Computational and Experimental Analysis of RNA structures in mRNA polyadenylation

描述（由申请人提供）：mRNA聚腺苷酸化是真核细胞中几乎所有mRNA的关键加工事件。它涉及成熟mRNA在3'末端的切割和添加聚（A）尾。poly（A）尾影响mRNA代谢的许多方面，包括mRNA稳定性、mRNA转运和翻译。超过一半的人类基因具有多个聚腺苷酸化位点或聚腺苷酸位点，导致含有不同mRNA顺式调节元件和/或编码蛋白质同种型的转录物变体。替代的多聚腺苷酸化已被证明是在组织和条件特异性的方式进行调节。越来越多的人类疾病与多聚腺苷酸化活性的改变有关。虽然多聚腺苷酸化的核心元件已被很好地表征，但对调节多聚腺苷酸化活性的辅助元件知之甚少。特别是，RNA二级结构在调节多聚腺苷酸化中的作用完全不清楚。长期目标是充分了解mRNA多聚腺苷酸化在不同生物条件下的调节机制。本研究的具体目的是：1）通过生物信息学系统地分析与哺乳动物poly（A）位点相关的不同类型的RNA结构; 2）通过实验分析来研究RNA结构如何调节mRNA聚腺苷酸化。 公共卫生相关性：mRNA聚腺苷酸化是真核细胞中几乎所有mRNA的关键加工事件。它涉及成熟mRNA在3'末端的切割和添加聚（A）尾。poly（A）尾影响mRNA代谢的许多方面，包括mRNA稳定性、mRNA转运和翻译。超过一半的人类基因具有多个聚腺苷酸化位点或聚腺苷酸位点，导致含有不同mRNA顺式调节元件和/或编码蛋白质同种型的转录物变体。替代的多聚腺苷酸化已被证明是在组织和条件特异性的方式进行调节。越来越多的人类疾病与多聚腺苷酸化活性的改变有关。虽然多聚腺苷酸化的核心元件已被很好地表征，但对调节多聚腺苷酸化活性的辅助元件知之甚少。特别是，RNA二级结构在调节多聚腺苷酸化中的作用完全不清楚。长期目标是充分了解mRNA多聚腺苷酸化在不同生物条件下的调节机制。本研究的具体目的是：1）通过生物信息学系统地分析与哺乳动物poly（A）位点相关的不同类型的RNA结构; 2）通过实验分析来研究RNA结构如何调节mRNA聚腺苷酸化。

DESCRIPTION (provided by applicant): mRNA polyadenylation is a key processing event for almost all mRNAs in eukaryotic cells. It involves cleavage of maturing mRNAs at the 3' end and addition of a poly(A) tail. The poly(A) tail influences many aspects of mRNA metabolism, including mRNA stability, mRNA transport, and translation. Over half of all human genes have multiple polyadenylation sites, or poly(A) sites, leading to transcript variants containing distinct mRNA cis- regulatory elements and/or encoding protein isoforms. Alternative polyadenylation has been shown to be regulated in tissue- and condition-specific manners. A growing number of human diseases have been associated with altered polyadenylation activity. While the core elements for polyadenylation have been well characterized, little is known about the auxiliary elements that modulate polyadenylation activity. In particular, the role of RNA secondary structures in regulation of polyadenylation is completely unclear. The long term goal is to fully understand the mechanisms by which mRNA polyadenylation is regulated under different biological conditions. The specific aims of this study are 1) to systematically analyze different types of RNA structures associated with mammalian poly(A) sites by bioinformatics, and 2) to examine how RNA structures regulate mRNA polyadenylation by experimental assays. PUBLIC HEALTH RELEVANCE: mRNA polyadenylation is a key processing event for almost all mRNAs in eukaryotic cells. It involves cleavage of maturing mRNAs at the 3' end and addition of a poly(A) tail. The poly(A) tail influences many aspects of mRNA metabolism, including mRNA stability, mRNA transport, and translation. Over half of all human genes have multiple polyadenylation sites, or poly(A) sites, leading to transcript variants containing distinct mRNA cis- regulatory elements and/or encoding protein isoforms. Alternative polyadenylation has been shown to be regulated in tissue- and condition-specific manners. A growing number of human diseases have been associated with altered polyadenylation activity. While the core elements for polyadenylation have been well characterized, little is known about the auxiliary elements that modulate polyadenylation activity. In particular, the role of RNA secondary structures in regulation of polyadenylation is completely unclear. The long term goal is to fully understand the mechanisms by which mRNA polyadenylation is regulated under different biological conditions. The specific aims of this study are 1) to systematically analyze different types of RNA structures associated with mammalian poly(A) sites by bioinformatics, and 2) to examine how RNA structures regulate mRNA polyadenylation by experimental assays.