COOPERATIVITY AND COLLECTIVE BINDING IN TRANSCRIPTION FACTOR-DNA INTERACTIONS

转录因子通过与基因组顺式调控元件结合来塑造基因表达， 然后募集核小体重塑因子、RNA聚合酶和其他 转录辅激活因子。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，Cbf 1和Tye 7，它们具有几乎相同的DNA 在体外结合偏好，但在体内结合在几乎完全不重叠的靶基因座。 我们发现Cbf 1利用同型协同性来实现其特异性，而Tye 7则结合同型协同性。 一个TF集体，一种最近才在果蝇中描述的现象， 不太了解。 我们假设同型协同性和集体结合被广泛使用， 真核TF以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的体内结合的贡献。 我们也将详细地剖析这些复合体中的一小部分。我们将调查 人bHLH转录因子Usf 1的结合特异性，这是一个候选药物靶点 因为它与肥胖和代谢疾病有关。这项工作的完成将 加深了我们对体内转录特异性调控因子的理解 因素此外，通过了解蛋白质-蛋白质接触， usf 1结合，我们将发现可以中断的相互作用的治疗效益。

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.