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Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution.

Yunyi Gao1, Jingyu Hou1,2, Saisai Wei3

  • 1Department of Clinical Laboratory of Sir Run-Run Shaw Hospital, and School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China.

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|March 12, 2025
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Summary
This summary is machine-generated.

Researchers mapped 3-Methylcytidine (m3C) modifications in the human transcriptome using m3C-IP-seq. This RNA modification is widespread in messenger RNAs (mRNAs) and linked to mRNA degradation.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • RNA Biology

Background:

  • 3-Methylcytidine (m3C) is a common modification in transfer RNAs (tRNAs).
  • The presence and function of m3C in eukaryotic messenger RNAs (mRNAs) were previously unknown.
  • Understanding m3C distribution and formation in mRNAs is crucial for RNA metabolism studies.

Purpose of the Study:

  • To develop a novel method for profiling m3C modifications in the transcriptome.
  • To investigate the distribution and formation of m3C in eukaryotic mRNAs and long noncoding RNAs (lncRNAs).
  • To explore the functional implications of m3C methylation in RNA metabolism.

Main Methods:

  • Developed m3C immunoprecipitation and sequencing (m3C-IP-seq) for single-nucleotide resolution profiling.
  • Utilized antibody enrichment to capture m3C-modified RNA molecules.
  • Analyzed m3C sites in tRNAs, mRNAs, and lncRNAs.

Main Results:

  • m3C-IP-seq successfully identified m3C modifications in 12 cytoplasmic and 2 mitochondrial tRNA isoacceptors.
  • Comprehensive profiling revealed widespread m3C sites in mRNAs and lncRNAs, dependent on a nuclear METTL8 isoform.
  • A significant number of m3C sites were found in mRNA 3' untranslated regions (3' UTRs) and correlated with mRNA degradation.
  • m3C methylation levels were observed to be dynamic and responsive to hypoxic conditions.

Conclusions:

  • Demonstrated the widespread presence of m3C modification across the human transcriptome.
  • Established m3C-IP-seq as a powerful tool for mapping RNA modifications.
  • Provided a valuable resource for future functional studies on m3C-mediated RNA metabolism and its regulation.