Journal Article

Coordinated Genome-Wide Modifications within Proximal Promoter <i>Cis</i>-regulatory Elements during Vertebrate Evolution

Ken Daigoro Yokoyama, Jeffrey L. Thorne and Gregory A. Wray

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 3, issue , pages 66-74
Published in print January 2011 |
Published online November 2010 | e-ISSN: 1759-6653 | DOI:

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There often exists a “one-to-many” relationship between a transcription factor and a multitude of binding sites throughout the genome. It is commonly assumed that transcription factor binding motifs remain largely static over the course of evolution because changes in binding specificity can alter the interactions with potentially hundreds of sites across the genome. Focusing on regulatory motifs overrepresented at specific locations within or near the promoter, we find that a surprisingly large number of cis-regulatory elements have been subject to coordinated genome-wide modifications during vertebrate evolution, such that the motif frequency changes on a single branch of vertebrate phylogeny. This was found to be the case even between closely related mammal species, with nearly a third of all location-specific consensus motifs exhibiting significant modifications within the human or mouse lineage since their divergence. Many of these modifications are likely to be compensatory changes throughout the genome following changes in protein factor binding affinities, whereas others may be due to changes in mutation rates or effective population size. The likelihood that this happened many times during vertebrate evolution highlights the need to examine additional taxa and to understand the evolutionary and molecular mechanisms underlying the evolution of protein–DNA interactions.

Keywords: gene expression; transcriptional regulation; protein–DNA coevolution; cis-regulatory evolution

Journal Article.  5689 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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