Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection

Xinyue Luo; Ruijie Song; David F Moreno; Hong-Yeoul Ryu; Mark Hochstrasser; Murat Acar

doi:10.1016/j.celrep.2020.108306

Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection

Cell Rep. 2020 Oct 27;33(4):108306. doi: 10.1016/j.celrep.2020.108306.

Authors

Xinyue Luo¹, Ruijie Song², David F Moreno¹, Hong-Yeoul Ryu³, Mark Hochstrasser⁴, Murat Acar⁵

Affiliations

¹ Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA.
² Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA.
³ Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
⁴ Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
⁵ Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA. Electronic address: murat.acar@yale.edu.

Abstract

How evolution can be facilitated by epigenetic mechanisms has received refreshed attention recently. To explore the role epigenetic inheritance plays in evolution, we subject isogenic wild-type yeast cells expressing P_GAL1-YFP (yellow fluorescent protein) to selection by daily sorting based on reporter expression. We observe expression-level reductions in multiple replicates sorted for the lowest expression that persist for several days, even after lifting the selection pressure. Reduced expression is due to factors in the galactose (GAL) network rather than global factors. Results using a constitutively active GAL network are in overall agreement with findings with the wild-type network. We find that the local chromatin environment of the reporter has a significant effect on the observed phenotype. Genome sequencing, chromatin immunoprecipitation (ChIP)-qPCR, and sporulation analysis provide further insights into the epigenetic and genetic contributors to the expression changes observed. Our work provides a comprehensive example of the role played by epigenetic mechanisms on gene network evolution.

Keywords: Darwinian evolution; Genetics; epigenetic inheritance; epigenetic memory; epigenetics; neo- Lamarckian evolution; real-time evolution; single-cell analysis; systems biology.

Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection

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