人类基因组编码了数十万条lncRNA，是蛋白质编码基因的8倍之多，但由于实验方法的限制，绝大多数lncRNA的功能及作用机制还不清楚。我们近期开发了可鉴定lncRNA靶标的新方法RNA-3C (RNA in situ three-dimensional contacts and conformation capture),借助RNA-RNA的原位连接，实现了非编码RNA靶标的全景式鉴定，并克服了已有方法的体外非特异性连接缺点。RNA-3C重现了NEAT1和MALAT1等已知lncRNA的体内作用靶标，并鉴定了一类hub-lncRNA，它们与周边数个Mb范围内的RNA或者不同染色体上的RNA相互作用，可能在DNA拓扑结构域组织和基因表达调控中发挥重要作用。我们计划继续完善RNA-3C，解析调节MYC的关键hub-lncRNA，揭示lncRNA调控基因表达的新规律、新功能和新机制。

Human genome encodes over hundreds of thousands long non-coding RNAs, which are more than eight-fold to the number of protein coding genes. Due to technical limits, the functional mechanism for most of the lncRNAs remains unknown. We recently developed a new technique, RNA-3C, to systematically identify lncRNA in vivo targets. By proximity ligation of direct contacting RNAs in situ, we simultaneously identified all the non-coding RNA targets in Hela cell, and largely excluded the false positive signals due to the in vitro ligations by published method. RNA-3C also revealed most of the targets identified by CHART-seq strategy for lncRNA NEAT1 and MALAT1. Unexpectedly, we identified many hub-lncRNAs, which can span over several mega-bases in the same chromosome or across many different chromosome regions. Within this proposal, we are planning to further improve RNA-3C method, and to decipher the functional mechanism of hun-lncRNA in MYC regulation. Moreover, RNA-3C will enable us to reveal new principals, functions and mechanisms for lncRNAs.