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Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline

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Epitranscriptomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1870))

Abstract

Circular RNAs (circRNAs) derived from back-spliced exons were sporadically identified about 25 years ago, and have been recently re-discovered genome-wide across different species. Interestingly, one gene locus can generate multiple circRNAs through alternative back-splicing and/or alternative splicing, thus expanding our understanding on the diversity and complexity of transcriptomes. Precise annotation of circRNAs with their alternative back-splicing and alternative splicing events is the basis for the functional characterization of different categories of circRNAs. Here we describe a step-by-step computational scheme to annotate circRNAs from publicly available RNA sequencing datasets with the CIRCexplorer2 pipeline.

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Authors and Affiliations

  1. CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China

    Rui Dong, Xu-Kai Ma & Li Yang

  2. State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China

    Ling-Ling Chen

Authors
  1. Rui Dong
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  2. Xu-Kai Ma
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  3. Ling-Ling Chen
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  4. Li Yang
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Corresponding author

Correspondence to Li Yang .

Editor information

Editors and Affiliations

  1. Department of Pathology, Yale University School of Medicine, New Haven, CT, USA

    Narendra Wajapeyee

  2. Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA

    Romi Gupta

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Dong, R., Ma, XK., Chen, LL., Yang, L. (2019). Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline. In: Wajapeyee, N., Gupta, R. (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8808-2_10

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  • DOI: https://doi.org/10.1007/978-1-4939-8808-2_10

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8807-5

  • Online ISBN: 978-1-4939-8808-2

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