Genome-wide Exploration of miRNA-mediated Network Motifs

MicroRNAs(MiRNAs)是一种非常小的(21-23个核苷酸)RNAs，不编码蛋白质，但作为重要的转录后调节因子。具体地说，miRNAs针对的是信使RNA，它们在降解方面与信使RNA完全互补，而在翻译抑制方面，miRNAs可以与内部错配配对。人们普遍认为miRNAs嵌入了一系列广泛的基因调控电路中，从而在发育和分化过程中建立和维持细胞功能方面发挥了重要作用。然而，缺乏支持这一提议的直接证据。鉴于miRNAs在基因调控中的重要性，一个关键问题是miRNA生物发生本身是如何在转录和加工水平上受到调控的。到目前为止，对miRNA基因的转录调控知之甚少，这主要是由于缺乏关于miRNA启动子的准确位置的信息。定位组成miRNA启动子的转录调控元件对于确定存在的序列基序以及它们相互作用开启和关闭miRNA合成的因素至关重要。本研究项目的目标是(1)使用高通量方法在全球范围内确定miRNA基因在人类细胞中的转录起始点；(2)使用计算策略来确定涉及miRNA转录调控的序列元件和调控因子。因此，这项研究将是解剖miRNA表达调控的分子机制的初步但也是关键的一步，使我们更接近于在网络/系统水平上完全理解miRNA介导的基因调控。更广泛的影响：拟议的项目为基因组科学方面的本科生、研究生和博士后研究员提供了独特的培训机会，包括但不限于基因组技术开发和计算生物学。此外，该研究计划将促进研究生和本科课程的课程开发，重点是基因组生物学。通过利用杜克大学现有的基础设施和推广计划，特别是基因组科学与政策研究所及其相关的NIGMS国家系统生物学中心，该项目将接触到不同背景的科学家，并教育公众。

MicroRNAs (miRNAs) are extremely small (21-23 nucleotide) RNAs that do not encode proteins but serve as important post-transcriptional regulators. Specifically, miRNAs target messenger RNAs to which they are perfectly complementary for degradation, and those to which they can base pair with internal mismatches for translational repression. It is widely believed that miRNAs are embedded in an extensive array of gene regulatory circuits, thereby playing essential roles in establishing and maintaining cellular functions during development and differentiation. However, direct evidence in support of this proposal is lacking. Given the importance of miRNAs in gene regulation, one key question is how miRNA biogenesis itself is regulated at the levels of transcription and processing. To date, little has been learned about transcriptional regulation of miRNA genes, mainly due to the lack of information about the precise location of miRNA promoters. Mapping the transcriptional regulatory elements that comprise miRNA promoters is critical for determining the sequence motifs present and the factors with which they interact to turn on and off miRNA synthesis. The goal of this research project is to (1) use high throughput methods to globally determine the transcription start sites of miRNA genes in human cells; and (2) to use computational strategies to identify the sequence elements and regulatory factors involved in miRNA transcriptional control. Therefore, this study will serve as an initial yet critical step towards dissecting the molecular mechanism underlying regulated miRNA expression, bringing us one step closer to fully understanding miRNA-mediated gene regulation at the network/system level. Broader Impacts: The proposed project provides unique training opportunities for undergraduate, graduate and postdoctoral fellows in genome science, including but not limited to genome technology development and computational biology. In addition, the research program will promote curriculum development for graduate and undergraduate courses with an emphasis on genome biology. By taking advantage of the existing infrastructure and outreach programs at Duke University, in particular at the Institute for Genome Sciences & Policy and its associated NIGMS National Center for Systems Biology, the project will reach out to scientists of diverse backgrounds as well as educate the general public.