2015 | Nian Liu, Qing Dai, Guanqun Zheng, Chuan He, Marc Parisien, and Tao Pan
RNA-binding proteins regulate cellular biology by interacting with RNA-binding motifs (RBM). However, RBMs can be hidden within RNA structures, inhibiting interactions. N⁶-methyladenosine (m⁶A) is a major modification in eukaryotic mRNA that can be recognized by YTHDF2, affecting mRNA stability. This study shows that m⁶A regulates RNA-protein interactions by altering RNA structure, termed "m⁶A-switch." m⁶A modifies mRNA and lncRNA to facilitate binding of hnRNP C, an RNA-binding protein involved in pre-mRNA processing. Using PAR-CLIP and m⁶A/MeRIP, 39,060 m⁶A-switches were identified among hnRNP C binding sites. Global m⁶A reduction decreased hnRNP C binding at 2,798 sites. These switches regulate mRNA abundance and alternative splicing, demonstrating m⁶A's role in gene expression and RNA maturation. m⁶A-dependent RNA structural remodeling allows RNA-binding proteins to access their RBMs. This study highlights the regulatory role of m⁶A in RNA-protein interactions and provides new insights into RNA modification's role in cellular biology. The findings show that m⁶A can alter RNA structure to enhance protein binding, influencing gene expression and RNA processing. The study also reveals that m⁶A-switches regulate alternative splicing and intron exclusion, affecting mRNA maturation. Overall, m⁶A plays a critical role in RNA-protein interactions, gene expression, and RNA processing.RNA-binding proteins regulate cellular biology by interacting with RNA-binding motifs (RBM). However, RBMs can be hidden within RNA structures, inhibiting interactions. N⁶-methyladenosine (m⁶A) is a major modification in eukaryotic mRNA that can be recognized by YTHDF2, affecting mRNA stability. This study shows that m⁶A regulates RNA-protein interactions by altering RNA structure, termed "m⁶A-switch." m⁶A modifies mRNA and lncRNA to facilitate binding of hnRNP C, an RNA-binding protein involved in pre-mRNA processing. Using PAR-CLIP and m⁶A/MeRIP, 39,060 m⁶A-switches were identified among hnRNP C binding sites. Global m⁶A reduction decreased hnRNP C binding at 2,798 sites. These switches regulate mRNA abundance and alternative splicing, demonstrating m⁶A's role in gene expression and RNA maturation. m⁶A-dependent RNA structural remodeling allows RNA-binding proteins to access their RBMs. This study highlights the regulatory role of m⁶A in RNA-protein interactions and provides new insights into RNA modification's role in cellular biology. The findings show that m⁶A can alter RNA structure to enhance protein binding, influencing gene expression and RNA processing. The study also reveals that m⁶A-switches regulate alternative splicing and intron exclusion, affecting mRNA maturation. Overall, m⁶A plays a critical role in RNA-protein interactions, gene expression, and RNA processing.