UPF1 promotes rapid degradation of m(6)A-containing RNAs

Abstract

N-6-methyladenosine (m(6)A) is the most prevalent internal modification in eukaryotic mRNAs and affects RNA processing and metabolism. When YTHDF2, an m(6)A-recognizing protein, binds to m(6)A, it facilitates the destabilization of m(6)A-containing RNAs (m(6)A RNAs). Here, we demonstrate that upstream frameshift 1 (UPF1), a key factor for nonsense-mediated mRNA decay, interacts with YTHDF2, thereby triggering rapid degradation of m(6)A RNAs. The UPF1-mediated m(6)A RNA degradation depends on a specific interaction between UPF1 and N-terminal residues 101-168 of YTHDF2. UPF1 ATPase/helicase activities, and UPF1 interaction with proline-rich nuclear receptor coactivator 2 (PNRC2), a decapping-promoting factor preferentially involved in nonsense-mediated mRNA decay. Furthermore, transcriptome-wide analyses show that YTHDF2-bound mRNAs that are not substrates for HRSP12-RNase P/MRP-mediated endoribonucleolytic cleavage are destabilized with a higher dependency on UPF1. Collectively, our data indicate dynamic and multilayered regulation of the stability of m(6)A RNAs and highlight the multifaceted role of UPF1 in mRNA decay.