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Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617956/ https://www.ncbi.nlm.nih.gov/pubmed/26290536 http://dx.doi.org/10.1101/gr.190868.115 |
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author | Bilgin Sonay, Tugce Carvalho, Tiago Robinson, Mark D. Greminger, Maja P. Krützen, Michael Comas, David Highnam, Gareth Mittelman, David Sharp, Andrew Marques-Bonet, Tomàs Wagner, Andreas |
author_facet | Bilgin Sonay, Tugce Carvalho, Tiago Robinson, Mark D. Greminger, Maja P. Krützen, Michael Comas, David Highnam, Gareth Mittelman, David Sharp, Andrew Marques-Bonet, Tomàs Wagner, Andreas |
author_sort | Bilgin Sonay, Tugce |
collection | PubMed |
description | Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation. |
format | Online Article Text |
id | pubmed-4617956 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-46179562016-05-01 Tandem repeat variation in human and great ape populations and its impact on gene expression divergence Bilgin Sonay, Tugce Carvalho, Tiago Robinson, Mark D. Greminger, Maja P. Krützen, Michael Comas, David Highnam, Gareth Mittelman, David Sharp, Andrew Marques-Bonet, Tomàs Wagner, Andreas Genome Res Research Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation. Cold Spring Harbor Laboratory Press 2015-11 /pmc/articles/PMC4617956/ /pubmed/26290536 http://dx.doi.org/10.1101/gr.190868.115 Text en © 2015 Bilgin Sonay et al.; 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 Bilgin Sonay, Tugce Carvalho, Tiago Robinson, Mark D. Greminger, Maja P. Krützen, Michael Comas, David Highnam, Gareth Mittelman, David Sharp, Andrew Marques-Bonet, Tomàs Wagner, Andreas Tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
title | Tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
title_full | Tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
title_fullStr | Tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
title_full_unstemmed | Tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
title_short | Tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
title_sort | tandem repeat variation in human and great ape populations and its impact on gene expression divergence |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617956/ https://www.ncbi.nlm.nih.gov/pubmed/26290536 http://dx.doi.org/10.1101/gr.190868.115 |
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