Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long.

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      Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE
    • Publication Information:
      Publication: New York Ny : Nature America Publishing
      Original Publication: New York, NY : Nature Pub. Co., [1996-
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    • Abstract:
      Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs. Here we describe a protocol for enrichment and full-length sequencing of circRNA isoforms using nanopore technology. Circular reverse transcription and size selection achieves a 20-fold higher enrichment of circRNAs from total RNA compared to previous methods. We developed an algorithm, called circRNA identifier using long-read sequencing data (CIRI-long), to reconstruct the sequence of circRNAs. The workflow was validated with simulated data and by comparison to Illumina sequencing as well as quantitative real-time RT-PCR. We used CIRI-long to analyze adult mouse brain samples and systematically profile circRNAs, including mitochondria-derived and transcriptional read-through circRNAs. We identified a new type of intronic self-ligated circRNA that exhibits special splicing and expression patterns. Our method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length circRNA sequences.
      (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc. part of Springer Nature.)
    • Comments:
      Erratum in: Nat Biotechnol. 2021 Apr 30;:. (PMID: 33941933)
      Comment in: Nat Biotechnol. 2021 Jul;39(7):811-812. (PMID: 33948001)
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    • Accession Number:
      0 (RNA Isoforms)
      0 (RNA, Circular)
    • Publication Date:
      Date Created: 20210312 Date Completed: 20210920 Latest Revision: 20230411
    • Publication Date:
      20231215
    • Accession Number:
      10.1038/s41587-021-00842-6
    • Accession Number:
      33707777