Evolution of transcription factor binding through sequence variations and turnover of binding sites

Variations in noncoding regulatory sequences play a central role in evolution but interpreting such variations remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, which contains two related genomes within the same nucleus. TFs localize preferentially to sites containing their known binding motifs, but occupy only a small fraction of the potential motif-coding genomic sites. Differential binding of TFs to the two orthologues is well explained by sequence variations that alter the consensus core motif, while changes in chromatin accessibility were of little apparent effect. Motif variations that abolish binding when present in one allele show only moderately reduced binding when common to both alleles, suggesting evolutionary compensation. At the promoter level, we report cases of turnover, where binding in the two orthologues localized to different promoter regions, yet most interspecies differences resulted from higher number of binding sites in one of the alleles. Our results suggest that cis variations affecting TF binding occur primarily through the gain and loss of cis-regulatory motifs at accessible regions. Examiniation of DNA binding of 27 yeast transcription factors to a hybrid genome (S. cerevisiae x S. paradoxus), with at least two biological replicates per TF.