Population genomics and transcriptional consequences of regulatory motif variation in globally diverse saccharomyces cerevisiae strains

Caitlin F. Connelly, Daniel A. Skelly, Maitreya J. Dunham, Joshua M. Akey

Research output: Contribution to journalArticle

8 Scopus citations

Abstract

Noncoding genetic variation is known to significantly influence gene expression levels in a growing number of specific cases; however, the patterns of genome-wide noncoding variation present within populations, the evolutionary forces acting on noncoding variants, and the relative effects of regulatory polymorphisms on transcript abundance are not well characterized. Here, we address these questions by analyzing patterns of regulatory variation in motifs for 177 DNA binding proteins in 37 strains of Saccharomyces cerevisiae. Between S. cerevisiae strains, we found considerable polymorphism in regulatory motifs across strains (mean π = 0.005) as well as diversity in regulatory motifs (mean 0.91 motifs differences per regulatory region). Population genetics analyses reveal that motifs are under purifying selection, and there is considerable heterogeneity in the magnitude of selection across different motifs. Finally, we obtained RNA-Seq data in 22 strains and identified 49 polymorphic DNA sequence motifs in 30 distinct genes that are significantly associated with transcriptional differences between strains. In 22 of these genes, there was a single polymorphic motif associated with expression in the upstream region. Our results provide comprehensive insights into the evolutionary trajectory of regulatory variation in yeast and the characteristics of a compendium of regulatory alleles.

Original languageEnglish (US)
Pages (from-to)1605-1613
Number of pages9
JournalMolecular biology and evolution
Volume30
Issue number7
DOIs
StatePublished - Jul 2013
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Keywords

  • adaptive evolution
  • evolution
  • regulatory variation
  • yeast

Fingerprint Dive into the research topics of 'Population genomics and transcriptional consequences of regulatory motif variation in globally diverse saccharomyces cerevisiae strains'. Together they form a unique fingerprint.

  • Cite this