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) is known to degrade EJC-bound mRNA, but the lack of a suitable methodology has prevented the identification of other potential degradation pathways. Here, we show that the RNA degradomes of Arabidopsis, rice, worm and human cells all exhibit an enrichment of 5' monophosphate (5'P) ends of degradation intermediates that map to the canonical EJC region. Inhibition of 5'-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 is dependent on an NMD factor, SMG7. 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。已知无义介导的mRNA衰变（NMD）可以降解EJC结合的mRNA，但是缺乏合适的方法已无法识别其他潜在的降解途径。在这里，我们显示了拟南芥，水稻，蠕虫和人类细胞的RNA降解组均表现出丰富的5'一磷酸（5'P）降解中间产物末端，这些末端映射到规范的EJC区。抑制拟南芥中5'-3'外切核糖核酸酶的活性和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足迹的观点。数百个拟南芥NMD目标拥有明显的EJC足迹，在翻译的先驱阶段验证他们的降级。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，由NMD而非microRNA靶产生EJC足迹的过程取决于NMD因子SMG7。总之，我们的结果证明了拟南芥中体内EJC的足迹揭示了RNA降解组的组成，并为研究NMD和其他靶向EJC结合的mRNA进行稳态翻译之前降解的机制提供了新途径。