Functional RNA elements in the human genome

项目摘要 本提案寻求多PI项目（Fu和Yeo）的竞争性更新，旨在开发创新的 基因组学方法来阐明RNA代谢调控中的调控途径。建立在我们的 在过去的供资周期中取得的成就，旨在解决监管方面的一些新概念， 在生物学方面，我们提出了四个具体目标：在目标1中，我们将开发一种新的基因组学技术， 在单细胞水平上测量新生RNA的产生。一旦完全开发，我们将利用这个 技术，以推进转录枢纽的概念，其中基因可以以协调的方式表达， 时尚和连接每个枢纽内的启动子和增强子，以了解长距离调控DNA 元件被环入基因启动子附近以控制爆发的幅度和频率 转录。在目标2中，我们将继续从上一个资助周期开始的项目， 选择性聚腺苷酸化（阿帕）的调节剂。从提出的全基因组筛选中，我们已经确定了5个 参与阿帕调控的基因网络，其中之一对应于一组成熟的剪接， 因素因此，我们建议追求剪接和阿帕之间串扰的机制 调控在目标3中，我们建议通过构建约1000个文库来开发新的系留功能测定法， 限制性商业惯例系统地描述和识别参与阿帕监管的限制性商业惯例。鉴于 哺乳动物基因组表达数百种含有锌指的蛋白质， RNA（基于我们以前的发现）和/或DNA，其中许多也是从我们的全基因组中鉴定出来的。 屏幕拼接和阿帕监管机构，我们建议致力于目标4开发一个大的集合， 基因组标记的细胞系，以能够表征它们与RNA和/或DNA的转录组范围的结合 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 发现驱动的研究，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.