Exon junction complexes (EJCs) are deposited on mRNAs during splicing and displaced by ribosomes during the pioneer round of translation. Nonsense-mediated mRNA decay (NMD) degrades EJC-bound mRNA, but the lack of suitable methodology has prevented the identification of other degradation pathways. Here, we show that the RNA degradomes of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), worm (Caenorhabditis elegans), and human (Homo sapiens) cells exhibit an enrichment of 5' monophosphate (5'P) ends of degradation intermediates that map to the canonical EJC region. Inhibition of 5' to 3' exoribonuclease activity and overexpression of an EJC disassembly factor in Arabidopsis reduced the accumulation of these 5'P ends, supporting the notion that they 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 requires the NMD factor SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN7. Together, our results demonstrating in vivo EJC footprinting in Arabidopsis unravel the composition of the RNA degradome and provide a new avenue for studying NMD and other mechanisms targeting EJC-bound mRNAs for degradation before steady state translation.

外显子连接复合物（EJC）在剪接过程中沉积在mRNA上，并在翻译的先驱阶段被核糖体置换。废话介导的mRNA降解（NMD）降解EJC绑定的mRNA，但缺乏合适的方法已阻止了其他降解途径的鉴定。在这里，我们显示了拟南芥（Arabidopsis thaliana），水稻（Oryza sativa），蠕虫（Caenorhabditis elegans）和人（Homo sapiens）的RNA降解组）细胞的降解中间体的5'单磷酸酯（5'P）末端富集，并映射到规范的EJC区域。抑制拟南芥中5'至3'外切核糖核酸酶的活性以及EJC分解因子的过表达减少了这些5'P末端的积累，支持了它们是体内EJC足迹的观念。数以百计的拟南芥NMD靶标​​具有明显的EJC足迹，验证了它们在翻译的先驱者过程中的降解。除过早终止密码子外，植物微RNA还可以指导EJC结合的mRNA的降解。但是，要从NMD产生EJC足迹，而不是从microRNA靶产生EJC足迹，就需要NMD因子抑制子，并具有对生殖器蛋白质7的形态学影响。一起，