Computational and experimental modeling of RNA Splicing

描述（由申请人提供）：真核基因“分裂”为外显子和内含子的发现对于我们理解基因表达和调控具有巨大的意义。现在人们认识到，超过一半的人类基因是通过选择性剪接表达的，通常以特定的空间/时间模式表达。选择性剪接在确定正常发育过程中分化的真核细胞类型的特殊特性方面发挥着重要作用，并且剪接的错误调节越来越被认为是许多人类疾病的原因。该项目的主要目标是组建一个由计算和实验分子生物学家组成的尖端研究团队，以模拟两个重要的生物学问题：c/s-元件如何调节前mRNA剪接？它们如何影响剪接位点的选择？针对这些问题，提出以下具体目标。 1) 在一些明确的系统中，通过数学和实验模拟前 mRNA 剪接活性对 SR 蛋白和 hnRNP A1 依赖的 ESE/ESS 的依赖性。 2) 研究组织特异性选择性剪接对顺式/顺式元件和反式作用剪接因子的依赖性。 3) 通过将更多增强器和消音器主题纳入数据库并为用户社区实施更多计算工具，改进和扩展我们基于网络的 ESEfinder 功能和服务。我们的方法是数学建模和实验测试的结合，使用小基因构建体和功能性前 mRNA 剪接测定。计算和实验分子生物学家之间的这种密切合作预计将有助于更好地理解前 mRNA 剪接调控机制，并改善公众对选择性剪接信息的获取。

DESCRIPTION (provided by applicant): The discovery that eukaryotic genes are "split" into exons and introns has had enormous implications for our understanding of gene expression and regulation. It is now recognized that more than half of human genes are expressed via alternative splicing, frequently in specific spatial/temporal patterns. Alternative splicing plays a fundamental role in determining the specialized properties of differentiated eukaryotic cell types during normal development, and misregulation of splicing is increasingly recognized as being responsible for many human diseases. The main goal of this project is to form a cutting-edge research team comprising computational and experimental molecular biologists to model two biologically important problems: How do c/s-elements regulate pre-mRNA splicing? How do they affect splice-site selection? To address these problems, the following specific aims are proposed. 1) To mathematically and experimentally model the dependency of pre-mRNA splicing activity upon SR protein- and hnRNP A1- dependent ESEs/ESSs in a few well defined systems. 2) To study the dependency of tissue-specific alternative splicing on c/s-elements and frans-acting splicing factors. 3) To improve and extend our web-based ESEfinder capability and service by including more enhancer and silencer motifs into the database and by implementing more computational tools for the user community. Our approach is a combination Of mathematical modeling and experimental testing, using minigene constructs and functional pre-mRNA splicing assays. This close collaboration between computational and experimental molecular biologists is expected to lead to a better understanding of the mechanism of pre- mRNA splicing regulation, as well as to improved public access to information about alternative splicing.