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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...

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Detalles Bibliográficos
Autores principales: Grishkevich, Vladislav, Yanai, Itai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
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.
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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
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