Identification of m6A and m5C RNA modifications at single-molecule resolution from Nanopore sequencing

  • The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.

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Author:Pablo Acera MateosORCiD, Aditya J. Sethi, Marco GuarnacciORCiD, Agin RavindranORCiD, Akanksha SrivastavaORCiD, Jiajia Xu, Katrina Woodward, William Hamilton, Jing Gao, Lora M. StarrsORCiD, Gaetan BurgioORCiD, Rippei HayashiORCiD, Vihandha WickramasingheORCiD, Nathalie DehorterORCiD, Thomas PreissORCiDGND, Nikolay ShirokikhORCiD, Eduardo Angel Eyras JiménezORCiDGND
URN:urn:nbn:de:hebis:30:3-830373
URL:https://www.biorxiv.org/content/10.1101/2022.03.14.484124v1
DOI:https://doi.org/10.1101/2022.03.14.484124
Parent Title (English):bioRxiv
Publisher:bioRxiv
Document Type:Preprint
Language:English
Date of Publication (online):2022/03/16
Date of first Publication:2022/03/16
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2024/04/30
Issue:2022.03.14.484124 Version 1
Edition:Version 1
Page Number:25
HeBIS-PPN:518934055
Institutes:Biowissenschaften / Biowissenschaften
Fachübergreifende Einrichtungen / Buchmann Institut für Molekulare Lebenswissenschaften (BMLS)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International