基于高通量测序数据发掘植物长非编码RNA及其调控网络研究

Recently Sanger sequencing of cDNA libraries, tilling array and RNA-seq have demonstrated that transcription is not limited to protein-coding regions but is pervasive instead. A growing body of literature has demonstrated that long noncoding RNA (lncRNA) constitutes a large fraction of the transcriptome in mammalian genomes and other organisms. At present, lncRNAs are operationally defined as RNA genes larger than 200 bp that do not appear to have coding potential. A number of lncRNAs have been shown to be involved in a wide range of biological functions. These findings have spurred a huge interest in elucidating the functions and mechanisms of lncRNAs. Clearly, lncRNA is an exciting field of ncRNA, with an increasing number of literatures published in the past years. However, a systematic analysis of lncRNAs expressed in Arabidopsis by integrating deep sequencing data is still missing. The regulatory network of lncRNA and other RNA molecules is also unexplored. In this project, we try to identify lncRNAs in Arabidopsis by mining next generation sequencing data. Genome-wide analysis will reveal the properties of lncRNAs, e.g. genomic features, poly A and GC content. Computational prediction and degradome-based analysis will indicate whether lncRNAs are targeted by miRNAs. Further, we will investigate if most lncRNAs can form natural antisense transcripts with protein coding transcripts as well as other lncRNAs. We will construct RNA regulatory networks mediated by novel lncRNAs in Arabidopsis. The genome wide of lncRNA identification and lncRNA-mediated RNA regulatory network in Arabidopsis will provide an insight into transcriptional regulations in plant.

近年来大规模的cDNA文库、tilling芯片和转录组测序的研究表明真核生物基因组绝大部分区域都是有转录活性的，不仅仅存在于蛋白编码区域。目前认为长非编码RNA（lncRNA）是长度大于200bp，而且不编码蛋白质的RNA。已知许多lncRNA参与诸多的生命活动过程，这使得人们开始关注长非编码RNA的功能和作用机制。lncRNA已成为一个热点研究领域，近几年的研究成果与文献数量不断增加。但目前为止人们对于植物中lncRNA的知识却所知甚少。本项目拟利用新一代测序的数据，结合已测序的基因组信息，系统地发掘植物拟南芥中的lncRNA。通过生物信息方法，构建lncRNA和其他生物分子，如染色质修饰蛋白、mRNA、miRNA等的RNA互作调控网络，从而对RNA的调控基因表达机制有更深入的了解。

本项目利用新一代测序的数据，结合已测序的基因组信息，系统地发掘植物拟南芥中的lncRNA。完成了植物高通量测序数据的进一步整合与挖掘；拟南芥的lncRNA的注释、NAT的分析及相关调控研究；植物lncRNA介导的不同类型的RNA之间调控网络的构建及其相关研究。开发完善相关的生物信息学工具，包括转录组分析的pipeline和植物lncRNA的网站的完善。通过生物信息方法，构建lncRNA和其他生物分子，如染色质修饰蛋白、mRNA、miRNA等的RNA互作调控网络，从而对RNA的调控基因表达机制有更深入的了解。受项目资助，已发表23篇论文，申报专利1项，并开发了多个生物信息学数据库。参加34次国内或国际学术会议，培养硕士生5名，博士生5名。