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Evolution and Genetic Architecture of Chromatin Accessibility and Function in Yeast

Author(s): Connelly, Caitlin F.; Wakefield, Jon; Akey, Joshua M.

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Abstract: Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign.
Publication Date: 3-Jul-2014
Electronic Publication Date: 3-Jul-2014
Citation: Connelly, Caitlin F., Wakefield, Jon, Akey, Joshua M. (2014). Evolution and Genetic Architecture of Chromatin Accessibility and Function in Yeast. PLoS Genetics, 10 (7), e1004427 - e1004427. doi:10.1371/journal.pgen.1004427
DOI: doi:10.1371/journal.pgen.1004427
EISSN: 1553-7404
Pages: e1004427 - e1004427
Type of Material: Journal Article
Journal/Proceeding Title: PLoS Genetics
Version: Final published version. This is an open access article.

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