气候变化领域集成服务门户(CCPortal): Transcriptome-wide investigation of circular RNAs in rice

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DOI	10.1261/rna.052282.115
	Transcriptome-wide investigation of circular RNAs in rice
	Lu, Tingting; Cui, Lingling; Zhou, Yan; Zhu, Chuanrang; Fan, Danlin; Gong, Hao; Zhao, Qiang; Zhou, Congcong; Zhao, Yan; Lu, Danfeng; Wo, Panghong; Wang, Yongchun; Tian, Qilin; Feng, Qi; Huang, Tao; Han, Bin
发表日期	2015
ISSN	1355-8382
EISSN	1469-9001
卷号	21 期号:12
英文摘要	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.
关键词	Oryza sativa circRNA ssRNA-seq ncRNA transcriptome
学科领域	Biochemistry & Molecular Biology
语种	英语
WOS研究方向	Biochemistry & Molecular Biology
来源期刊	RNA
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/111791
作者单位	Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Plant Physiol & Ecol, Natl Ctr Gene Res, Shanghai 200233, Peoples R China
推荐引用方式 GB/T 7714	Lu, Tingting,Cui, Lingling,Zhou, Yan,et al. Transcriptome-wide investigation of circular RNAs in rice[J]. 中国科学院西北生态环境资源研究院,2015,21(12).
APA	Lu, Tingting.,Cui, Lingling.,Zhou, Yan.,Zhu, Chuanrang.,Fan, Danlin.,...&Han, Bin.(2015).Transcriptome-wide investigation of circular RNAs in rice.RNA,21(12).
MLA	Lu, Tingting,et al."Transcriptome-wide investigation of circular RNAs in rice".RNA 21.12(2015).