Targets and functions of the mammalian snoRNAome

哺乳动物 snoRNAome 的目标和功能

• 批准号: 10565187
• 负责人: CHUAN HE
• 金额: $ 77.38万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-22 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10565187
• 关键词: Address; Antisense Oligonucleotides; Binding; Binding Sites; Biological Process; Biology; Cell Line; Cells; Complex; Gene Expression; Gene Expression Regulation; Genes; Genetic Translation; Guide RNA; Human; Human Genome; Individual; Investigation; Knowledge; Maps; Messenger RNA; Methods; Modification; Mus; Mutation; Nucleotides; Orphan; Pathway interactions; Proteins; Pseudouridine; RNA; RNA Binding; RNA Splicing; RNA-Binding Proteins; Regulation; Research; Resolution; Ribonucleoproteins; Ribosomal RNA; Ribosomes; Role; Small Nucleolar RNA; Small Nucleolar Ribonucleoproteins; Stress; Technology; Time; Tissues; Translations; Untranslated RNA; base; biological systems; bisulfite; cell type; human disease; invention; kethoxal; knock-down; mRNA Precursor; mRNA Stability; nanopore; novel sequencing technology; novel strategies; protein complex; response; tool; transcriptome; transcriptomics

Project Abstract: Small nucleolar RNA (snoRNA) are natural guide non-coding RNAs derived from over 900 annotated snoRNA genes in the human genome. The major known function of about one-third of snoRNAs is to install 2’O-methyl and pseudouridine modifications in the ribosomal RNA. These rRNA modifications guide ribosome assembly and maturation, and fine-tune translation in a cell type and cell state dependent manner. However, the majority of snoRNAs do not have a well described function; they are called orphans because their cellular RNA targets are not known. How snoRNA interacts with the human transcriptome and the functional consequences of these potential non-canonical snoRNA-RNA interactions in gene expression regulation and human diseases remain to be determined. We recently developed several new sequencing technologies that are directly relevant to studying snoRNA biology. They include methods to robustly identify inter-molecular RNA-RNA interactions in cells and transcriptome-wide sequencing of 2’O-methyl and pseudouridine modifications. These new tools will allow us to address mysteries of snoRNA biology. Aim 1 will identify the cellular RNA targets of the snoRNAome through an advanced version of kethoxal-assisted RNA-RNA interaction sequencing (KARR-seq) approach to enable comprehensive capture and identification of snoRNA-RNA interactions at the transcriptomic scale. These results will be used to identify the rules of snoRNA-guided targeting of mRNA sequences. Aim 2 will investigate two types of snoRNA-mRNA interactions transcriptome-wide and the consequences on regulating gene expression through the application of new sequencing methods to map 2’O-methyl and pseudouridine modifications in pre-mRNA and mature mRNA, and associate these results with the snoRNA-mRNA interactome. We will also selectively delete snoRNA genes or knockdown snoRNA levels, alter the expression of snoRNP components to investigate the consequence of specific snoRNA-mRNA interaction. All together these results will provide the first comprehensive snoRNA-RNA interactome and derive the guiding principles of snoRNA-mRNA interactions and the associated biological functions.

项目摘要： 小核仁RNA（snoRNA）是从900多种已标记的snoRNA中分离出来的天然非编码RNA 人类基因组中的基因大约三分之一的snoRNA的主要已知功能是安装2 'O-甲基 和核糖体RNA中的假尿苷修饰。这些rRNA修饰引导核糖体组装 和成熟，并以细胞类型和细胞状态依赖性方式微调翻译。但是大部分 的snoRNA没有一个很好的描述功能;他们被称为孤儿，因为他们的细胞RNA目标 不知道。snoRNA如何与人类转录组相互作用以及这些相互作用的功能后果 在基因表达调控和人类疾病中潜在的非经典snoRNA-RNA相互作用仍然存在， 被确定。我们最近开发了几种新的测序技术， 研究snoRNA生物学。它们包括稳健地鉴定分子间RNA-RNA相互作用的方法， 细胞和2 'O-甲基和假尿苷修饰的全转录组测序。这些新工具将 让我们能够解开snoRNA生物学的谜团。目的1：确定snoRNAome的细胞RNA靶点 通过一种先进的酮基化辅助RNA-RNA相互作用测序（KARR-seq）方法， 能够在转录组学规模上全面捕获和鉴定snoRNA-RNA相互作用。这些 结果将被用于确定snoRNA引导的mRNA序列靶向的规则。目标2将调查 两种类型的snoRNA-mRNA相互作用的转录组范围和调节基因的后果 通过应用新的测序方法来定位2 'O-甲基和假尿苷， 在前mRNA和成熟mRNA的修饰，并将这些结果与snoRNA-mRNA相互作用组。 我们还将选择性地删除snoRNA基因或敲低snoRNA水平，改变snoRNP的表达， 组分以研究特异性snoRNA-mRNA相互作用的结果。所有这些结果将 提供了第一个全面的snoRNA-RNA相互作用组，并推导出snoRNA-mRNA的指导原则 相互作用和相关的生物功能。