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Updated: Jun 26, 2025

Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis
Published on: May 14, 2020
Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA
P Acera Mateos1,2,3, A J Sethi1,2,3, A Ravindran1,2,3
1EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
Abstract:
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
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