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Title: Large-scale turnover of functional transcription factor bindingsites in Drosophila

Abstract

The gain and loss of functional transcription-factor bindingsites has been proposed as a major source of evolutionary change incis-regulatory DNA and gene expression. We have developed an evolutionarymodel to study binding site turnover that uses multiple sequencealignments to assess the evolutionary constraint on individual bindingsites, and to map gain and loss events along a phylogenetic tree. Weapply this model to study the evolutionary dynamics of binding sites ofthe Drosophila melanogaster transcription factor Zeste, using genome-widein vivo (ChIP-chip) binding data to identify functional Zeste bindingsites, and the genome sequences of D. melanogaster, D. simulans, D.erecta and D. yakuba to study their evolution. We estimate that more than5 percent of functional Zeste binding sites in D. melanogaster weregained along the D. melanogaster lineage or lost along one of the otherlineages. We find that Zeste bound regions have a reduced rate of bindingsite loss and an increased rate of binding site gain relative to flankingsequences. Finally, we show that binding site gains and losses areasymmetrically distributed with respect to D. melanogaster, consistentwith lineage-specific acquisition and loss of Zeste-responsive regulatoryelements.

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
COLLABORATION - UCBerkeley
OSTI Identifier:
913276
Report Number(s):
LBNL-61357
R&D Project: GHEIS2; BnR: 400412000; TRN: US200802%%739
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
PLoS Computational Biology
Additional Journal Information:
Journal Volume: 2; Journal Issue: 10; Related Information: Journal Publication Date: 2006
Country of Publication:
United States
Language:
English
Subject:
60; DNA; DROSOPHILA; FUNCTIONALS; GENES; IN VIVO; TRANSCRIPTION FACTORS

Citation Formats

Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, VenkyN, Li, Xiao-Yong, Biggin, Mark D, and Eisen, Michael B. Large-scale turnover of functional transcription factor bindingsites in Drosophila. United States: N. p., 2006. Web. doi:10.1371/journal.pcbi.0020130.
Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, VenkyN, Li, Xiao-Yong, Biggin, Mark D, & Eisen, Michael B. Large-scale turnover of functional transcription factor bindingsites in Drosophila. United States. https://doi.org/10.1371/journal.pcbi.0020130
Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, VenkyN, Li, Xiao-Yong, Biggin, Mark D, and Eisen, Michael B. 2006. "Large-scale turnover of functional transcription factor bindingsites in Drosophila". United States. https://doi.org/10.1371/journal.pcbi.0020130. https://www.osti.gov/servlets/purl/913276.
@article{osti_913276,
title = {Large-scale turnover of functional transcription factor bindingsites in Drosophila},
author = {Moses, Alan M and Pollard, Daniel A and Nix, David A and Iyer, VenkyN and Li, Xiao-Yong and Biggin, Mark D and Eisen, Michael B},
abstractNote = {The gain and loss of functional transcription-factor bindingsites has been proposed as a major source of evolutionary change incis-regulatory DNA and gene expression. We have developed an evolutionarymodel to study binding site turnover that uses multiple sequencealignments to assess the evolutionary constraint on individual bindingsites, and to map gain and loss events along a phylogenetic tree. Weapply this model to study the evolutionary dynamics of binding sites ofthe Drosophila melanogaster transcription factor Zeste, using genome-widein vivo (ChIP-chip) binding data to identify functional Zeste bindingsites, and the genome sequences of D. melanogaster, D. simulans, D.erecta and D. yakuba to study their evolution. We estimate that more than5 percent of functional Zeste binding sites in D. melanogaster weregained along the D. melanogaster lineage or lost along one of the otherlineages. We find that Zeste bound regions have a reduced rate of bindingsite loss and an increased rate of binding site gain relative to flankingsequences. Finally, we show that binding site gains and losses areasymmetrically distributed with respect to D. melanogaster, consistentwith lineage-specific acquisition and loss of Zeste-responsive regulatoryelements.},
doi = {10.1371/journal.pcbi.0020130},
url = {https://www.osti.gov/biblio/913276}, journal = {PLoS Computational Biology},
number = 10,
volume = 2,
place = {United States},
year = {Fri Jul 14 00:00:00 EDT 2006},
month = {Fri Jul 14 00:00:00 EDT 2006}
}