Targets and functions of the mammalian snoRNAome

哺乳动物 snoRNAome 的目标和功能

基本信息

批准号：
10708950
负责人：
CHUAN HE
金额：
$ 69.66万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
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/10708950
关键词：
Address Antisense Oligonucleotides Binding Binding Sites Biological Process Biology Cell Line Cells Complex Gene Expression Gene Expression Regulation Genes 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 Spliceosomes Stress Technology Time Tissues Translations Untranslated RNA biological systems bisulfite cell type human disease invention kethoxal knock-down mRNA Precursor mRNA Stability mRNA Translation nanopore novel sequencing technology novel strategies protein complex response tool transcriptome transcriptomics

项目摘要

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) 是源自 900 多种带注释的 snoRNA 的天然引导非编码 RNA 人类基因组中大约三分之一的 snoRNA 的主要已知功能是安装 2’O-甲基。核糖体 RNA 中的假尿苷修饰这些 rRNA 修饰指导核糖体组装。和成熟，并以细胞类型和细胞状态依赖的方式微调翻译。的 snoRNA 没有被充分描述的功能；它们被称为孤儿，因为它们的细胞 RNA 目标 snoRNA 如何与人类转录组相互作用以及其功能后果尚不清楚。基因表达调控和人类疾病中潜在的非典型 snoRNA-RNA 相互作用仍有待研究我们最近开发了几种与直接相关的新测序技术。研究 snoRNA 生物学，其中包括可靠识别分子间 RNA-RNA 相互作用的方法。这些新工具将用于对 2’O-甲基和假尿苷修饰进行细胞和全转录组测序。让我们解开 snoRNA 生物学的谜团，目标 1 将识别 snoRNAome 的细胞 RNA 靶点。通过先进版本的酮醛辅助 RNA-RNA 相互作用测序 (KARR-seq) 方法能够在转录组规模上全面捕获和鉴定 snoRNA-RNA 相互作用。结果将用于确定 snoRNA 引导的 mRNA 序列靶向规则。目标 2 将进行研究。两种类型的 snoRNA-mRNA 转录组范围内的相互作用及其对调节基因的影响通过应用新的测序方法来定位 2’O-甲基和假尿苷的表达前体 mRNA 和成熟 mRNA 的修饰，并将这些结果与 snoRNA-mRNA 相互作用组相关联。我们还将选择性删除 snoRNA 基因或敲低 snoRNA 水平，改变 snoRNP 的表达研究特定 snoRNA-mRNA 相互作用的结果的成分将所有这些结果结合起来。提供第一个全面的 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学功能。