N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

N-6-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m(6)A modification to control mRNA maturation, translation and decay. m(6)A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m(6)A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m(6)A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro. The Arg-Gly-Gly repeats within the low-complexity region are required for binding to the RNA motif exposed by m(6)A methylation. We identified 13,191 m(6)A sites in the transcriptome that regulate RNA-HNRNPG interaction and thereby alter the expression and alternative splicing pattern of target mRNAs. Low-complexity regions are pervasive among mRNA binding proteins. Our results show that m(6)A-dependent RNA structural alterations can promote direct binding of m(6)A-modified RNAs to low-complexity regions in RNA binding proteins.