GSE118215
Widespread EJC footprints in the RNA degradome mark mRNA degradation before steady-state translation
Exon junction complexes (EJCs) are deposited to mRNAs during splicing and displaced from mRNAs by ribosomes in the pioneer round of translation. The understanding of EJC-bound mRNA degradation before steady-state translation has been limited to nonsense-mediated mRNA decay (NMD) due to a lack of suitable methodologies. Here, we show that RNA degradome data of Arabidopsis, rice, worm and human cells all exhibit a predominant accumulation of 5' monophosphate (5'P) ends in the canonical EJC region. Inhibition of 5'-3' exoribonuclease activity and overexpression of an EJC disassembly factor in Arabidopsis reduced the 5'P ends accumulating in the EJC region, supporting the notion that these 5'P ends are in vivo EJC footprints. Hundreds of Arabidopsis NMD targets possess evident EJC footprints, validating their degradation during the pioneer round of translation. In addition to premature termination codons, plant microRNAs can also direct the degradation of EJC-bound mRNAs. However, the production of EJC footprints from NMD but not microRNA targets is dependent on an NMD factor, SMG7. Together, our finding demonstrating in vivo EJC footprinting unravels the composition of the RNA degradome, and provides a new avenue for studying NMD and other mechanisms, such as microRNAs, targeting EJC-bound mRNAs for degradation before steady-state translation. Overall design: Profiling 5' ends of RNA degradation intermediates in Arabidopsis thaliana by parallel analysis of RNA ends (PARE)