基于大规模RNA-Seq数据的植物胁迫响应的可变剪接规律研究

结合申请人在植物转录组学和系统生物学方面的基础，本项目将以拟南芥、水稻和玉米为研究体系，利用大规模RNA-Seq数据开展植物响应生物和非生物胁迫过程中可变剪接（alternative splicing, AS）事件的计算研究。首先，根据植物外显子以及内含子的特征，开发一个为植物定制化的AS检测工具，精确计算可变外显子的保留比例。利用该工具对RNA-Seq数据进行挖掘，鉴定出胁迫特异的可变外显子以及基因，分析胁迫特异的可变外显子对蛋白序列基序、结构域以及无序区的影响，分析对应基因的生物学功能。 进一步，将构建基因-可变外显子的共关联网络，通过网络分析去推断AS上游的剪接调控因子。最后，将整合植物蛋白互作组数据，系统地探究胁迫响应AS事件对蛋白互作网络的重塑效应。本项目的实施将获得适用于植物的AS检测工具及数据库，有助于全面深入理解植物响应胁迫的AS调控机制，进而为作物改良提供新的思路。

In this proposed project, we will use large-scale RNA-Seq data of Arabidopsis thaliana, Oryza sativa and Zea mays to decipher the roles of alternative splicing (AS) in plant biotic and abiotic stress responses from a computational perspective. Firstly, we will develop a specialized tool based on the characteristics of plant exons and introns in plants to accurately calculate percent spliced in (PSI) of alternative exons (AEs). Next, we will use this tool to detect stress-specific alternative exons and genes from RNA-Seq data related to biotic and abiotic stresses. We will characterize sequence motifs, protein domains and disordered regions that are affected by AEs. We will also investigate the biological processes targeted by AS through analyzing functions of alternatively spliced genes under stresses. Furthermore, we will construct gene-AE co-association networks to infer splicing regulators in plant stress responses. Additionally, we will combine the plant protein interactome data with AS profiles to characterize how AS remodels plant protein-protein interaction network from a global perspective. It is hoped that the proposed project will provide a customized tool and database for plant AS detection and help to improve our systems understanding of AS landscape in plant biotic and abiotic stress responses. In the meantime, the results may provide some new hints for breeding new crop varieties that have effective resistance to environmental stresses.