113 |
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author | Grishkevich, Vladislav Yanai, Itai |
author_facet | Grishkevich, Vladislav Yanai, Itai |
author_sort | Grishkevich, Vladislav |
collection | PubMed |
description | Gene duplication and alternative splicing are important mechanisms in the production of genomic novelties. Previous work has shown that a gene’s family size and the number of splice variants it produces are inversely related, although the underlying reason is not well understood. Here, we report that gene length and expression level together explain this relationship. We found that gene lengths correlate with both gene duplication and alternative splicing: Longer genes are less likely to produce duplicates and more likely to exhibit alternative splicing. We show that gene length is a dynamic property, increasing with evolutionary time—due in part to the insertions of transposable elements—and decreasing following partial gene duplications. However, gene length alone does not account for the relationship between alternative splicing and gene duplication. A gene’s expression level appears both to impose a strong constraint on its length and to restrict gene duplications. Furthermore, high gene expression promotes alternative splicing, in particular for long genes, and alternatively, short genes with low expression levels have large gene families. Our analysis of the human and mouse genomes shows that gene length and expression level are primary genic properties that together account for the relationship between gene duplication and alternative splicing and bias the origin of novelties in the genome. |
format | Online Article Text |
id | pubmed-4158763 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-41587632015-03-01 Gene length and expression level shape genomic novelties Grishkevich, Vladislav Yanai, Itai Genome Res Research Gene duplication and alternative splicing are important mechanisms in the production of genomic novelties. Previous work has shown that a gene’s family size and the number of splice variants it produces are inversely related, although the underlying reason is not well understood. Here, we report that gene length and expression level together explain this relationship. We found that gene lengths correlate with both gene duplication and alternative splicing: Longer genes are less likely to produce duplicates and more likely to exhibit alternative splicing. We show that gene length is a dynamic property, increasing with evolutionary time—due in part to the insertions of transposable elements—and decreasing following partial gene duplications. However, gene length alone does not account for the relationship between alternative splicing and gene duplication. A gene’s expression level appears both to impose a strong constraint on its length and to restrict gene duplications. Furthermore, high gene expression promotes alternative splicing, in particular for long genes, and alternatively, short genes with low expression levels have large gene families. Our analysis of the human and mouse genomes shows that gene length and expression level are primary genic properties that together account for the relationship between gene duplication and alternative splicing and bias the origin of novelties in the genome. Cold Spring Harbor Laboratory Press 2014-09 /pmc/articles/PMC4158763/ /pubmed/25015383 http://dx.doi.org/10.1101/gr.169722.113 Text en © 2014 Grishkevich and Yanai; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Research Grishkevich, Vladislav Yanai, Itai Gene length and expression level shape genomic novelties |
title | Gene length and expression level shape genomic novelties |
title_full | Gene length and expression level shape genomic novelties |
title_fullStr | Gene length and expression level shape genomic novelties |
title_full_unstemmed | Gene length and expression level shape genomic novelties |
title_short | Gene length and expression level shape genomic novelties |
title_sort | gene length and expression level shape genomic novelties |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158763/ https://www.ncbi.nlm.nih.gov/pubmed/25015383 http://dx.doi.org/10.1101/gr.169722.113 |
work_keys_str_mv | AT grishkevichvladislav genelengthandexpressionlevelshapegenomicnovelties AT yanaiitai genelengthandexpressionlevelshapegenomicnovelties |