A potentially abundant junctional RNA motif stabilized by m(6)A and Mg(2+)

N(6)-Methyladenosine (m(6)A) is an abundant post-transcriptional RNA modification that influences multiple aspects of gene expression. In addition to recruiting proteins, m(6)A can modulate RNA function by destabilizing base pairing. Here, we show that when neighbored by a 5ʹ bulge, m(6)A stabilizes m(6)A–U base pairs, and global RNA structure by ~1 kcal mol(−1). The bulge most likely provides the flexibility needed to allow optimal stacking between the methyl group and 3ʹ neighbor through a conformation that is stabilized by Mg(2+). A bias toward this motif can help explain the global impact of methylation on RNA structure in transcriptome-wide studies. While m(6)A embedded in duplex RNA is poorly recognized by the YTH domain reader protein and m(6)A antibodies, both readily recognize m(6)A in this newly identified motif. The results uncover potentially abundant and functional m(6)A motifs that can modulate the epitranscriptomic structure landscape with important implications for the interpretation of transcriptome-wide data.