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High-stoichiometry m6A sites are evolutionarily conserved.

Hamish Nc Pike1, Schraga Schwartz2

  • 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.

RNA (New York, N.Y.)
|December 18, 2025
PubMed
Summary
This summary is machine-generated.

N6-methyladenosine (m6A) modification sites are functionally important, not neutral byproducts. Highly methylated m6A sites show significant evolutionary conservation, indicating purifying selection and a role in gene regulation.

Keywords:
RNA methylationepitranscriptomeevolutionphylogenetic analysispurifying selection

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genomics

Background:

  • N6-methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes.
  • The functional significance and evolutionary conservation of m6A sites remain debated, with conflicting previous findings.

Purpose of the Study:

  • To definitively determine if m6A sites are under evolutionary selection.
  • To reconcile inconsistent results from previous evolutionary analyses of m6A sites.

Main Methods:

  • Development of novel motif-level conservation metrics incorporating m6A biogenesis.
  • Analysis of ~500,000 m6A sites using quantitative, single-nucleotide resolution measurements across 447 mammalian species.
  • Controlling for proximity to exon-junctions to isolate selection pressures on m6A sites.

Main Results:

  • A clear, dose-dependent relationship between m6A stoichiometry and evolutionary conservation was observed in both coding sequences (CDS) and untranslated regions (UTRs).
  • Highly methylated m6A sites (>60%) displayed significantly greater conservation than lowly methylated sites.
  • The observed conservation provides definitive evidence for purifying selection acting on m6A sites.

Conclusions:

  • Highly m6A-modified sites are functionally important for gene regulation, challenging the notion of neutral byproduct.
  • Established a methodological framework for evolutionary analysis of RNA modifications using quantitative data and phylogenetic sampling.