Potential G-Quadruplex Forming Sequences and N(6)-Methyladenosine Colocalize at Human Pre-mRNA Intron Splice Sites

[Image: see text] Maturation of mRNA in humans involves modifying the 5′ and 3′ ends, splicing introns, and installing epitranscriptomic modifications that are essential for mRNA biogenesis. With respect to epitranscriptomic modifications, they are usually installed in specific consensus motifs, although not all sequences are modified suggesting a secondary structural component to site selection. Using bioinformatic analysis of published data, we identify in human mature-mRNA that potential RNA G-quadruplex (rG4) sequences colocalize with the epitranscriptomic modifications N(6)-methyladenosine (m(6)A), pseudouridine (Ψ), and inosine (I). Using the only available pre-mRNA data sets from the literature, we demonstrate colocalization of potential rG4s and m(6)A was greatest overall and occurred in introns near 5′ and 3′ splice sites. The loop lengths and sequence context of the m(6)A-bearing potential rG4s exhibited short loops most commonly comprised of single A nucleotides. This observation is consistent with a literature report of intronic m(6)A found in SAG (S = C or G) consensus motifs that are also recognized by splicing factors. The localization of m(6)A and potential rG4s in pre-mRNA at intron splice junctions suggests that these features could function together in alternative splicing. A similar analysis for potential rG4s around sites of Ψ installation or A-to-I editing in mRNA also found a colocalization; however, the frequency was less than that observed with m(6)A. These bioinformatic analyses guide a discussion of future experiments to understand how noncanonical rG4 structures may collaborate with epitranscriptomic modifications in the human cellular context to impact cellular phenotype.