High throughput identification of cis-regulatory rewiring events in yeast.

A co-regulated module of genes ("regulon") can have evolutionarily conserved expression patterns and yet have diverged upstream regulators across species. For instance, the ribosomal genes regulon is regulated by the transcription factor (TF) TBF1 in C. albicans, while in S. cerevisiae it is regulated by RAP1. Only a handful of such rewiring events have been established, and the prevalence or conditions conducive to such events are not well known. Here, we develop a novel probabilistic scoring method to comprehensively screen for regulatory rewiring within regulons across 23 yeast species. Investigation of 1713 regulons and 176 TFs yielded 5353 significant rewiring events at 5% FDR. Besides successfully recapitulating known rewiring events, our analyses also suggests TF candidates for certain processes reported to be under distinct regulatory controls in S. cerevisiae and C. albicans, for which the implied regulators are not known: 1) oxidative stress response (Sc-MSN2 to Ca-FKH2),and 2) nutrient modulation (Sc-RTG1 to Ca-GCN4/Ca-UME6). Further, a stringent screen to detect TF rewiring at individual genes identified 1446 events at 10% FDR. Overall, these events are supported by strong co-expression between the predicted regulator and its target gene(s) in a species-specific fashion (>50-fold). Independent functional analyses of rewiring TF pairs revealed greater functional interactions and shared biological processes between them (p=1e-03).Our study represents the first comprehensive assessment of regulatory rewiring; with a novel approach that has generated a unique high-confidence resource of several specific events, suggesting that evolutionary rewiring is relatively frequent and may be a significant mechanism of regulatory innovation.