植物非编码RNA多层级调控网络的构建与分析

Non-coding RNAs (ncRNAs) include long non-coding RNA (lncRNAs), medium-size RNAs and small RNAs (smRNAs). LncRNAs and smRNAs play important roles in the regulation of gene expression as regulatory RNAs. Recently, studies have suggested that tRNAs are involved in gene regulation as smRNA precursors to produce smRNA, namely tRF. In addition, circRNAs are enriching the RNA world. At present, the high-throughput studies focus solely on the roles of miRNAs and lncRNAs in stress response, and the accumulating evidence also points that some siRNA and circRNA are involved in plant stress adaptation. In this project, we try to identify ncRNAs, including miRNA, siRNA, tRF, circRNA and lncRNA in Arabidopsis by means of integrative bioinformatics. Through integrating bioinformatics tools, multilevel regulatory network will be reconstructed, including transfator factors regulatory network, epigenetic regulatory network, long-range interaction network, competing endogenous RNA (ceRNA) network, NAT pairs and smRNA regulating network. Further, the combination with high-throughput sequencing data under several stress conditions, we will construct dynamic multilevel regulatory network. Together, our project will provide further insight into the role of ncRNAs in transcription regulations in plant.

非编码RNA（ncRNA）包括长非编码RNA（lncRNA）、中间长度非编码RNA和小RNA（smRNA）。其中lncRNA和smRNA可以作为调控型的RNA，在基因表达中起到重要作用。tRNA可以作为smRNA的前体从而产生smRNA，即tRF，参与基因的表达调控。circRNA的发现，更加丰富了ncRNA的世界。目前对于植物抗逆应答的研究，只针对其中一、两类ncRNA的调控，而没有全面的ncRNA参与的调控网络。本项目拟利用多组学数据，系统挖掘植物拟南芥中各类ncRNA，包括miRNA、siRNA、tRF、circRNA和lncRNA。通过生物信息学方法，构建多层级调控网络，包括：转录因子调控网络、表观调控网络、染色质长距离互作网络、内源性竞争RNA（ceRNA）网络、NAT对和siRNA与其靶点调控。结合拟南芥多种逆境胁迫下的数据，构建并验证动态的ncRNA多层级调控网络。

本项目利用多组学数据，系统挖掘拟南芥、水稻等植物中各类ncRNA，包括miRNA、siRNA、circRNA和lncRNA。通过生物信息学方法，构建多层级调控网络，包括：转录因子调控网络、表观调控网络、内源性竞争RNA（ceRNA）网络等等。并结合拟南芥多种逆境胁迫下的数据，构建全面的ncRNA多层次调控网络，预测非编码RNA参与的生物学功能。在此基础上，建立非编码RNA的预测平台和分析工具，并方便相关科研人员使用。受项目资助，已发表24篇期刊论文，并开发了多个生物信息学数据库。参加30多次国内或国际学术会议，培养硕士生5名，博士生8名。