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

Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Molecular Systems Biology (Impact Factor: 10.87). 12/2011; 7(1):555. DOI: 10.1038/msb.2011.89
Source: PubMed


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.

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Available from: Trevor Siggers, Aug 08, 2014
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    • "As a rule, TFs function through interactions with a wide range of proteins, including other TFs, cofactors, and chromatin modifiers (D'Alessio et al., 2009; Grove and Walhout 2008; Nä a ¨ r et al., 2001; Spitz and Furlong 2012). The biological activity of each TF depends upon these protein interactions, which ultimately govern DNA-binding affinity, activation of chromatin remodeling, and DNA-binding-sequence specificity (Siggers et al., 2011; Slattery et al., 2011). Given the importance of the cooperative action of TFs, defining their protein interaction profile is essential for understanding the regulation of cellular gene expression. "
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