Uncovering a new role of nucleosomes in gene regulation

项目总结：揭示核小体在基因调控中的新作用 转录因子和核小体是基因调控的两个主要决定因素 在真核细胞中。传统上，转录因子和核小体被认为是相互排斥的。 最近的研究已经确定了越来越多的蛋白质，包括肿瘤抑制因子p53 能够在不破坏整个核小体结构的情况下与核小体DNA结合。在… 至少对于这些TF来说，核小体不再是障碍，在某些情况下，核小体不再是障碍 可以促进甚至稳定TF-DNA的相互作用。然而，目前尚不清楚是否会出现这种情况 (转铁蛋白和核小体之间的)相互作用具有任何生物学意义。我们的预赛 研究表明，核小体中p53靶点的可及性与 关于p53如何调节其靶基因，这突显了核小体在 介导转铁蛋白结合，调控基因表达。拟议的研究旨在获得充分的 了解核小体在基因调控中的这一新作用。在目标1中，我们将重点放在 P53，意在建立在以下背景下P53结合位点的可及性之间的联系 染色质和邻近基因的表达模式。在《目标2》中，我们将发现一个 全套潜在的人类和模型核小体DNA结合蛋白 有机体。感兴趣的核小体-转铁蛋白的相互作用将通过体外试验进行验证。在 总结这些研究，我们将重新定义核小体在转铁蛋白结合和 基因调控，发展了检测核小体转铁蛋白的理论和实验方法 相互作用，并建立了一条识别核小体的计算/实验管道 DNA结合蛋白。

Project Summary: Uncovering a new role of nucleosomes in gene regulation Transcriptional factors (TFs) and nucleosomes are two major determinants for gene regulation in eukaryotic cells. Traditionally, TFs and nucleosomes are considered to be mutually exclusive. Recent studies have identified a growing list of proteins including the tumor suppressor p53 that are able to bind to nucleosomal DNA without disrupting the overall nucleosome structure. At least for these TFs, nucleosomes are no longer obstacles, and in some cases, nucleosomes can facilitate or even stabilize TF-DNA interactions. However, it was not clear if such interactions (between TFs and nucleosomes) have any biological significance. Our preliminary studies have shown that the extent of accessibility of p53 target sites in nucleosomes correlates with how p53 regulates its target genes, which highlights the importance of nucleosomes in mediating TF binding and controlling gene expression. The proposed research aims to gain full understanding of this new role of nucleosomes in gene regulation. In the Aim 1, we will focus on p53, intending to establish the link between accessibility of p53 binding sites in the context of chromatin and expression patterns of nearby genes. In the Aim 2, we will discover a comprehensive set of potential nucleosomal DNA-binding proteins in humans and model organisms. Nucleosome-TF interactions of interest will be validated by in vitro assays. At the conclusion of these studies, we will have re-defined the roles of nucleosomes in TF binding and gene regulation, developed theoretical and experimental method for testing nucleosome-TF interactions, and established a computational/experimental pipeline to identify nucleosomal DNA-binding proteins.