Reconstruction of full-length circular RNAs enables isoform-level quantification
Reconstruction of full-length circular RNAs enables isoform-level quantification
复制标题
全长环状 RNA 的重建可实现异构体水平的定量
DOI：
10.1186/s13073-019-0614-1
复制
发表时间：
2019
期刊：
影响因子：
12.3
通讯作者：
Zhao Fangqing
中科院分区：
文献类型：
--
作者：
Zheng Yi;Ji Peifeng;Chen Shuai;Hou Lingling;Zhao Fangqing
目前，circRNA研究正在从鉴定环状转录物转向了解其生物学功能。然而，这种努力受到了限制，大规模确定其全长序列，也无法准确定量的异构体水平。在这里，我们提出了一个新的功能，反向重叠（RO），circRNA检测，它优于后剪接连接（BSJ）为基础的方法在识别低丰度circRNA。通过结合RO和BSJ特征，我们提出了一种新的方法，用于有效地重建全长circRNA和转录组的异构体水平定量。我们系统地比较了使用人肝肿瘤和正常组织的BSJ水平和亚型水平差异表达分析之间的差异，并强调了深化circRNA研究到亚型水平分辨率的必要性。CIRI完整软件可在 https://sourceforge.net/projects/ciri .
Currently, circRNA studies are shifting from the identification of circular transcripts to understanding their biological functions. However, such endeavors have been limited by large-scale determination of their full-length sequences and also by the inability of accurate quantification at the isoform level. Here, we propose a new feature, reverse overlap (RO), for circRNA detection, which outperforms back-splice junction (BSJ)-based methods in identifying low-abundance circRNAs. By combining RO and BSJ features, we present a novel approach for effective reconstruction of full-length circRNAs and isoform-level quantification from the transcriptome. We systematically compared the difference between the BSJ-level and isoform-level differential expression analyses using human liver tumor and normal tissues and highlight the necessity of deepening circRNA studies to the isoform-level resolution. The CIRI-full software can be accessed at https://sourceforge.net/projects/ciri .