N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions

RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBM)(1-3). However, RBMs can be buried within their local RNA structures(4-7), thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA(8-19), can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs(15), but how m(6)A achieves wide-ranging physiological significance needs further exploration. Here we show that m(6)A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism “m(6)A-switch”. We found that m(6)A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (hnRNP C), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing(20-24). Combining PAR-CLIP and m(6)A/MeRIP approaches enabled us to identify 39,060 m(6)A-switches among hnRNP C binding sites; and global m(6)A reduction decreased hnRNP C binding at 2,798 high confidence m(6)A-switches. We determined that these m(6)A-switch-regulated hnRNP C binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m(6)A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m(6)A-dependent RNA structural remodeling, and provide a new direction for investigating RNA-modification-coded cellular biology.