Most m6A RNA Modifications in Protein-Coding Regions Are Evolutionarily Unconserved and Likely Nonfunctional

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Epigenetics

Background:

• N6-methyladenosine (m6A) is the most common internal mRNA modification in eukaryotes.
• While m6A mapping and functions are increasingly understood, the functional relevance of most m6A sites remains unclear.

Purpose of the Study:

• To investigate the evolutionary conservation of m6A modifications in yeast and human protein-coding regions.
• To determine if m6A modifications are generally functional or nonadaptive.

Main Methods:

• Comparative analysis of evolutionary conservation between methylated and unmethylated adenosine sites in yeast and human genomes.
• Examination of single nucleotide polymorphism (SNP) density and frequency spectrum for m6A sites versus unmethylated sites.

Main Results:

• m6A sites showed no significant increase in conservation compared to unmethylated sites in yeast, and only slight conservation in mammals.
• No significant differences in SNP density or frequency spectrum were observed between m6A and unmethylated sites in either yeast or humans.
• Purifying selection acts on the methylation status of genes, not necessarily specific sites, for a minority of m6A-modified genes.
• A recent claim of positive selection for newly acquired human m6A modifications was invalidated.

Conclusions:

• The majority of m6A modifications in protein-coding regions are likely nonfunctional and nonadaptive, potentially due to off-target methyltransferase activity.
• A small subset of evolutionarily conserved m6A sites are likely functional and should be prioritized for future research.
• These findings impact the understanding of m6A's biological significance and other posttranscriptional modifications.