The frequency and fitness of m6A-associated variants may be modulated by thermodynamic stability of the overlapping G-quadruplex

Background: Post-transcriptional modifications like m6A, and secondary structures like G-quadruplex (G4), play an important role in RNA processing. Despite an emerging number of studies focusing on m6A and G4 separately, there are less studies about their synergy. Since m6A is known to be enzymatically created in DRACH-motif, and genetic variants may create a novel DRACH-motif or abolish a pre-existing DRACH-motif, we can suppose that the variants may affect gene product level through modulating m6A-G4 colocalization, which consequently may affect fitness and change allele frequency. To test this hypothesis, rare and common variants in selected human genes were investigated in terms of their effect on m6A-G4 colocalization. Methods: : Genomic sequences and variant features were fetched from GRCh37/hg19 and Biomart-Ensembl databases, respectively. Genomic coordinates of experimentally identified G4 sequences were yielded from two studies. Counting the number of putative motifs and statistical analysis were performed with appropriate libraries of Python3.7. Results: : Common variants creating novel m6A-motif were found more frequently inside than outside G4, and displayed unequal distribution throughout pre-mRNA. Unequal distribution of m6A-creating variants seemed to be related to their effect on thermodynamic stability of the overlapping-G4. Conclusions: : Selective m6A-G4 colocalization suggests that m6A-motifs are favorable when overlapping with G4. Besides, thermodynamic stability may lead to unequal distribution of m6A-G4 colocalization, favorable in 5-prime-side, but not in 3-prime-side. We can conclude that the fitness, and consequently frequency of an m6A-creating variant is prone to become higher or lower depending on its position and effect on the overlapping-G4 stability.