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

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 () and Matthew D. Weitzman ()
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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
Nandan S. Gokhale: Duke University Medical Center
Jonathan S. Abebe: New York University School of Medicine
Ashley N. Fera: The Children’s Hospital of Philadelphia
Christopher E. Mason: Weill Cornell Medicine
Stacy M. Horner: 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

Nature Communications, 2020, vol. 11, issue 1, 1-17

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19787-6

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