Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of...

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Main Authors:	Stefflova, Klara, Thybert, David, Wilson, Michael D., Streeter, Ian, Aleksic, Jelena, Karagianni, Panagiota, Brazma, Alvis, Adams, David J., Talianidis, Iannis, Marioni, John C., Flicek, Paul, Odom, Duncan T.
Format:	Online
Language:	English
Published:	Cell Press 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732390/

id	pubmed-3732390
recordtype	oai_dc
spelling	pubmed-37323902013-08-05 Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals Stefflova, Klara Thybert, David Wilson, Michael D. Streeter, Ian Aleksic, Jelena Karagianni, Panagiota Brazma, Alvis Adams, David J. Talianidis, Iannis Marioni, John C. Flicek, Paul Odom, Duncan T. Article To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence TF binding, most binding differences occur in the absence of nearby sequence variations. Instead, combinatorial binding was found to be significant for genetic and evolutionary stability; cobound TFs tend to disappear in concert and were sensitive to genetic knockout of partner TFs. The large, qualitative differences in genomic regions bound between closely related mammals, when contrasted with the smaller, quantitative TF binding differences among Drosophila species, illustrate how genome structure and population genetics together shape regulatory evolution. Cell Press 2013-08-01 /pmc/articles/PMC3732390/ /pubmed/23911320 http://dx.doi.org/10.1016/j.cell.2013.07.007 Text en © 2013 ELL & Excerpta Medica. https://creativecommons.org/licenses/by/3.0/ Open Access under CC BY 3.0 (https://creativecommons.org/licenses/by/3.0/) license
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Stefflova, Klara Thybert, David Wilson, Michael D. Streeter, Ian Aleksic, Jelena Karagianni, Panagiota Brazma, Alvis Adams, David J. Talianidis, Iannis Marioni, John C. Flicek, Paul Odom, Duncan T.
spellingShingle	Stefflova, Klara Thybert, David Wilson, Michael D. Streeter, Ian Aleksic, Jelena Karagianni, Panagiota Brazma, Alvis Adams, David J. Talianidis, Iannis Marioni, John C. Flicek, Paul Odom, Duncan T. Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
author_facet	Stefflova, Klara Thybert, David Wilson, Michael D. Streeter, Ian Aleksic, Jelena Karagianni, Panagiota Brazma, Alvis Adams, David J. Talianidis, Iannis Marioni, John C. Flicek, Paul Odom, Duncan T.
author_sort	Stefflova, Klara
title	Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
title_short	Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
title_full	Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
title_fullStr	Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
title_full_unstemmed	Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
title_sort	cooperativity and rapid evolution of cobound transcription factors in closely related mammals
description	To mechanistically characterize the microevolutionary processes active in altering transcription factor (TF) binding among closely related mammals, we compared the genome-wide binding of three tissue-specific TFs that control liver gene expression in six rodents. Despite an overall fast turnover of TF binding locations between species, we identified thousands of TF regions of highly constrained TF binding intensity. Although individual mutations in bound sequence motifs can influence TF binding, most binding differences occur in the absence of nearby sequence variations. Instead, combinatorial binding was found to be significant for genetic and evolutionary stability; cobound TFs tend to disappear in concert and were sensitive to genetic knockout of partner TFs. The large, qualitative differences in genomic regions bound between closely related mammals, when contrasted with the smaller, quantitative TF binding differences among Drosophila species, illustrate how genome structure and population genetics together shape regulatory evolution.
publisher	Cell Press
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732390/
_version_	1612000252123938816

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

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