Zhang Jinyang, Zhao Fangqing
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
Methods. 2021 Dec;196:17-22. doi: 10.1016/j.ymeth.2021.03.017. Epub 2021 Mar 27.
High-throughput RNA sequencing has enabled the extensive detection of circular RNAs (circRNAs) in eukaryotic organisms. However, most circRNAs are derived from exonic regions and possess sequences that are highly overlapped to their cognate linear mRNAs, which makes the reconstruction of the internal structure and full-length circular transcripts a challenging aspect in circRNA studies. To solve this problem, we provide a step-by-step protocol for the full-length reconstruction of circRNAs using CIRI-full and CIRI-long in Illumina and Nanopore RNA-seq libraries. By combining experimental and computational methods, we are able to effectively characterize the full-length landscape of circRNAs, which provide an important basis to explore the biogenesis and biological function of circRNAs.
高通量RNA测序能够在真核生物中广泛检测环状RNA（circRNA）。然而，大多数circRNA来源于外显子区域，并且拥有与它们对应的线性mRNA高度重叠的序列，这使得环状RNA内部结构和全长环状转录本的重建成为circRNA研究中的一个具有挑战性的方面。为了解决这个问题，我们提供了一个逐步方案，用于在Illumina和Nanopore RNA-seq文库中使用CIRI-full和CIRI-long对circRNA进行全长重建。通过结合实验和计算方法，我们能够有效地描绘circRNA的全长图谱，这为探索circRNA的生物发生和生物学功能提供了重要依据。
