Ma Xu-Kai, Xue Wei, Chen Ling-Ling, Yang Li
CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
Methods. 2021 Dec;196:3-10. doi: 10.1016/j.ymeth.2021.02.008. Epub 2021 Feb 12.
Covalently closed circular RNAs (circRNAs) produced by back-splicing of exon(s) are co-expressed with their cognate linear RNAs from the same gene loci. Most circRNAs are fully overlapped with their cognate linear RNAs in sequences except the back-spliced junction (BSJ) site, thus challenging the computational detection, experimental validation and hence functional evaluation of circRNAs. Nevertheless, specific bioinformatic pipelines were developed to identify fragments mapped to circRNA-featured BSJ sites, and circRNAs were pervasively identified from non-polyadenylated RNA-seq datasets in different cell lines/tissues and across species. Precise identification and quantification of circRNAs provide a basis to further understand their functions. Here, we describe detailed computational steps to annotate and quantify circRNAs using a series of CIRCexplorer pipelines.
由外显子反向剪接产生的共价闭合环状RNA（circRNA）与其来自相同基因座的同源线性RNA共表达。除反向剪接连接（BSJ）位点外，大多数circRNA在序列上与其同源线性RNA完全重叠，这给circRNA的计算检测、实验验证以及功能评估带来了挑战。尽管如此，人们开发了特定的生物信息学流程来识别映射到circRNA特征性BSJ位点的片段，并且在不同细胞系/组织以及跨物种的非聚腺苷酸化RNA测序数据集中广泛鉴定出了circRNA。circRNA的精确鉴定和定量为进一步了解其功能提供了基础。在此，我们描述了使用一系列CIRCexplorer流程注释和定量circRNA的详细计算步骤。
