Redundancy and the evolution of cis-regulatory element multiplicity.

PLoS Computational Biology
Tiago Paixão, Ricardo B R Azevedo

Abstract

The promoter regions of many genes contain multiple binding sites for the same transcription factor (TF). One possibility is that this multiplicity evolved through transitional forms showing redundant cis-regulation. To evaluate this hypothesis, we must disentangle the relative contributions of different evolutionary mechanisms to the evolution of binding site multiplicity. Here, we attempt to do this using a model of binding site evolution. Our model considers binding sequences and their interactions with TFs explicitly, and allows us to cast the evolution of gene networks into a neutral network framework. We then test some of the model's predictions using data from yeast. Analysis of the model suggested three candidate nonadaptive processes favoring the evolution of cis-regulatory element redundancy and multiplicity: neutral evolution in long promoters, recombination and TF promiscuity. We find that recombination rate is positively associated with binding site multiplicity in yeast. Our model also indicated that weak direct selection for multiplicity (partial redundancy) can play a major role in organisms with large populations. Our data suggest that selection for changes in gene expression level may have contributed to the e...Continue Reading

References

Apr 1, 1991·Molecular and Cellular Biology·G M Anderson, S O Freytag
May 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·D B KabackP de Jonge
Jan 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·E Giniger, M Ptashne
Nov 1, 1993·Trends in Genetics : TIG·J H Thomas
Jul 10, 1997·Nature·M A NowakJ M Smith
Apr 30, 1998·Genetics·J W DrakeJ F Crow
May 15, 1998·Trends in Biochemical Sciences·G D Stormo, D S Fields
Dec 9, 1998·Cell·F C HolstegeR A Young
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·E van NimwegenM Huynen
Aug 16, 2001·Molecular Biology and Evolution·J R Stone, G A Wray
Nov 8, 2001·Proceedings of the National Academy of Sciences of the United States of America·G M Edelman, J A Gally
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
Jun 26, 2002·Molecular Biology and Evolution·Emmanouil T Dermitzakis, Andrew G Clark
Jul 26, 2002·Nature·Guri GiaeverMark Johnston
Sep 10, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ulrich GerlandTerence Hwa
Oct 2, 2002·Journal of Molecular Evolution·Ulrich Gerland, Terence Hwa
Oct 18, 2002·Nucleic Acids Research·Panayiotis V BenosGary D Stormo
Jan 4, 2003·Nature·Zhenglong GuWen-Hsiung Li
Jun 5, 2003·Molecular Biology and Evolution·Gregory A WrayLaura A Romano
Oct 17, 2003·Nature·Sina GhaemmaghamiJonathan S Weissman
Mar 10, 2004·Cell·Andrew D BasehoarB Franklin Pugh
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Oct 30, 2004·BMC Evolutionary Biology·Johannes BergMichael Lässig
Jan 25, 2005·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Andreas Wagner
Feb 25, 2005·The American Naturalist·Stephen R Proulx, Patrick C Phillips
Mar 11, 2005·Molecular Biology and Evolution·Andreas Wagner
Aug 10, 2005·Proceedings of the National Academy of Sciences of the United States of America·Andreas Wagner
Feb 21, 2006·Journal of Theoretical Biology·Andy Gardner, Alex T Kalinka
Mar 9, 2006·BMC Bioinformatics·Kenzie D MacIsaacErnest Fraenkel
Apr 18, 2006·Proceedings. Biological Sciences·Dusan MisevicRichard E Lenski
Feb 6, 2007·PLoS Computational Biology·Stefano CilibertiAndreas Wagner
May 4, 2007·Journal of Theoretical Biology·Günter P WagnerPeter F Stadler
May 29, 2007·PLoS Computational Biology·Scott W Doniger, Justin C Fay
Aug 11, 2007·Science·Anthony R BornemanMichael Snyder
Sep 18, 2007·Nature Genetics·William LeeCorey Nislow
Sep 20, 2007·Nature Reviews. Genetics·Michael Lynch

❮ Previous
Next ❯

Citations

May 31, 2012·TheScientificWorldJournal·Rajesh MehrotraSandhya Mehrotra
Nov 15, 2011·Molecular Biology and Evolution·Xin HeSaurabh Sinha
Sep 1, 2012·BMC Evolutionary Biology·Troy Ruths, Luay Nakhleh
Oct 20, 2012·Bioinformatics·Cho-Yi ChenHsuan-Cheng Huang
Aug 16, 2013·Proceedings. Biological Sciences·Alexander J Stewart, Joshua B Plotkin
Nov 16, 2011·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Scott Barolo
Jun 4, 2014·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Mikhail Spivakov
Jan 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yanglan GanWeixiong Zhang
May 11, 2015·Cell·Trevor R Sorrells, Alexander D Johnson
Aug 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Tobias SikosekErich Bornberg-Bauer
Aug 10, 2013·Aging·Anna VlantiPopi Syntichaki
Nov 19, 2015·Frontiers in Genetics·Joshua L Payne, Andreas Wagner
Mar 24, 2021·Briefings in Functional Genomics·François Giudicelli, Hugues Roest Crollius

❮ Previous
Next ❯

Software Mentioned

R
Mathematica
REML
Bioconductor

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

Related Papers

Journal of Molecular Evolution
Ulrich Gerland, Terence Hwa
Current Opinion in Genetics & Development
Dana J WohlbachAviv Regev
© 2021 Meta ULC. All rights reserved