Diverse alternative back-splicing and alternative splicing landscape of circular RNAs
Zhang, Xiao-Ou1,2; Dong, Rui1,2; Zhang, Yang2,3; Zhang, Jia-Lin1,2,3; Luo, Zheng1,2; Zhang, Jun3; Chen, Ling-Ling2,3,4; Yang, Li1,2,4
2016-09
发表期刊GENOME RESEARCH
ISSN1088-9051
卷号26期号:9页码:1277-1287
发表状态已发表
DOI10.1101/gr.202895.115
摘要Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or alternative splice site selection; however, a detailed map of alternative back-splicing/splicing in circRNAs is lacking. Here, with the upgraded CIRCexplorer2 pipeline, we systematically annotated different types of alternative back-splicing and alternative splicing events in circRNAs from various cell lines. Compared with their linear cognate RNAs, circRNAs exhibited distinct patterns of alternative back-splicing and alternative splicing. Alternative back-splice site selection was correlated with the competition of putative RNA pairs across introns that bracket alternative back-splice sites. In addition, all four basic types of alternative splicing that have been identified in the (linear) mRNA process were found within circRNAs, and many exons were predominantly spliced in circRNAs. Unexpectedly, thousands of previously unannotated exons were detected in circRNAs from the examined cell lines. Although these novel exons had similar splice site strength, they were much less conserved than known exons in sequences. Finally, both alternative back-splicing and circRNA-predominant alternative splicing were highly diverse among the examined cell lines. All of the identified alternative back-splicing and alternative splicing in circRNAs are available in the CIRCpedia database (http://www.picb.ac.cn/rnomics/circpedia). Collectively, the annotation of alternative back -splicing and alternative splicing in circRNAs provides a valuable resource for depicting the complexity of circRNA biogenesis and for studying the potential functions of circRNAs in different cells.
收录类别SCI
语种英语
资助项目National Natural Science Foundation of China (NSFC)[91540115] ; National Natural Science Foundation of China (NSFC)[91440202] ; National Natural Science Foundation of China (NSFC)[31471241] ; National Natural Science Foundation of China (NSFC)[31322018]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号WOS:000382421000013
出版者COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
WOS关键词EXON CIRCULARIZATION ; CIRCRNA BIOGENESIS ; TRANSCRIPTION ; REVEALS ; REPEATS ; CELLS
原始文献类型Article
引用统计
文献类型期刊论文
条目标识符https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/1729
专题生命科学与技术学院_特聘教授组_陈玲玲组
生命科学与技术学院_特聘教授组_杨力组
通讯作者Chen, Ling-Ling; Yang, Li
作者单位1.Chinese Acad Sci, Shanghai Inst Biol Sci, CAS Ctr Excellence Brain Sci & Intelligence Techn, CAS MPG Partner Inst Computat Biol,Key Lab Comput, Shanghai 200031, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, CAS Ctr Excellence Mol Cell Sci,State Key Lab Mol, Shanghai 200031, Peoples R China
4.ShanghaiTech Univ, Sch Life Sci, Shanghai 20003, Peoples R China
通讯作者单位上海科技大学
推荐引用方式
GB/T 7714
Zhang, Xiao-Ou,Dong, Rui,Zhang, Yang,et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs[J]. GENOME RESEARCH,2016,26(9):1277-1287.
APA Zhang, Xiao-Ou.,Dong, Rui.,Zhang, Yang.,Zhang, Jia-Lin.,Luo, Zheng.,...&Yang, Li.(2016).Diverse alternative back-splicing and alternative splicing landscape of circular RNAs.GENOME RESEARCH,26(9),1277-1287.
MLA Zhang, Xiao-Ou,et al."Diverse alternative back-splicing and alternative splicing landscape of circular RNAs".GENOME RESEARCH 26.9(2016):1277-1287.
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