使用CIRCexplorer流程对环状RNA进行全基因组注释及其可变反向剪接/剪接
Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline.
作者信息
Dong Rui, Ma Xu-Kai, Chen Ling-Ling, Yang Li
机构信息
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 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, Shanghai, China.
出版信息
Methods Mol Biol. 2019;1870:137-149. doi: 10.1007/978-1-4939-8808-2_10.
Circular RNAs (circRNAs) derived from back-spliced exons were sporadically identified about 25 years ago, and have been recently re-discovered genome-wide across different species. Interestingly, one gene locus can generate multiple circRNAs through alternative back-splicing and/or alternative splicing, thus expanding our understanding on the diversity and complexity of transcriptomes. Precise annotation of circRNAs with their alternative back-splicing and alternative splicing events is the basis for the functional characterization of different categories of circRNAs. Here we describe a step-by-step computational scheme to annotate circRNAs from publicly available RNA sequencing datasets with the CIRCexplorer2 pipeline.
大约25年前，人们偶然发现了由反向剪接外显子产生的环状RNA（circRNA），最近在不同物种中通过全基因组范围重新发现了它们。有趣的是，一个基因座可以通过可变反向剪接和/或可变剪接产生多个circRNA，从而拓展了我们对转录组多样性和复杂性的认识。对circRNA及其可变反向剪接和可变剪接事件进行精确注释，是不同类型circRNA功能表征的基础。在此，我们描述了一种逐步计算方案，用于使用CIRCexplorer2管道从公开可用的RNA测序数据集中注释circRNA。
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