Coevolution within a transcriptional network by compensatory trans and cis mutations

Handle URI:
http://hdl.handle.net/10754/555797
Title:
Coevolution within a transcriptional network by compensatory trans and cis mutations
Authors:
Kuo, D.; Licon, K.; Bandyopadhyay, S.; Chuang, R.; Luo, C.; Catalana, J.; Ravasi, Timothy ( 0000-0002-9950-465X ) ; Tan, K.; Ideker, T.
Abstract:
Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “coevolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners.
KAUST Department:
Red Sea Research Center (RSRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Coevolution within a transcriptional network by compensatory trans and cis mutations 2010, 20 (12):1672 Genome Research
Journal:
Genome Research
Issue Date:
26-Oct-2010
DOI:
10.1101/gr.111765.110
PubMed ID:
20978140
PubMed Central ID:
PMC2989993
Type:
Article
ISSN:
1088-9051
Additional Links:
http://genome.cshlp.org/cgi/doi/10.1101/gr.111765.110
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKuo, D.en
dc.contributor.authorLicon, K.en
dc.contributor.authorBandyopadhyay, S.en
dc.contributor.authorChuang, R.en
dc.contributor.authorLuo, C.en
dc.contributor.authorCatalana, J.en
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorTan, K.en
dc.contributor.authorIdeker, T.en
dc.date.accessioned2015-05-26T08:04:54Zen
dc.date.available2015-05-26T08:04:54Zen
dc.date.issued2010-10-26en
dc.identifier.citationCoevolution within a transcriptional network by compensatory trans and cis mutations 2010, 20 (12):1672 Genome Researchen
dc.identifier.issn1088-9051en
dc.identifier.pmid20978140en
dc.identifier.doi10.1101/gr.111765.110en
dc.identifier.urihttp://hdl.handle.net/10754/555797en
dc.description.abstractTranscriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “coevolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners.en
dc.relation.urlhttp://genome.cshlp.org/cgi/doi/10.1101/gr.111765.110en
dc.rightsArchived with thanks to Genome Researchen
dc.titleCoevolution within a transcriptional network by compensatory trans and cis mutationsen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGenome Researchen
dc.identifier.pmcidPMC2989993en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartments of Bioengineering and Medicine, University of California, San Diego, La Jolla, California 92093, USAen
dc.contributor.institutionDepartments of Internal Medicine and Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USAen
kaust.authorRavasi, Timothyen

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