拟南芥种子萌发过程中差异表达基因的识别和pre-mRNA可变剪接图谱的构建  

The detection of differentially expressed gene and atlas construction of pre-mRNA alternative splicing during seed germination of Arabidopsis thaliana

作　　者：邢永强 王延新 何泽学 崔向军 刘国庆 孟虎 赵宏宇 赵秀娟 蔡禄 Yongqiang Xing;Yanxin Wang;Zexue He;Xiangjun Cui;Guoqing Liu;Hu Meng;Hongyu Zhao;Xiujuan Zhao;Lu Cai(School of Life Science and Technology,Inner Mongolia University of Science and Technology,Baotou 014010,China;The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics,Inner Mongolia University of Science and Technology,Baotou 014010,China)

机构地区：[1]内蒙古科技大学生命科学与技术学院,包头014010 [2]内蒙古自治区功能基因组生物信息学重点实验室,包头014010

出　　处：《科学通报》2019年第36期3844-3855,共12页Chinese Science Bulletin

基　　金：国家自然科学基金(61662055,61671256,31660322,31760247,21767020);内蒙古自然科学基金(2018MS03024)资助

摘　　要：种子的萌发是植物新生命的开始,也是决定植物种群更新、物种延续的关键环节和影响粮食作物产量的重要因素.种子萌发事件是一个极其复杂的过程,其调控机制至今仍未完全知晓.本文基于拟南芥种子不同萌发过程的RNA-seq测序数据,分别从基因表达和pre-mRNA可变剪接层面系统地剖析了种子萌发过程中的组学特征和调控机制.首先,通过组学数据分析方法得到拟南芥的基因表达矩阵,系统地识别了种子不同萌发阶段间的差异表达基因,并解析了其生物学功能.结果显示,随着种子的萌发,一方面大量与糖酵解、DNA合成等代谢过程密切相关的基因被激活,保证了种子新陈代谢和基本的细胞活性的重新激活;另一方面,与氧化应激胁迫响应、有毒物质响应、热响应、水响应等相关的基因活性被抑制,保证了种子能够从休眠态顺利活化.其次,使用rMATS系统描绘了种子萌发过程中各阶段的pre-mRNA可变剪接图谱,鉴定了不同萌发阶段间的差异可变剪接事件,并分析了种子萌发过程中的可变剪接特征及差异可变剪接事件的生物学功能.该工作的开展将进一步促进种子萌发过程中的调控机制的阐明,并为相关实验工作的开展提供一定的帮助.Seed germination is the initial phase of life cycle for plants and plays a pivotal role in regeneration of plant population,continuation of plant species and crop yield.However,seed germination is an extremely complex biological process and its regulatory mechanisms remain unclear.It is well known that gene expression and pre-mRNA alternative splicing are vital to the central dogma.In Arabidopsis genome,~60%multi-exon genes are alternatively spliced.Alternative splicing is involved in the response to environmental cues,including abiotic and biotic stresses,in the regulation of crucial developmental processes such as flowering,and in circadian timekeeping.The present paper studies the effect of gene expression and alternative splicing on seed germination in Arabidopsis.We constructed RNA-seq datasets from dry seeds,germinating seeds 1–3,Young seeds and Seeds in Arabidopsis and carried out quality control for the raw reads by using FastQC and Trimmomatic.StringTie estimated transcript and gene expression from a mapping to the Arabidopsis genome obtained from Hisat2.We next created the gene expression matrix for Arabidopsis,which includes 37336 genes along the rows and 12 samples along the columns,and employed DESeq2 to systematically identify differentially expressed genes between different stages during seed germination.To elucidate the biological functions of differentially expressed genes,we performed a functional enrichment analysis of these genes using clusterProfiler tool.The results showed that many genes involved in metabolic processes,such as glycolysis and DNA synthesis,were activated during the seed germination.It ensures the reactivation of metabolism and basic cellular activities of seeds.Some genes involved in environmental responses,such as oxidative stress,toxic substance,heat,and water,were inhibited.This is essential for seeds to be successfully activated from a dormant state.Furthermore,rMATS was utilized to detect the pre-mRNA alternative splicing events and differential alternative splicing e

关 键 词：拟南芥 种子 差异表达基因 可变剪接 富集分析 

分 类 号：Q943.2[生物学—植物学]