Mechanistic studies on HNRNPA2B1 suggest binding but not selective recognition of m⁶A

HNRNPA2B1 contains two RRM domains and has been investigated for its possible role as an m⁶A reader protein. The targetome of HNRNPA2B1 was shown to overlap with the m⁶A methylation motif, but further investigations of its binding affinity for m⁶A-containing RNAs have been less clear on the relative selectivity of HNRNPA2B1 for methylated transcripts. Our computational and experimental studies depict that when an m⁶A modification is positioned in between the two RRM domains, and in the context of the GGACU motif that can be written by methyltransferases, the binding affinity is nearly identical and slightly less favourable to the unmodified sequence. Our study suggests that HNRNPA2B1 is not a (selective) reader but has high affinity for m⁶A in a sequence-dependent manner. This can be attributed to the strong interactions conferred by AGG and UAG motifs rather than adenine or m⁶A in the GGACU motif which are predicted to interact weakly, intercalating between the two RRMs or positioned outwards. Overall, our findings highlight the higher complexity of HNRNPA2B1 and RRM recognition properties compared to well-studied YTH domains in the recognition of m⁶A, as well as modified and unmodified sequences.