title: Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice.
abstract: Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.
authors.affiliation: a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.affiliation: a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.
authors.forename: Xingchen
authors.initials: X
authors.lastname: Zhang
authors.affiliation: a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.
authors.forename: Qinjie
authors.initials: Q
authors.lastname: Chu
authors.affiliation: a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.
authors.forename: Chen
authors.initials: C
authors.lastname: Liu
authors.affiliation: a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.
authors.forename: Yongyi
authors.initials: Y
authors.lastname: Yu
authors.affiliation: c The First Affiliated Hospital, Zhejiang University , Hangzhou , China.
authors.forename: Weiqin
authors.initials: W
authors.lastname: Jiang
authors.affiliation: d CSIRO Agriculture and Food, Black Mountain Laboratories , Canberra , Australia.
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.affiliation: a Institute of Crop Sciences, Zhejiang University , Hangzhou , China.|b Institute of Bioinformatics, Zhejiang University , Hangzhou , China.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
authors.affiliation: e China National Rice Research Institute, Chinese Academy of Agricultural Sciences , Hangzhou , China.
authors.forename: Longbiao
authors.initials: L
authors.lastname: Guo
mesh_terms: D017398:Alternative Splicing; D001483:Base Sequence; D066264:Datasets as Topic; D005095:Exoribonucleases / Q000737:chemistry; D018745:Genome, Plant; D006801:Humans; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D022821:RNA Splice Sites; D020871:RNA Stability; D000079962:RNA, Circular; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry; D017423:Sequence Analysis, RNA
chemical_list: D022821:RNA Splice Sites; D000079962:RNA, Circular; D018749:RNA, Plant; D012335:RNA, Ribosomal; D012313:RNA; D005095:Exoribonucleases; C080868:ribonuclease R
keywords: Alternative circularization; circular RNAs; full-length circRNAs; rice; splicing signals