Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
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- dc.contributor.author van Dijk, Davidca
- dc.contributor.author Sharon, Elionca
- dc.contributor.author Lotan Pompan, Mayaca
- dc.contributor.author Weinberger, Adinaca
- dc.contributor.author Segal, Eranca
- dc.contributor.author Carey, Lucas, 1980-ca
- dc.date.accessioned 2017-05-26T07:52:42Z
- dc.date.issued 2017
- dc.description.abstract Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA sequence, TF concentration, and gene expression output, we have conducted in budding yeast a large-scale measurement of the activity of thousands of designed promoters at six different levels of TF. We observe that maximum promoter activity is determined by TF concentration and not by the number of binding sites. Surprisingly, the addition of an activator site often reduces expression. A thermodynamic model that incorporates competition between neighboring binding sites for a local pool of TF molecules explains this behavior and accurately predicts both absolute expression and the amount by which addition of a site increases or reduces expression. Taken together, our findings support a model in which neighboring binding sites interact competitively when TF is limiting but otherwise act additively.
- dc.description.sponsorship This work was supported by the Spanish Ministerio de Economía y Competitividad and FEDER through project BFU2015-68351-P to L.B.C. and by grant 2014SGR0974 from the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) to L.B.C. This work was supported by grants from the European Research Council (ERC) and the US National Institutes of Health (NIH) to E.S. D.vD. was supported by Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) Rubicon fellowship 825.14.016.
- dc.format.mimetype application/pdfca
- dc.identifier.citation van Dijk D, Sharon E, Lotan Pompan M, Weinberger A, Segal E, Carey L. Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators. Genome Research. 2017;27:87-94. DOI: 10.1101/gr.212316.116
- dc.identifier.doi http://dx.doi.org/10.1101/gr.212316.116
- dc.identifier.issn 1088-9051
- dc.identifier.uri http://hdl.handle.net/10230/32169
- dc.language.iso eng
- dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)ca
- dc.relation.ispartof Genome Research. 2017;27:87-94
- dc.rights © 2017 van Dijk et al.; Published by Cold Spring Harbor Laboratory Press. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.title Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activatorsca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion