CHEUI: transcriptome-wide identification of m6A and m5C RNA modifications at single-molecule resolution

The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. However, the transcriptome-wide identification of multiple modification types in individual RNAs remains challenging. We present CHEUI, a new method that 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, using nanopore signals. CHEUI processes observed and expected signals with convolutional neural networks to achieve high single-molecule accuracy and outperform other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI unlocks the capability of studying links between multiple RNA modifications and phenotypes and is adaptable to other modifications, making it a versatile RNA technology for the discovery of new epitranscriptome functions.CHEUI is made available under an Academic Public License (please see license at https://github.com/comprna/CHEUI-public