Computational and experimental modeling of RNA Splicing

描述（由申请人提供）：真核生物基因被“分裂”为外显子和内含子的发现对我们对基因表达和调控的理解具有巨大的意义。现在认识到，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。在正常发育过程中，选择性剪接在决定分化真核细胞类型的特化特性方面起着重要作用，剪接的错误调节越来越被认为是导致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前沿研究团队，模拟两个生物学上重要的问题：c/s-elements如何调节pre-mRNA剪接？它们如何影响剪接位点的选择？为了解决这些问题，提出了以下具体目标。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依赖性ESEs/ESSs的依赖性。2)研究c/s-element和trans -acting剪接因子对组织特异性选择性剪接的依赖性。3)通过在数据库中加入更多的增强器和消音器主题，以及为用户社区实现更多的计算工具，改进和扩展我们基于web的ESEfinder功能和服务。我们的方法是结合数学建模和实验测试，使用迷你基因构建和功能性前mrna剪接分析。计算分子生物学家和实验分子生物学家之间的密切合作有望使人们更好地理解前mRNA剪接调节的机制，并改善公众对可选剪接信息的获取。

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.