全基因组环状 RNA 鉴定和定量的方法与挑战。

Approaches and challenges in genome-wide circular RNA identification and quantification.

机构信息

Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

出版信息

Trends Genet. 2023 Dec;39(12):897-907. doi: 10.1016/j.tig.2023.09.006. Epub 2023 Oct 13.

DOI:10.1016/j.tig.2023.09.006

PMID:37839990

Abstract

Numerous circular RNAs (circRNAs) produced from back-splicing of exon(s) have been recently revealed on a genome-wide scale across species. Although generally expressed at a low level, some relatively abundant circRNAs can play regulatory roles in various biological processes, prompting continuous profiling of circRNA in broader conditions. Over the past decade, distinct strategies have been applied in both transcriptome enrichment and bioinformatic tools for detecting and quantifying circRNAs. Understanding the scope and limitations of these strategies is crucial for the subsequent annotation and characterization of circRNAs, especially those with functional potential. Here, we provide an overview of different transcriptome enrichment, deep sequencing and computational approaches for genome-wide circRNA identification, and discuss strategies for accurate quantification and characterization of circRNA.

摘要

最近在全基因组范围内，在不同物种中发现了大量由外显子反向剪接产生的环状 RNA（circRNA）。尽管一般表达水平较低，但一些相对丰富的 circRNA 可以在各种生物过程中发挥调节作用，这促使人们在更广泛的条件下不断对 circRNA 进行分析。在过去的十年中，在转录组富集和生物信息学工具方面都应用了不同的策略来检测和定量 circRNA。了解这些策略的范围和局限性对于随后对 circRNA 进行注释和表征至关重要，特别是那些具有功能潜力的 circRNA。在这里，我们概述了用于全基因组 circRNA 鉴定的不同转录组富集、深度测序和计算方法，并讨论了准确定量和表征 circRNA 的策略。