Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

Acera Mateos, P; Sethi, AJ; Ravindran, A; Srivastava, A; Woodward, K; Mahmud, S; Kanchi, M; Guarnacci, M; Xu, J; Yuen, ZWS; Zhou, Y; Sneddon, A; Hamilton, W; Gao, J; Starrs, LM; Hayashi, R; Wickramasinghe, V; Zarnack, K; Preiss, T; Burgio, G; Dehorter, N; Shirokikh, NE; Eyras, E

Author(s): Acera Mateos, P; Sethi, AJ; Ravindran, A; Srivastava, A; Woodward, K; Mahmud, S; Kanchi, M; Guarnacci, M; Xu, J; Yuen, ZWS; Zhou, Y; Sneddon, A; Hamilton, W; Gao, J; Starrs, LM; Hayashi, R; Wickramasinghe, V; Zarnack, K; Preiss, T; Burgio, G; Dehorter, N; Shirokikh, NE; Eyras, E;
Details: Publication Year 2024-05-09,Volume 15,Issue #1,Page 3899
Journal Title: Nature Communications
Publication Type: Research article
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.
Publisher: Springer Nature
Keywords: *Adenosine/analogs & derivatives/metabolism; *Transcriptome; *5-Methylcytosine/metabolism/analogs & derivatives; Humans; Methylation; *Sequence Analysis, RNA/methods; RNA Processing, Post-Transcriptional; RNA, Messenger/metabolism/genetics; RNA/metabolism/genetics
Department(s): Laboratory Research
Publisher's Version: https://doi.org/10.1038/s41467-024-47953-7
Open Access at Publisher's Site: https://doi.org/10.1038/s41467-024-47953-7
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2024-06-25 07:58:41

Last Modified: 2024-06-25 08:02:37