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Comprehensive identification of internal structure and alternative splicing events in circular RNAs

Author

Listed:
  • Yuan Gao

    (Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jinfeng Wang

    (Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences)

  • Yi Zheng

    (Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jinyang Zhang

    (Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Shuai Chen

    (Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Fangqing Zhao

    (Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences)

Abstract

Although previous studies demonstrated circular RNAs (circRNAs) does not exclusively comprise mRNA exons, no study has extensively explored their internal structure. By combining an algorithm with long-read sequencing data and experimental validation, we, for the first time, comprehensively investigate internal components of circRNAs in 10 human cell lines and 62 fruit fly samples, and reveal the prevalence of alternative splicing (AS) events within circRNAs. Significantly, a large proportion of circRNA AS exons can hardly be detected in mRNAs and are enriched with binding sites of distinct splicing factors from those enriched in mRNA exons. We find that AS events in circRNAs have a preference towards nucleus localization and exhibit tissue- and developmental stage-specific expression patterns. This study suggests an independent regulation on the biogenesis or decay of AS events in circRNAs and the identified circular AS isoforms provide targets for future studies on circRNA formation and function.

Suggested Citation

  • Yuan Gao & Jinfeng Wang & Yi Zheng & Jinyang Zhang & Shuai Chen & Fangqing Zhao, 2016. "Comprehensive identification of internal structure and alternative splicing events in circular RNAs," Nature Communications, Nature, vol. 7(1), pages 1-13, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12060
    DOI: 10.1038/ncomms12060
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    Cited by:

    1. Wanying Wu & Jinyang Zhang & Xiaofei Cao & Zhengyi Cai & Fangqing Zhao, 2022. "Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Xiaojuan Fan & Yun Yang & Chuyun Chen & Zefeng Wang, 2022. "Pervasive translation of circular RNAs driven by short IRES-like elements," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

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