融合RNA结构组和分子变构效应研究lncRNA-TF协同转录调控机制

With the rapid development of the next generation sequencing technology, a comprehensive picture of the modular organization on ‘RNA structurome’ has been sketched and interpreted. Our understanding of lncRNAs gradually changes from linear relationship of sequence characteristics and quantitative expression relationship, to three-dimensional analysis of the combination of structure and function. It become an important research field at present by exploring the interactions of bio-molecules and functional mechanisms, based on considering the structures of RNAs. We aim to explore the cooperation regulation mechanism of lncRNA-TF in the process of transcriptional regulation and develop the strategy for lncRNAs structure analyzing and mapping in the genome scale via the RNA structurome information. By exploring SMART algorithm based on molecular structural interaction features, we could identify interaction domains of lncRNA-TF and specifically combination interface (landing pad), construct triple interaction model (lncRNA-TF-DNA), and investigate the disturbance effects mediated by Single Nucleotide Polymorphic Sites in cooperative transcriptional regulation process. It is could provide useful clues for the study of lncRNA structure-function interrelationships and potential disturbance mechanism in the transcriptional regulation, mediated by allosteric effects of lncRNA. The detailed architectural context could yield broad biological insights of lncRNA molecular mechanism, and provides a framework for feature comprehending cellular function and pathogenesis of disease, especially in the process of transcriptional regulation.

新一代测序技术推动了人类转录组层面RNA结构特征的广泛认知，“RNA结构组”初现端倪。对lncRNA的理解逐渐从线性的序列、表达数量关系向立体化的结构-功能相结合的分析层次转变，以RNA结构为基础的分子互作与功能机制研究成为前沿热点。本课题关注转录调控过程的lncRNA-TF协同机制，在融合RNA结构组学信息基础上构建基因组范围lncRNA二级结构图谱，开发以分子结构互作为特征的SMART算法，深入挖掘具有鉴别意义的lncRNA-TF特异性结合位点（landing-pad），剖析lncRNA-TF-DNA三元调控模型，并探讨SNP介导的lncRNA分子变构效应对协同调控的影响，从而实现lncRNA结构介导的lncRNA-TF协同关系和潜在扰动机制研究。本课题对于深入理解lncRNA作用机制，特别是在转录调控过程的重要功能有一定指导意义，并为进一步阐明细胞功能和疾病发生发展机制提供有用线索。

转录调控是细胞内复杂生物学功能和信号应激应答的关键过程。研究表明lncRNAs协同作用于转录因子，参与细胞内转录调控。结构及其与大分子的相互作用研究丰富了我们对分子生物世界的认知，特别是RNA结构组学的提出及RNAs与其他生物大分子相互作用的高通量实验技术发展，对于我们从基因组层面描绘转录调控的崭新画面创造了条件。本课题正是基于目前快速发展的RNA结构、RNA与蛋白质等生物大分子相互作用研究的基础上，关注以分子结构为导向的转录调控过程中的lncRNA-TF协同调控机制。首先实现人类lncRNAs、参考基因组、SNPs和侧翼序列数据标准化处理流程，建立标准基因组lncRNAs序列比对文库，完成SNPs精准化定位。其次开发基于最小自由能的动态规划算法，完成基于组学数据的二级结构元件修正，构建人类lncRNA二级结构图谱，设计SMART算法框架流程，开发滑动窗口算法模型，识别基因组landing pad，完成landing pad侧翼序列可及性分析。最后，设计基于结构特征的互作强度打分机制，评价二级结构元件暴露或屏蔽等分子过程在互作模式中的作用。构建lncRNA-TF-DNA三元调控复合物模型，分析lncRNA-TF协同转录调控特征。实现SNPs在lncRNAs转录本上的靶向比对，设计打分函数衡量单位点或不连续多位点改变引起的变构效应，探索其与复杂疾病发生机理的关联性。本项目为进一步理解lncRNA行使的生物学功能、转录调控的复杂过程，联系转录过程中的分子调控作用与生理和病理关系提供有益借鉴。