Widespread Exon Junction Complex Footprints in the RNA Degradome Mark mRNA Degradation before Steady State Translation

The RNA degradome is composed of assorted RNA degradation intermediates derived from diverse RNA degradation pathways. However, meanings behind different degradation intermediates remain largely obscure. This is the first report that in vivo exon junction complex (EJC) footprints are present in the degradomes of Arabidopsis, rice, worm and human cells. EJCs are deposited on mRNAs during splicing and displaced by ribosomes in the pioneer round of translation. If spliced RNAs are degraded before completing the pioneer round of translation, EJCs can block 5’ to 3’ RNA decay, leading the decay intermediates with 5’ ends protected by EJCs, the EJC footprints. Hence, EJC footprints can serve as markers for the mRNA degradation before steady-state translation. The analysis of EJC footprints showed that the mRNA degradation before steady-state translation occurs on hundreds of putative nonsense-mediated mRNA decay targets and some microRNA targets in plants. The finding brings new insight and tools into the study of when RNA degradation occurs.