Targets and functions of the mammalian snoRNAome

项目摘要： 小核仁RNA(SnoRNA)是从900多个注释的snoRNA中衍生的自然引导的非编码RNA 人类基因组中的基因。约三分之一的snoRNAs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 以及成熟，并以依赖于细胞类型和细胞状态的方式微调翻译。然而，大多数人 的snoRNA没有很好的描述功能；它们被称为孤儿，因为它们的细胞RNA靶标 都是未知的。SnoRNA如何与人类转录组相互作用及其功能后果 在基因表达调控和人类疾病中潜在的非典型snoRNA-RNA相互作用仍然存在 要下定决心。我们最近开发了几种新的测序技术，这些技术直接与 研究snoRNA生物学。它们包括强有力地识别分子间RNA-RNA相互作用的方法 2‘O-甲基和假尿苷修饰的细胞和转录组范围的测序。这些新工具将 让我们来解开snoRNA生物学的谜团。目标1将识别snoRNAome的细胞RNA靶标 通过高级版本的酮氧醛辅助的RNA-RNA相互作用测序(Karr-seq)方法 能够在转录水平上全面捕获和鉴定snoRNA-RNA相互作用。这些 结果将被用来确定snoRNA引导的mRNA序列靶向的规则。AIM 2将调查 转录范围内两种类型的snoRNA-mRNA相互作用及其对调控基因的影响 应用新的测序方法表达2‘O-甲基和假尿嘧啶 前-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。 我们还将选择性地删除snoRNA基因或下调snoRNA水平，改变snoRNP的表达 成分，以研究特异性snoRNA-mRNA相互作用的结果。所有这些结果都将 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。

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.