Large-scale characterization of the function of RNA regulatory elements

RNA调控元件功能的大规模表征

• 批准号: 10293392
• 负责人: Eric Lyman Van Nostrand
• 金额: $ 48万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-10 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10293392
• 关键词: Address; Affect; Antisense Oligonucleotides; Area; Binding Sites; Biological Assay; Biology; Catalogs; Cell Nucleus; Databases; Development; Disease; Elements; Foundations; Genetic Variation; Genomic approach; Genomics; Half-Life; Human; Human Genetics; Individual; Knowledge; Location; Maps; Mediation; Methods; Pharmaceutical Preparations; Physiological; Proteins; RNA; RNA Binding; RNA Decay; RNA Processing; RNA Splicing; RNA Stability; RNA-Binding Proteins; RNA-Protein Interaction; Regulation; Regulatory Element; Reporter; Research; Research Personnel; Ribosomes; Site; Small Nuclear RNA; Small Nucleolar RNA; Spinal Muscular Atrophy; Techniques; Transcript; Translations; Work; improved; insight; interest; knock-down; tool

PROJECT SUMMARY Once an RNA is transcribed in the nucleus, it is bound by RNA binding proteins and other regulatory RNAs which control its sequence (by altering splicing), half-life (by modulating RNA stability and decay) and translation (through mediation of ribosome initiation and elongation) among other RNA processing steps. Individual RBP binding sites can have significant physiological importance, as emphasized by the recent example of the drug Spinraza, which is an antisense oligonucleotide that blocks a single RBP:RNA interaction in order to cure Spinal Muscular Atrophy. Recent advances in genomics techniques have dramatically increased our ability to identify the interaction sites for these regulatory RBPs and RNAs, and we now have catalogs of over a million such interaction sites that are candidate RNA regulatory elements. However, it is clear that only a small fraction of these elements truly function as regulatory modules, as few show differences in RNA processing when the RBP is knocked down or otherwise altered. As such, large-scale assays to sift through these elements to identify the subset that are function are an essential missing piece in converting these element databases into a useful tool for researchers interested in understanding whether human genetic variation will alter RNA biology. In this proposal, I describe my research group’s proposed efforts to address this major knowledge gap in two areas: 1. Using orthogonal approaches (rapid degradation of RBPs followed by genomics profiling to identify direct regulatory targets of RBPs and massively parallel reporter assays) to characterize which RBP binding sites confer regulation. 2. Large-scale identification of regulatory targets for snoRNAs, snRNAs, and other regulatory RNAs through improved genomics techniques. My extensive expertise in developing experimental and computational genomics methods to map and understand RNA processing regulatory networks makes my newly founded lab an ideal location to undertake these efforts, and build an improved global picture of the RNA processing regulatory landscape. Further, it will support my efforts to develop an independent research group that will lay the foundation to the broader effort to understand how human genetic variation affects disease through mis-regulation of RNA processing.

项目概要 一旦RNA在细胞核中转录，它就会被RNA结合蛋白结合并 其他控制其序列（通过改变剪接）、半衰期（通过调节 RNA稳定性和衰变）和翻译（通过核糖体起始和转录的介导） 延伸）以及其他 RNA 加工步骤中可以有单独的 RBP 结合位点。 正如该药物最近的例子所强调的那样，具有重要的生理重要性 Spinraza，一种反义寡核苷酸，可阻断单个 RBP:RNA 相互作用 为了治愈脊髓性肌萎缩症，基因组学技术取得了最新进展。 极大地提高了我们识别这些监管 RBP 相互作用位点的能力， RNA，我们现在拥有超过一百万个此类相互作用位点的目录，它们是候选 RNA 然而，很明显，这些要素中只有一小部分是真正的。 作为调节模块，当 RBP 处于调节状态时，RNA 加工很少表现出差异 因此，需要进行大规模的分析来筛选这些元素。 识别函数的子集是转换这些函数时必不可少的缺失部分 元素数据库成为有兴趣了解人类是否存在的研究人员的有用工具 遗传变异将改变RNA生物学。 在这份提案中，我描述了我的研究小组为解决这一重大问题而提出的努力 两个领域的知识差距： 1. 使用正交方法（RBP 快速降解，然后进行基因组学分析） 分析以确定 RBP 和大规模并行报告器的直接监管目标 分析）来表征哪些 RBP 结合位点具有调节作用。 2. snoRNA、snRNA等调控靶点的大规模鉴定 通过改进的基因组技术来调节RNA。 我在开发实验和计算基因组学方法方面拥有丰富的专业知识 绘制并了解 RNA 加工调控网络使我新成立的实验室成为 开展这些工作并建立改进的 RNA 全球图景的理想地点 此外，它将支持我发展独立的努力。 研究小组将为更广泛的努力奠定基础，以了解人类如何 遗传变异通过 RNA 加工的错误调节来影响疾病。