Article abstract
Nature Genetics 41, 438 - 445 (2009)
Published online: 1 March 2009 | doi:10.1038/ng.324
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
Yair Field1,5, Yvonne Fondufe-Mittendorf2,5, Irene K Moore2, Piotr Mieczkowski3, Noam Kaplan1, Yaniv Lubling1, Jason D Lieb3, Jonathan Widom2 & Eran Segal1,4
Abstract
Eukaryotic transcription occurs within a chromatin environment, whose organization has an important regulatory function and is partly encoded in cis by the DNA sequence itself. Here, we examine whether evolutionary changes in gene expression are linked to changes in the DNA-encoded nucleosome organization of promoters. We find that in aerobic yeast species, where cellular respiration genes are active under typical growth conditions, the promoter sequences of these genes encode a relatively open (nucleosome-depleted) chromatin organization. This nucleosome-depleted organization requires only DNA sequence information, is independent of any cofactors and of transcription, and is a general property of growth-related genes. In contrast, in anaerobic yeast species, where cellular respiration genes are relatively inactive under typical growth conditions, respiration gene promoters encode relatively closed (nucleosome-occupied) chromatin organizations. Our results suggest a previously unidentified genetic mechanism underlying phenotypic diversity, consisting of DNA sequence changes that directly alter the DNA-encoded nucleosome organization of promoters.
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel.
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA.
- Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
- These authors contributed equally to this work.
Correspondence to: Eran Segal1,4 e-mail: eran@weizmann.ac.il
Correspondence to: Jonathan Widom2 e-mail: j-widom@northwestern.edu
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