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CompasSeq: epitranscriptome-wide percentage assessment of metabolite-capped RNA at the transcript resolution
Yuanbo Liu1,2, Dean Li1,2, Xueting Wang1,2
1Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
Nature Communications
|July 19, 2025
Summary
Nucleotide metabolites like NAD can initiate transcription, forming noncanonical initiating nucleotide-RNAs (NCIN-RNAs). A new platform, CompasSeq, quantifies these NCIN-RNAs and their ratios with standard caps across the epitranscriptome.
Area of Science:
- Molecular Biology
- RNA Biology
- Genomics
Background:
- Nucleotide metabolites, such as NAD, can function as noncanonical initiating nucleotides (NCIN).
- This process yields NCIN-capped RNAs (NCIN-RNAs), representing a distinct RNA modification.
- Existing methods for profiling NCIN-RNAs are limited and lack epitranscriptome-wide quantitative capabilities.
Purpose of the Study:
- To develop a comprehensive analytical platform for quantifying NCIN-RNAs.
- To enable transcript-resolution assessment of NCIN-RNA capping.
- To investigate the dynamics and functional implications of NCIN-RNA capping.
Main Methods:
- Development of the CompasSeq analytical platform, integrating experimental and computational approaches.
- Utilizing selective enzymatic reactions for NCIN-RNA capture and spike-ins for stoichiometry analysis.
- Employing a quantitative exoribonuclease reduction assay for orthogonal validation of NCIN-RNAs and capping ratios.
Main Results:
- CompasSeq enables comprehensive, quantitative assessment of NCIN-RNAs at the transcript level.
- Quantification of previously uncharacterized NCIN capping percentages in mouse liver.
- Illustration of age-associated dynamics in NCIN capping and identification of gene-specific dichotomies related to aging pathways.
Conclusions:
- CompasSeq provides a robust solution for analyzing NCIN-RNA abundance and capping stoichiometry.
- The study reveals novel insights into the prevalence and age-related changes of NCIN-RNA capping.
- This work facilitates future functional studies of NCIN-RNAs in biological processes, particularly aging.
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