Changes in gene expression predictably shift and switch genetic interactions

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  • dc.contributor.author Li, Xianghua
  • dc.contributor.author Lalić, Jasna
  • dc.contributor.author Baeza Centurión, Pablo, 1989-
  • dc.contributor.author Dhar, Riddhiman
  • dc.contributor.author Lehner, Ben, 1978-
  • dc.date.accessioned 2019-10-25T11:12:05Z
  • dc.date.available 2019-10-25T11:12:05Z
  • dc.date.issued 2019
  • dc.description.abstract Non-additive interactions between mutations occur extensively and also change across conditions, making genetic prediction a difficult challenge. To better understand the plasticity of genetic interactions (epistasis), we combine mutations in a single protein performing a single function (a transcriptional repressor inhibiting a target gene). Even in this minimal system, genetic interactions switch from positive (suppressive) to negative (enhancing) as the expression of the gene changes. These seemingly complicated changes can be predicted using a mathematical model that propagates the effects of mutations on protein folding to the cellular phenotype. More generally, changes in gene expression should be expected to alter the effects of mutations and how they interact whenever the relationship between expression and a phenotype is nonlinear, which is the case for most genes. These results have important implications for understanding genotype-phenotype maps and illustrate how changes in genetic interactions can often-but not always-be predicted by hierarchical mechanistic models.
  • dc.description.sponsorship This work was supported by a European Research Council (ERC) Consolidator grant (616434), the Spanish Ministry of Economy and Competitiveness (BFU2017-89488-P and SEV-2012-0208), the Bettencourt Schueller Foundation, Agencia de Gestio d’Ajuts Universitaris i de Recerca (AGAUR, 2017 SGR 1322.), and the CERCA Program/Generalitat de Catalunya. X. Li was supported in part by a fellowship from the Ramón Areces Foundation. We also acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership and the Centro de Excelencia Severo Ochoa.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Li X, Lalić J, Baeza-Centurion P, Dhar R, Lehner B. Changes in gene expression predictably shift and switch genetic interactions. Nat Commun. 2019;10(1):3886. DOI: 10.1038/s41467-019-11735-3
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-019-11735-3
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/42511
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nature Communications. 2019;10(1):3886
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/616434
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-89488-P
  • dc.rights © The Author(s) 2019. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Computational models
  • dc.subject.keyword Epistasis
  • dc.subject.keyword Genetics
  • dc.subject.keyword Systems biology
  • dc.title Changes in gene expression predictably shift and switch genetic interactions
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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