title: Transcriptome-wide investigation of circular RNAs in rice.
abstract: Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs.
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Lu
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Cui
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Chuanrang
authors.initials: C
authors.lastname: Zhu
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Danlin
authors.initials: D
authors.lastname: Fan
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Gong
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Congcong
authors.initials: C
authors.lastname: Zhou
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Danfeng
authors.initials: D
authors.lastname: Lu
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Jianghong
authors.initials: J
authors.lastname: Luo
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Qilin
authors.initials: Q
authors.lastname: Tian
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D018749:RNA, Plant
keywords: Oryza sativa; circRNA; ncRNA; ssRNA-seq; transcriptome