Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis

Messenger RNAs transmit the genetic information that dictates protein production, and are a nexus for numerous pathways that regulate gene expression. The prevailing view of canonical mRNA decay is that it is mediated by deadenylation and decapping followed by exonucleolysis from the 3′ and 5′ ends. By developing Akron-Seq, a novel approach that captures native 3′ and 5′ ends of capped and polyadenylated RNAs respectively, we show that canonical human mRNAs are subject to repeated, cotranslational, ribosome-phased, endonucleolytic cuts at the exit site of the mRNA ribosome channel, in a process that we term ribothrypsis. We uncover RNA G-quadruplexes among likely ribothrypsis triggers, and show that ribothrypsis is a conserved process. Strikingly, we find that mRNA fragments are prevalent in living cells with important implications for the interpretation of experiments, such as RNA-Seq, that rely on the assumption that mRNAs exist largely as full-length molecules in vivo.