基于CLIP-Seq数据解析环状RNA与RNA结合蛋白的互作网络和功能机制

Circular RNAs (circRNAs) have been shown to contribute to the physiological and pathological processes through interaction with RNA-binding proteins (RBPs). More than 100000 circRNAs have been identified, however, for the majority of circRNAs, the mechanisms and functions underlying their interaction with RBPs remain unknown. In our previous studies, we have developed two platforms, starBase and deepBase (ESI highly cited papers), for the identification of circRNAs as well as their interactions with microRNAs (miRNAs). In the present study, by integrating cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) data, we aim to develop novel algorithms and softwares that combine circRNAs’ sequence feature and probabilistic models to systematically identify the interaction networks between circRNAs and RBPs, and predict the novel functions of circRNAs. We will further confirm the biological functions and mechanisms of candidate circRNAs by using experimental methods, including RNA immunoprecipitation (RIP) and CRISPR/Cas9. This study will promote our understanding of the roles of circRNAs and RBPs in physiological and pathological processes.

环状RNA（circRNA）与RNA结合蛋白（RBP）相互作用形成调控网络系统，参与生物体生理和病理过程的调控。虽然已有超过10万个的circRNA被鉴定，但是绝大多数circRNA与RBP之间的互作规律及功能机制仍有待阐明。我们前期开发了starBase和deepBase平台（ESI高引用论文）实现对circRNA的大规模鉴定和circRNA-miRNA互作组的研究。在此基础上，本项目拟通过整合研究蛋白与RNA互作的CLIP-Seq高通量实验数据，开发基于circRNA跨环接口序列特征及概率罚分模型的新算法和软件，系统鉴定circRNA与RBP的互作关系，预测circRNA的新功能。我们将进一步采用RNA免疫共沉淀和CRISPR/Cas9等方法验证它们的生物学功能和作用机制，从而扩展对circRNA与RBP功能调控网络在生理与疾病中作用的认识。

环状RNA（circRNA）与RNA结合蛋白（RBP）相互作用形成调控网络系统，参与生物体生理和病理过程的调控。虽然已有超过10万个的circRNA被鉴定，但是绝大多数circRNA与RBP之间的互作规律及功能机制仍有待阐明。我们项目通过整合研究蛋白与RNA互作的CLIP-Seq高通量实验数据，我们开发新一代测序数据的deepBase、RMBase、colorCells、Pol3Base、dreamBase和tsRFun等工具和平台在细胞、组织、肿瘤样本及单细胞系统鉴定circRNA的表达图谱及其与RBP的互作关系，预测circRNA的新功能。我们进一步采用RNA免疫共沉淀和CRISPR/Cas9等方法验证6个RNA结合蛋白的生物学功能和作用机制，揭示转座子来源的lncRNA与RNF169互作促进同源重组修复的分子机制，从而扩展对circRNA等非编码RNA与RBP功能调控网络在生理与疾病中作用的认识。以上的研究成果在Nucleic Acid Research、Cell Reports、EMBO Reports等杂志发表了9篇研究论文。