环形RNA A-to-I编辑与m6A表观修饰互作的计算生物学研究

Computational analyzes of large transcriptome data indicate that a large number of exonic circular RNAs are present in the Human body. Although the processing mechanism and function of circular RNA has been reported by many papers, its distribution and regulation over more than 100 epigenetic modification and RNA editing levels have not yet been clarified. In the meantime, a series of efficient algorithms for computational biology were established by the applicant, the combination with the experiment was further systematically revealed that circular RNAs were coupling with transcriptional, and the important functions and mechanisms of circular RNAs in anti-viral immunity. This project aims to systematically study the epitranscriptomics modifications of circular RNA based on previous studies. Mainly through the combination of computational biology and experimental biology, 1) Exploring the A-to-I RNA editing sites and distribution in circular RNAs and the differential regulation of tissue specific, 2) Discovering and validating m6A modification sites and distribution of circular RNAs including modification characteristics, 3) to detect the interaction between A-to-I editing and m6A in circular RNA and its potential regulation on the production and function of circular RNA, by comprehensively mapping of the circular RNA modifications and epitranscriptomics atlas, ultimately provides the basis and clues for the epitranscriptomics level studies of the processing and function of circular RNAs.

对海量转录组数据的计算分析表明人体内存在大量的外显子来源环形RNA。虽然已有对环形RNA生成加工机制及其功能的研究报道，但对其在已知100多种表观转录组学修饰和编辑水平上的分布和调控等尚不清楚。申请人前期建立了一系列高效计算生物学算法，并进一步与实验相结合，系统揭示了环形RNA与转录偶联及其在抗病毒免疫中发挥的重要功能和机制。本项目旨在前期研究基础上，系统研究环形RNA的表观转录组学修饰。主要是利用计算生物学和实验生物学相结合的交叉方法，1）发掘环形RNA中A-to-I编辑位点，分布及组织差异调控，2）发现和进一步验证环形RNA中m6A修饰位点，分布及表观修饰特征，3）检测环形RNA中A-to-I与m6A的互作及其对环形RNA产生和功能的潜在调控作用，通过全面绘制环形RNA的表观修饰图谱，最终为环形RNA的生成加工和功能作用研究提供表观转录组水平的基础和线索。

环形RNA（circRNA）是一类通过外显子反向剪接形成，即下游5'剪接位点反向与上游3'剪接位点连接所形成的具有闭合环形结构的RNA分子。近年来，通过对海量转录组数据的计算生物学深度解析，在真核生物中发现了大量外显子来源的环形RNA。本研究围绕环形RNA功能研究和碱基编辑系统的开发，开展了一系列计算生物学研究，包括，对环形RNA A-to-I编辑进行筛选，研究特定细胞系中环形RNA的m6A分布及表观修饰特征，进一步构建了CRISPR-RfxCas13d/BSJ-gRNA体系，并开发了全新的环形RNA功能筛选计算流程CDCscreen，为全面和深入理解环形RNA的生物学功能建立了新的技术体系和研究范式。此外，受项目资助还开发了新型变形碱基编辑系统tBE及全基因组脱靶检测流程BEIDOU，揭示了tBE在in vivo水平的治疗潜能，且仅发生与本底水平相一致的全基因组和全转录组水平脱靶。上述研究，发现和解析了环形RNA在生理和病理条件下所发挥的功能调控作用及其新机制，并拓展了碱基编辑器在个性化治疗和精准医疗领域应用的新方向。