CircAST:Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs
- Author:
Wu JING
1
;
Li YAN
;
Wang CHENG
;
Cui YIQIANG
;
Xu TIANYI
;
Wang CHANG
;
Wang XIAO
;
Sha JIAHAO
;
Jiang BIN
;
Wang KAI
;
Hu ZHIBIN
;
Guo XUEJIANG
;
Song XIAOFENG
Author Information
1. Department of Biomedical Engineering
- Keywords:
Circular RNA;
Full-length reconstruction;
Isoform quantification;
Multiple splice graph model;
Transcriptome
- From:
Genomics, Proteomics & Bioinformatics
2019;17(5):522-534
- CountryChina
- Language:Chinese
-
Abstract:
Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may gener-ate different circRNA isoforms at the same locus. However, the challenges of reconstruction and quantification of alternatively spliced full-length circRNAs remain unresolved. On the basis of the internal structural characteristics of circRNAs, we developed CircAST, a tool to assemble alter-natively spliced circRNA transcripts and estimate their expression by using multiple splice graphs.Simulation studies showed that CircAST correctly assembled the full sequences of circRNAs with a sensitivity of 85.63％-94.32％and a precision of 81.96％-87.55％. By assigning reads to specific iso-forms, CircAST quantified the expression of circRNA isoforms with correlation coefficients of 0.85-0.99 between theoretical and estimated values. We evaluated CircAST on an in-house mouse testis RNA-seq dataset with RNase R treatment for enriching circRNAs and identified 380 cir-cRNAs with full-length sequences different from those of their corresponding cognate linear RNAs. RT-PCR and Sanger sequencing analyses validated 32 out of 37 randomly selected isoforms, thus further indicating the good performance of CircAST, especially for isoforms with low abundance. We also applied CircAST to published experimental data and observed substantial diversity in circular transcripts across samples, thus suggesting that circRNA expression is highly regulated. CircAST can be accessed freely at https://github.com/xiaofengsong/CircAST.
