Divergence of transcription factor binding sites across related yeast species.
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.
Borneman
Anthony R
AR
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
Gianoulis
Tara A
TA
Zhang
Zhengdong D
ZD
Yu
Haiyuan
H
Rozowsky
Joel
J
Seringhaus
Michael R
MR
Wang
Lu Yong
LY
Gerstein
Mark
M
Snyder
Michael
M
D001483:Base Sequence; D001665:Binding Sites; D002176:Candida albicans / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D012045:Regulatory Sequences, Nucleic Acid; D012440:Saccharomyces / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
C090837:CPH1 protein, Candida albicans; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; C489432:TEC1 protein, Candida albicans; C069926:TEC1 protein, S cerevisiae; D014157:Transcription Factors