Chromatin-mediated mechanisms of transcription regulation in ES cells

项目总结/摘要 我们的研究兴趣集中在不同的染色体之间染色质结构的相似性和差异 细胞类型以及调节这些差异的染色质重塑因子如何调节细胞命运。很长的- 我们实验室的长期目标是全面了解功能，目标，调控， 非编码RNA（ncRNA）和染色质调节因子在细胞凋亡中的作用机制 基因调控网络 大约75%的哺乳动物基因组被转录。虽然编码区只占 ~2%的基因组，其余的基因间和基因内转录产生大量的非- 编码RNA（ncRNA）。两个富含非编码转录的区域是活性增强子（其中ncRNA 双向产生）和启动子（其中ncRNA以反义方向产生， 蛋白质编码基因）。虽然一些单独的ncRNA已被证明在基因激活中起作用，但它们的 基因调控中的活动尚未得到系统的阐述。最近，我们发现esBAF， 结合增强子和启动子的核小体重塑复合物，是抑制 在胚胎干细胞的基因组中有大量的ncRNA。在耗尽esBAF后，核小体占据 开放染色质的侧翼区域减少，导致ncRNA转录升高。基于这些 研究中，我们处于独特的地位，可以通过核小体重塑因子构建ncRNA调控网络 在ES细胞中。具体来说，我们将确定（1）esBAF如何调节高阶染色质结构，（2） 增强子特异性ncRNA（eRNA）在增强子环和基因调控中的作用;（3）增强子特异性ncRNA的作用机制 ncRNA对mRNA的潜在调控，以及（4）核小体重塑复合物网络 调节ncRNA表达。这些研究将加深我们对以染色质为中心的 ncRNA的调控。 在接下来的五年里，我们的实验室将确定调节ncRNA的核小体重塑 表达，探讨核小体重塑因子在调节高级染色质结构中的作用， 增强子-启动子环的水平，并确定两类未表征的ncRNA的功能 在ES细胞中。这项拟议中的研究意义重大，因为它将揭示 设计染色质动力学与ncRNA功能的相互作用，从而提供了关键的一步， 了解胚胎干细胞的命运决定

PROJECT SUMMARY/ABSTRACT Our research interests focus on the similarities and differences in chromatin structure among different cell types and how chromatin remodeling factors that modulate these differences regulate cell fate. The long- term goals of our laboratory are to comprehensively understand the functions, targets, regulation, and mechanisms of action of non-coding RNAs (ncRNAs) and chromatin regulatory factors with critical functions in gene regulatory networks. Approximately 75% of the mammalian genome is transcribed. While coding regions account for only ~2% of the genome, the remaining intergenic and intragenic transcription generates a large collection of non- coding RNAs (ncRNAs). Two regions rich with non-coding transcription are active enhancers (where ncRNAs are generated bi-directionally) and promoters (where ncRNAs are generated in the antisense orientation from protein-coding genes). While a few individual ncRNAs have been shown to function in gene activation, their activities in gene regulation have not been systematically addressed. Recently, we showed that esBAF, a nucleosome remodeling complex that binds enhancers and promoters, is necessary for repression of numerous ncRNAs throughout the genome in ES cells. Upon depletion of esBAF, nucleosome occupancy flanking regions of open chromatin was reduced, resulting in elevated ncRNA transcription. Based on these studies, we are in a unique position to build a network of ncRNA regulation by nucleosome remodeling factors in ES cells. Specifically, we will determine (1) how esBAF regulates higher order chromatin structure, (2) the functions of enhancer-specific ncRNAs (eRNAs) in enhancer looping and gene regulation, (3) the mechanisms underlying regulation of mRNAs by ncRNAs, and (4) the network of nucleosome remodeling complexes regulating ncRNA expression. These studies will enhance our understanding of the chromatin-centered regulation of ncRNAs. Over the next five years, our laboratory will identify nucleosome remodelers that regulate ncRNA expression, explore the role of nucleosome remodeling factors in regulating higher order chromatin structure at the level of enhancer-promoter looping, and determine the function of two uncharacterized classes of ncRNAs in ES cells. The proposed research is significant because it will uncover fundamental mechanisms that choreograph the interplay of chromatin dynamics with ncRNA function, consequently providing a crucial step in understanding ES cell fate decisions.