Populational landscape of INDELs affecting transcription factor-binding sites in humans

Background Differences in gene expression have a significant role in the diversity of phenotypes in humans. Here we integrated human public data from ENCODE, 1000 Genomes and Geuvadis to explore the populational landscape of INDELs affecting transcription factor-binding sites (TFBS). A significant...

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Principais autores: Ribeiro-dos-Santos, André M., Silva, Vandeclécio L. da, Souza, Jorge E.S. de, Souza, Sandro José de
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Idioma:eng
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Transcription factor
Transcription factor-binding site
INDEL
Population genetics
Endereço do item:https://repositorio.ufrn.br/jspui/handle/123456789/23189
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spelling ri-123456789-231892021-07-09T22:46:52Z Populational landscape of INDELs affecting transcription factor-binding sites in humans Ribeiro-dos-Santos, André M. Silva, Vandeclécio L. da Souza, Jorge E.S. de Souza, Sandro José de Transcription factor Transcription factor-binding site INDEL Population genetics Background Differences in gene expression have a significant role in the diversity of phenotypes in humans. Here we integrated human public data from ENCODE, 1000 Genomes and Geuvadis to explore the populational landscape of INDELs affecting transcription factor-binding sites (TFBS). A significant fraction of TFBS close to the transcription start site of known genes is affected by INDELs with a consequent effect at the expression of the associated gene. Results Hundreds of TFBS-affecting INDELs (TFBS-ID) show a differential frequency between human populations, suggesting a role of natural selection in the spread of such variant INDELs. A comparison with a dataset of known human genomic regions under natural selection allowed us to identify several cases of TFBS-ID likely involved in populational adaptations. Ontology analyses on the differential TFBS-ID further indicated several biological processes under natural selection in different populations. Conclusion Together, our results strongly suggest that INDELs have an important role in modulating gene expression patterns in humans. The dataset we make available, together with other data reporting variability at both regulatory and coding regions of genes, represent a powerful tool for studies aiming to better understand the evolution of gene regulatory networks in humans. 2017-05-29T17:50:25Z 2017-05-29T17:50:25Z 2015 article https://repositorio.ufrn.br/jspui/handle/123456789/23189 10.1186/s12864-015-1744-5 eng Acesso Aberto application/pdf
institution Repositório Institucional
collection RI - UFRN
language eng
topic Transcription factor
Transcription factor-binding site
INDEL
Population genetics
spellingShingle Transcription factor
Transcription factor-binding site
INDEL
Population genetics
Ribeiro-dos-Santos, André M.
Silva, Vandeclécio L. da
Souza, Jorge E.S. de
Souza, Sandro José de
Populational landscape of INDELs affecting transcription factor-binding sites in humans
description Background Differences in gene expression have a significant role in the diversity of phenotypes in humans. Here we integrated human public data from ENCODE, 1000 Genomes and Geuvadis to explore the populational landscape of INDELs affecting transcription factor-binding sites (TFBS). A significant fraction of TFBS close to the transcription start site of known genes is affected by INDELs with a consequent effect at the expression of the associated gene. Results Hundreds of TFBS-affecting INDELs (TFBS-ID) show a differential frequency between human populations, suggesting a role of natural selection in the spread of such variant INDELs. A comparison with a dataset of known human genomic regions under natural selection allowed us to identify several cases of TFBS-ID likely involved in populational adaptations. Ontology analyses on the differential TFBS-ID further indicated several biological processes under natural selection in different populations. Conclusion Together, our results strongly suggest that INDELs have an important role in modulating gene expression patterns in humans. The dataset we make available, together with other data reporting variability at both regulatory and coding regions of genes, represent a powerful tool for studies aiming to better understand the evolution of gene regulatory networks in humans.
format article
author Ribeiro-dos-Santos, André M.
Silva, Vandeclécio L. da
Souza, Jorge E.S. de
Souza, Sandro José de
author_facet Ribeiro-dos-Santos, André M.
Silva, Vandeclécio L. da
Souza, Jorge E.S. de
Souza, Sandro José de
author_sort Ribeiro-dos-Santos, André M.
title Populational landscape of INDELs affecting transcription factor-binding sites in humans
title_short Populational landscape of INDELs affecting transcription factor-binding sites in humans
title_full Populational landscape of INDELs affecting transcription factor-binding sites in humans
title_fullStr Populational landscape of INDELs affecting transcription factor-binding sites in humans
title_full_unstemmed Populational landscape of INDELs affecting transcription factor-binding sites in humans
title_sort populational landscape of indels affecting transcription factor-binding sites in humans
publishDate 2017
url https://repositorio.ufrn.br/jspui/handle/123456789/23189
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