title: Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.
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.
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Siggers
authors.forename: Michael H
authors.initials: MH
authors.lastname: Duyzend
authors.forename: Jessica
authors.initials: J
authors.lastname: Reddy
authors.forename: Sidra
authors.initials: S
authors.lastname: Khan
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D019540:Area Under Curve; D001483:Base Sequence; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; D001665:Binding Sites; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal / Q000235:genetics; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012680:Sensitivity and Specificity; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C064042:CBF1 protein, S cerevisiae; D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors