Divergence of transcription factor binding sites across related yeast species

Anthony R Borneman; Tara A Gianoulis; Zhengdong D Zhang; Haiyuan Yu; Joel Rozowsky; Michael R Seringhaus; Lu Yong Wang; Mark Gerstein; Michael Snyder

doi:10.1126/science.1140748

Divergence of transcription factor binding sites across related yeast species

Science. 2007 Aug 10;317(5839):815-9. doi: 10.1126/science.1140748.

Authors

Anthony R Borneman¹, Tara A Gianoulis, Zhengdong D Zhang, Haiyuan Yu, Joel Rozowsky, Michael R Seringhaus, Lu Yong Wang, Mark Gerstein, Michael Snyder

Affiliation

¹ Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

PMID: 17690298
DOI: 10.1126/science.1140748

Abstract

Characterization of interspecies differences in gene regulation is crucial for understanding the molecular basis of both phenotypic diversity and evolution. By means of chromatin immunoprecipitation and DNA microarray analysis, the divergence in the binding sites of the pseudohyphal regulators Ste12 and Tec1 was determined in the yeasts Saccharomyces cerevisiae, S. mikatae, and S. bayanus under pseudohyphal conditions. We have shown that most of these sites have diverged across these species, far exceeding the interspecies variation in orthologous genes. A group of Ste12 targets was shown to be bound only in S. mikatae and S. bayanus under pseudohyphal conditions. Many of these genes are targets of Ste12 during mating in S. cerevisiae, indicating that specialization between the two pathways has occurred in this species. Transcription factor binding sites have therefore diverged substantially faster than ortholog content. Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Binding Sites
Candida albicans / genetics
Candida albicans / growth & development
Candida albicans / metabolism
Chromatin Immunoprecipitation
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
Evolution, Molecular*
Fungal Proteins / genetics
Fungal Proteins / metabolism*
Gene Expression Regulation, Fungal
Gene Regulatory Networks
Genes, Fungal
Oligonucleotide Array Sequence Analysis
Regulatory Sequences, Nucleic Acid*
Saccharomyces / genetics*
Saccharomyces / growth & development
Saccharomyces / metabolism
Saccharomyces cerevisiae / genetics*
Saccharomyces cerevisiae / growth & development
Saccharomyces cerevisiae / metabolism
Saccharomyces cerevisiae Proteins / genetics
Saccharomyces cerevisiae Proteins / metabolism
Transcription Factors / genetics
Transcription Factors / metabolism*

Substances

CPH1 protein, Candida albicans
DNA-Binding Proteins
Fungal Proteins
Saccharomyces cerevisiae Proteins
TEC1 protein, Candida albicans
TEC1 protein, S cerevisiae
Transcription Factors