Computational and Experimental Analysis of RNA structures in mRNA polyadenylation

描述(申请人提供)：信使核糖核酸化是真核细胞中几乎所有信使核糖核酸的关键加工事件。它包括在3‘端切割成熟的mRNAs和添加Poly(A)尾巴。Poly(A)尾巴影响着信使核糖核酸代谢的许多方面，包括信使核糖核酸的稳定性、信使核糖核酸的转运和翻译。超过一半的人类基因有多个多聚腺苷酸化位点，或多聚(A)位点，导致转录变异体包含不同的mRNA顺式调节元件和/或编码蛋白质异构体。选择性多聚腺苷已被证明是以组织和条件特定的方式调节的。越来越多的人类疾病与多聚腺苷酸化活性改变有关。虽然多聚腺苷化的核心元件已经被很好地描述，但对调节多腺苷化活性的辅助元件却知之甚少。特别是，RNA二级结构在调节多聚腺苷基化中的作用还完全不清楚。长期的目标是充分了解在不同的生物条件下，信使核糖核酸多腺苷被调节的机制。本研究的具体目的是：1)用生物信息学的方法系统地分析与哺乳动物PolyA位点相关的不同类型的RNA结构；2)通过实验研究RNA结构如何调节mRNA的多糖化作用。 公共卫生相关性：在真核细胞中，几乎所有的mRNAs都是一个关键的处理事件。它包括在3‘端切割成熟的mRNAs和添加Poly(A)尾巴。Poly(A)尾巴影响着信使核糖核酸代谢的许多方面，包括信使核糖核酸的稳定性、信使核糖核酸的转运和翻译。超过一半的人类基因有多个多聚腺苷酸化位点，或多聚(A)位点，导致转录变异体包含不同的mRNA顺式调节元件和/或编码蛋白质异构体。选择性多聚腺苷已被证明是以组织和条件特定的方式调节的。越来越多的人类疾病与多聚腺苷酸化活性改变有关。虽然多聚腺苷化的核心元件已经被很好地描述，但对调节多腺苷化活性的辅助元件却知之甚少。特别是，RNA二级结构在调节多聚腺苷基化中的作用还完全不清楚。长期的目标是充分了解在不同的生物条件下，信使核糖核酸多腺苷被调节的机制。本研究的具体目的是：1)用生物信息学的方法系统地分析与哺乳动物PolyA位点相关的不同类型的RNA结构；2)通过实验研究RNA结构如何调节mRNA的多糖化作用。

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.