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Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

Author

Listed:
  • Alexander M. Price

    (The Children’s Hospital of Philadelphia)

  • Katharina E. Hayer

    (The Children’s Hospital of Philadelphia)

  • Alexa B. R. McIntyre

    (Weill Cornell Medicine
    Tri-Institutional Program in Computational Biology and Medicine
    University of Zurich)

  • Nandan S. Gokhale

    (Duke University Medical Center
    University of Washington)

  • Jonathan S. Abebe

    (New York University School of Medicine)

  • Ashley N. Fera

    (The Children’s Hospital of Philadelphia
    University of Maryland)

  • Christopher E. Mason

    (Weill Cornell Medicine
    Weill Cornell Medicine
    Weill Cornell Medicine
    Weill Cornell Medicine)

  • Stacy M. Horner

    (Duke University Medical Center
    Duke University Medical Center)

  • Angus C. Wilson

    (New York University School of Medicine)

  • Daniel P. Depledge

    (New York University School of Medicine)

  • Matthew D. Weitzman

    (The Children’s Hospital of Philadelphia
    University of Pennsylvania Perelman School of Medicine)

Abstract

Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.

Suggested Citation

  • Alexander M. Price & Katharina E. Hayer & Alexa B. R. McIntyre & Nandan S. Gokhale & Jonathan S. Abebe & Ashley N. Fera & Christopher E. Mason & Stacy M. Horner & Angus C. Wilson & Daniel P. Depledge , 2020. "Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing," Nature Communications, Nature, vol. 11(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19787-6
    DOI: 10.1038/s41467-020-19787-6
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    Cited by:

    1. P Acera Mateos & A J Sethi & A Ravindran & A Srivastava & K Woodward & S Mahmud & M Kanchi & M Guarnacci & J Xu & Z W S Yuen & Y Zhou & A Sneddon & W Hamilton & J Gao & L M Starrs & R Hayashi & V Wick, 2024. "Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Ziyuan Wang & Yinshan Fang & Ziyang Liu & Ning Hao & Hao Helen Zhang & Xiaoxiao Sun & Jianwen Que & Hongxu Ding, 2024. "Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Adrien Leger & Paulo P. Amaral & Luca Pandolfini & Charlotte Capitanchik & Federica Capraro & Valentina Miano & Valentina Migliori & Patrick Toolan-Kerr & Theodora Sideri & Anton J. Enright & Konstant, 2021. "RNA modifications detection by comparative Nanopore direct RNA sequencing," Nature Communications, Nature, vol. 12(1), pages 1-17, December.

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