A multi-transcriptomics approach reveals the coordinated action of the endoribonuclease DNE1 and the decapping machinery in orchestrating mRNA decay

Decapping is a crucial step of mRNA degradation in eucaryotes and requires the formation of the holoenzyme complex between the decapping enzyme DCP2 and the decapping enhancer DCP1. In Arabidopsis, we recently identified DNE1, a NYN domain endoribonuclease, as a direct protein partner of DCP1. The function of both DNE1 and decapping are necessary to maintain phyllotaxis, the regularity of organ emergence in the apex. In this study we combined in vivo mRNA editing, RNA degradome, transcriptomics and small RNA-omics to identify targets of DNE1 and study how DNE1 and DCP2 cooperate in controlling mRNA fate. Our data reveal that DNE1 mainly contacts and cleaves mRNAs in the CDS and has sequence cleavage preferences. We found that DNE1 targets are also degraded through decapping, and that both RNA degradation pathways influence the production of mRNA-derived siRNAs. Finally, we detected mRNA features enriched in DNE1 targets including RNA G-quadruplexes and translated upstream-ORFs. Combining these four complementary high-throughput sequencing strategies greatly expands the range of DNE1 targets and allowed us to build a conceptual framework describing the influence of DNE1 and decapping on mRNA fate. These data will be crucial to unveil the specificity of DNE1 action and understand its importance for developmental patterning.