从转录组数据中检测和重建环状RNA

Detection and Reconstruction of Circular RNAs from Transcriptomic Data.

作者信息

Zheng Yi, Zhao Fangqing

机构信息

Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.

出版信息

Methods Mol Biol. 2018;1724:1-8. doi: 10.1007/978-1-4939-7562-4_1.

DOI:10.1007/978-1-4939-7562-4_1

PMID:29322436

Abstract

Recent studies have shown that circular RNAs (circRNAs) are a novel class of abundant, stable, and ubiquitous noncoding RNA molecules in eukaryotic organisms. Comprehensive detection and reconstruction of circRNAs from high-throughput transcriptome data is an initial step to study their biogenesis and function. Several tools have been developed to deal with this issue, but they require many steps and are difficult to use. To solve this problem, we provide a protocol for researchers to detect and reconstruct circRNA by employing CIRI2, CIRI-AS, and CIRI-full. This protocol can not only simplify the usage of above tools but also integrate their results.

摘要

最近的研究表明，环状RNA（circRNA）是真核生物中一类新型的丰富、稳定且普遍存在的非编码RNA分子。从高通量转录组数据中全面检测和重建circRNA是研究其生物发生和功能的第一步。已经开发了几种工具来处理这个问题，但它们需要很多步骤且使用困难。为了解决这个问题，我们为研究人员提供了一个使用CIRI2、CIRI-AS和CIRI-full检测和重建circRNA的方案。该方案不仅可以简化上述工具的使用，还能整合它们的结果。