title: CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.
abstract: Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function. Here, we present a novel chiastic clipping signal-based algorithm, CIRI, to unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies. By applying CIRI to ENCODE RNA-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circRNAs as well as fragments specific to them in the human transcriptome.
authors.affiliation: Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. gaoyuan06@mails.ucas.ac.cn.|University of Chinese Academy of Sciences, Beijing, 100049, China. gaoyuan06@mails.ucas.ac.cn.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. wangjf@mail.biols.ac.cn.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. zhfq@mail.biols.ac.cn.
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D005091:Exons / Q000235:genetics; D005095:Exoribonucleases / Q000378:metabolism; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D000079962:RNA, Circular; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D000079962:RNA, Circular; D012313:RNA; D005095:Exoribonucleases; C080868:ribonuclease R