Non‐DNA‐binding cofactors enhance DNA‐binding specificity of a transcriptional regulatory complex

Abstract

Abstract Recruitment of cofactors to specific DNA sites is integral for specificity in gene regulation. As a model system, we examined how targeting and transcriptional control of the sulfur metabolism genes in Saccharomyces cerevisiae is governed by recruitment of the transcriptional co‐activator Met4. We developed genome‐scale approaches to measure transcription factor (TF) DNA‐binding affinities and cofactor recruitment to >1300 genomic binding site sequences. We report that genes responding to the TF Cbf1 and cofactor Met28 contain a novel ‘recruitment motif’ (RYAAT), adjacent to Cbf1 binding sites, which enhances the binding of a Met4–Met28–Cbf1 regulatory complex, and that abrogation of this motif significantly reduces gene induction under low‐sulfur conditions. Furthermore, we show that correct recognition of this composite motif requires both non‐DNA‐binding cofactors Met4 and Met28. Finally, we demonstrate that the presence of an RYAAT motif next to a Cbf1 site, rather than Cbf1 binding affinity, specifies Cbf1‐dependent sulfur metabolism genes. Our results highlight the need to examine TF/cofactor complexes, as novel specificity can result from cofactors that lack intrinsic DNA‐binding specificity.

Keywords

• cofactor
• DNA‐binding affinities
• DNA binding site
• sulfur metabolism
• transcription factor