COOPERATIVITY AND COLLECTIVE BINDING IN TRANSCRIPTION FACTOR-DNA INTERACTIONS

转录因子通过结合基因组顺式调节元件和 然后招募核小体重塑因子，RNA聚合酶全酶和其他 转录辅活化子。是什么决定了转录因子在体内的结合位置？为 大多数真核转录因子(TF)，这个问题的答案是未知的。我们有 最近分析了两种酵母bHLH蛋白CBF1和Tye7，它们的DNA几乎相同 在体外结合偏好，但在体内结合在几乎完全不重叠的靶点。 我们发现CBF1利用同型协作性来实现其特异性，而Tye7结合在 一个TF集体，这一现象最近才在果蝇中描述，但 人们对此知之甚少。 我们假设同型协作性和集体绑定被广泛使用 真核生物转录因子在体内实现其特异性。我们将通过量化来检验这一假设 这两种机制对所有酵母转录因子在体内结合的贡献。 我们还将详细剖析这些复合体中的一小部分。我们将调查 候选药物靶点人bHLH转录因子USF1的结合特异性 因为它与肥胖和代谢性疾病有关。这项工作的完成将 加深对控制体内转录特异性的因素的理解 各种因素。此外，通过了解调节蛋白质的蛋白质-蛋白质接触 USF1结合，我们将发现可以为了治疗利益而中断的相互作用。

Transcription factors shape gene expression by binding to genomic cis-regulatory elements and then recruiting nucleosome remodeling factors, the RNA polymerase holoenyzme, and other transcriptional coactivators. What determines where a transcription factor binds in vivo? For most eukaryotic transcription factors (TFs), the answer to this question is not known. We have recently analyzed two yeast bHLH proteins, Cbf1 and Tye7, which have nearly identical DNA binding preferences in vitro, but bind at almost completely non-overlapping target loci in vivo. We found that Cbf1 utilizes homotypic cooperativity to achieve its specificity, while Tye7 binds in a TF collective, a phenomenon that has been described only recently in Drosophila, but is poorly understood. We hypothesize that homotypic cooperativity and collective binding are widely used by eukaryotic TFs to achieve their specificities in vivo. We will test this hypothesis by quantifying the contribution of these two mechanisms to the in vivo binding of all yeast transcription factors. We will also dissect a small number of these complexes in detail. We will investigate the binding specificity of the human bHLH transcription factor Usf1, which is a candidate drug target because of its involvement in obesity and metabolic disease. The completion of this work will deepen our understanding of the factors that govern the in vivo specificities of transcription factors. Furthermore, by gaining an understanding of the protein-protein contacts that regulate Usf1 binding, we will uncover interactions that can be disrupted for therapeutic benefit.