A potentially abundant junctional RNA motif stabilized by mA and Mg.

N-Methyladenosine (mA) is an abundant post-transcriptional RNA modification that influences multiple aspects of gene expression. In addition to recruiting proteins, mA can modulate RNA function by destabilizing base pairing. Here, we show that when neighbored by a 5' bulge, mA stabilizes mA-U base pairs, and global RNA structure by ~1 kcal mol. The bulge most likely provides the flexibility needed to allow optimal stacking between the methyl group and 3' neighbor through a conformation that is stabilized by Mg. A bias toward this motif can help explain the global impact of methylation on RNA structure in transcriptome-wide studies. While mA embedded in duplex RNA is poorly recognized by the YTH domain reader protein and mA antibodies, both readily recognize mA in this newly identified motif. The results uncover potentially abundant and functional mA motifs that can modulate the epitranscriptomic structure landscape with important implications for the interpretation of transcriptome-wide data.