Mechanistic Investigation of RNA-Mediated Gene Regulation and Immunity

RNA介导的基因调控和免疫的机制研究

• 批准号: 10798509
• 负责人: Ailong Ke
• 金额: $ 23.26万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10798509
• 关键词: Adopted; Antibiotics; Area; Bacteria; Bacterial Physiology; Biochemical; Biological Process; Biology; Biophysics; Biotechnology; CRISPR interference; Clustered Regularly Interspaced Short Palindromic Repeats; Development; Essential Genes; Eukaryota; Gene Expression Regulation; Genetic Screening; Immunity; Integrase; Investigation; Ligands; Mediating; Medicine; Molecular Conformation; Molecular Genetics; Operon; Orphan; Proliferating; Proteins; RNA; RNA Interference; Research; Resolution; Structure; System; Virulence; Work; genome editing; genomic tools; human pathogen; insight; novel; pathogenic microbe

Project Summary The proposed research combines biophysics, molecular genetics, and genomics tools to provide high- resolution mechanisms for RNA-dominated biological processes. Our study focuses on two central themes in RNA biology. (1) RNA can serve as an information carrier to guide the action of proteins. Such systems are inherently precise and programmable, therefore carry great potential in biotechnology and medicine, as exemplified by RNAi and CRISPR-Cas. My lab spent more than ten years dissecting the mechanisms of CRISPR-Cas, and more recently has been developing genome editing applications based on our mechanistic insights. (2) RNA can adopt defined tertiary structures to exert important functions. My lab has elucidated the structure, function, and conformation dynamics of many riboswitches. The high-resolution information may enable new antibiotics development. We now aim to combine genetic screen with biochemical purification to systematically identify ligands for orphan riboswitches. Such studies often reveal novel aspects of bacterial physiology, which may even be conserved in eukaryotes. We propose to work on the following four areas of research: 1) Structure, mechanism, and genome editing applications of Type I CRISPR (CRISPR-Cas3); 2) Mechanism of CRISPR immunity establishment by Cas1-Cas2 integrase; 3) Mechanism and genome editing application of CRISPR-Tn7; 4) Dissecting riboswitch-controlled mechanism and bacterial physiology.

项目概要 拟议的研究结合了生物物理学、分子遗传学和基因组学工具，以提供高 RNA主导的生物过程的解析机制。我们的研究集中于两个中心主题 RNA生物学。 (1)RNA可以作为信息载体指导蛋白质的作用。此类系统是 本质上是精确和可编程的，因此在生物技术和医学领域具有巨大的潜力， 以 RNAi 和 CRISPR-Cas 为例。我的实验室花了十多年的时间来剖析其机制 CRISPR-Cas，最近一直在开发基于我们机​​制的基因组编辑应用程序 见解。 (2)RNA可以采用明确的三级结构来发挥重要的功能。我的实验室已经阐明了 许多核糖开关的结构、功能和构象动力学。高分辨率信息可能 促进新抗生素的开发。我们现在的目标是将基因筛选与生化纯化相结合 系统地鉴定孤儿核糖开关的配体。此类研究经常揭示细菌的新方面 生理学，甚至可能在真核生物中保守。我们建议从以下四个方面开展工作 研究方向：1）I型CRISPR（CRISPR-Cas3）的结构、机制及基因组编辑应用； 2） Cas1-Cas2整合酶建立CRISPR免疫机制； 3）机制和基因组编辑 CRISPR-Tn7的应用； 4）剖析核糖开关控制机制和细菌生理学。

项目成果

Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

• DOI: 10.1016/j.cell.2017.06.012
• 发表时间: 2017-06-29
• 期刊: Cell
• 影响因子: 64.5
• 作者: Xiao Y;Luo M;Hayes RP;Kim J;Ng S;Ding F;Liao M;Ke A
• 通讯作者: Ke A

Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli.

• DOI: 10.1038/nature16995
• 发表时间: 2016-02-25
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Hayes, Robert P.;Xiao, Yibei;Ding, Fran;van Erp, Paul B. G.;Rajashankar, Kanagalaghatta;Bailey, Scott;Wiedenheft, Blake;Ke, Ailong
• 通讯作者: Ke, Ailong

Structure basis for RNA-guided DNA degradation by Cascade and Cas3.

• DOI: 10.1126/science.aat0839
• 发表时间: 2018-07-06
• 期刊: Science (New York, N.Y.)
• 作者: Xiao Y;Luo M;Dolan AE;Liao M;Ke A
• 通讯作者: Ke A

Structural basis for guanidine sensing by the ykkC family of riboswitches.

• DOI: 10.1261/rna.060186.116
• 发表时间: 2017-04
• 期刊: RNA (New York, N.Y.)
• 作者: Battaglia RA;Price IR;Ke A
• 通讯作者: Ke A

How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.

• DOI: 10.1038/nature24020
• 发表时间: 2017-10-05
• 期刊: Nature
• 影响因子: 64.8
• 作者: Xiao Y;Ng S;Nam KH;Ke A
• 通讯作者: Ke A