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.
|Number of pages
|Published - Apr 2009
Bibliographical noteFunding Information:
We acknowledge with gratitude the gift of strains, protocols and advice from J. Berman (University of Minnesota), and thank H. Kelkar (University of North Carolina) for help with the Illumina sequencing data and the members of our respective laboratories for discussions and comments on the manuscript. This work was supported by grants from the US National Institutes of Health to J.D.L., from the NIH to J.W., and from the European Research Council (ERC) and NIH to E.S. N.K. is a Clore scholar. E.S. is the incumbent of the Soretta and Henry Shapiro career development chair.
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