Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

Arielle L. Yablonovitch, Jeremy Fu, Kexin Li, Simpla Mahato, Lin Kang, Eugenia Rashkovetsky, Abraham B. Korol, Hua Tang, Pawel Michalak, Andrew C. Zelhof, Eviatar Nevo, Jin Billy Li

Research output: Contribution to journalArticlepeer-review

Abstract

Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust to different environmental conditions. Here we study Drosophila melanogaster from 'Evolution Canyon' in Israel, which consists of two opposing slopes with divergent microclimates. We identify several hundred differentially expressed genes and dozens of differentially edited sites between flies from each slope, correlate these changes with genetic differences, and use CRISPR mutagenesis to validate that an intronic SNP in prominin regulates its editing levels. We also demonstrate that while temperature affects editing levels at more sites than genetic differences, genetically regulated sites tend to be less affected by temperature. This work shows the extent to which gene expression and RNA editing differ between flies from different microclimates, and provides insights into the regulation responsible for these differences.

Original languageEnglish
Article number1570
JournalNature Communications
Volume8
Issue number1
DOIs
StatePublished - 1 Dec 2017

Bibliographical note

Funding Information:
We thank members of the Li lab for comments, as well as Hunter Fraser, Tom Clandinin, Joe Lipsick, and Stephen Montgomery for helpful discussions. We also thank Drew Stenesen and Helmut Kramer for assistance with phenotyping flies. This work was supported by an NIH Molecular Biophysics Predoctoral Research Training Grant T32 GM008294 (A.L.Y.), Binational USA-Israel Science Foundation Grant BSF # 2011438 (K. L., E.R., A.B.K., E.N.), NIH grant R21EY024125 (S.M. and A.C.Z.), Research Foundation of Ancell-Teicher for Genetics and Molecular Evolution (E.N.), and NIH grants R01 GM102484, R01 GM124215, and R01 MH115080 and the Ellison Medical Foundation (J. B.L.).

Publisher Copyright:
© 2017 The Author(s).

ASJC Scopus subject areas

  • Chemistry (all)
  • Biochemistry, Genetics and Molecular Biology (all)
  • Physics and Astronomy (all)

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