Functional RNA elements in the human genome

项目摘要 该提案寻求竞争性地更新一个多PI项目(Fu和Yeo)，该项目旨在开发创新 基因组学方法阐明调节RNA新陈代谢的调节途径。建立在我们的 在过去的供资周期中取得的成就，并旨在解决监管中的一些新概念 生物学方面，我们计划追求四个具体目标：在目标1中，我们将开发一种新的基因组学技术来 在单细胞水平上测量新生RNA的产量。一旦完全开发，我们将利用这一点 促进转录中心概念的技术，在转录中心中，基因可能以协调的方式表达 每个枢纽内的时尚和链接启动子和增强子，以了解远程调控DNA 元件被环到基因启动子的附近，以控制猝发的幅度和频率 抄写。在目标2中，我们将继续上一个资金周期启动的项目，以描述小说 替代聚乙二醇化(APA)的调节剂。从拟议的全基因组筛查中，我们确定了5个 参与APA调控的基因网络，其中一个对应于一组成熟的剪接 各种因素。因此，我们建议探索剪接和APA之间串扰的潜在机制 监管。在目标3中，我们建议通过构建一个1000人的文库来开发新的系留功能分析 系留的限制性商业惯例能够系统地描述和识别参与APA监管的限制性商业惯例。考虑到 哺乳动物基因组表达数百种具有结合能力的含锌指蛋白 RNA(基于我们之前的发现)和/或DNA，其中许多也是从我们的基因组范围内识别出来的 用于剪接和APA调节器的屏幕，我们建议将Aim 4投入到开发一大批 基因组标记的细胞系，使其能够表征其转录组与RNA和/或DNA的结合 并确定它们对基因表达的功能影响。这一建议结合了假设驱动和 以发现为导向的研究，以解决基因表达调控中的这些突出问题。

Project Summary This proposal seeks competitive renewal of a multi-PI project (Fu and Yeo), which aims to develop innovative genomics approaches to elucidate regulatory pathways in the regulation of RNA metabolism. Built upon our accomplishments in the past funding cycles and aiming at addressing some emerging concepts in regulatory biology, we propose to pursue four specific aims: In Aim 1, we will develop a novel genomics technology to measure nascent RNA production at the level of single cells. Once fully developed, we will utilize this technology to advance the concept of transcription hubs in which genes may be expressed in a coordinated fashion and link promoters and enhancers within each hub to understand how long-distance regulatory DNA elements are looped into the proximity of gene promoters to control the amplitude and frequency of burst transcription. In Aim 2, we will continue the project initiated from the last funding cycle to characterize novel regulators for alternative polyadneylation (APA). From the proposed genome-wide screen, we have identified 5 gene networks involved in APA regulation, one of which correspond to a group of well-established splicing factors. We thus propose to pursue the mechanisms underlying the crosstalk between splicing and APA regulation. In Aim 3, we propose to develop new tethered function assays by constructing a library of ~1000 tethered-enabled RBPs to systematically characterize and identify RBPs involved in APA regulation. Given that mammalian genomes express several hundred zinc finger-containing proteins that have the capacity to bind RNA (based in our previous findings) and/or DNA, many of which were also identified from our genome-wide screens for splicing and APA regulators, we propose to devote Aim 4 to develop a large collection of genomically tagged cell lines to enable characterization of their transcriptome-wide binding to RNA and/or DNA and determine their functional impact on gene expression. This proposal combines both hypothesis-driven and discovery-driven research to address these outstanding problems in the regulation of gene expression.