Genome-wide mapping of DCP2-dependent 5′ cap footprints in Arabidopsis thaliana

Abstract

Messenger RNA (mRNA) decapping mediated by DCP2 is a key mechanism controlling RNA stability and gene expression in eukaryotes, including plants. Despite its central role in regulating plant development and stress responses, the repertoire of mRNA 5′ caps targeted by DCP2 remains undefined. Here, we combined in vitro decapping with 5′-end enriched and full-length transcriptome sequencing of DCP2-deficient mutants to comprehensively characterize the mRNA capping landscape in Arabidopsis thaliana. We mapped over 13 000 high-confidence capped transcripts at nucleotide resolution, revealing distinct 5′ cap signatures in wild-type and dcp2 seedlings. Most caps localized near annotated transcription start sites, validating the accuracy of our approach. Loss of DCP2 led to substantial expansion of detectable capped 5′-ends, including 275 caps from previously unannotated loci, and an increased prevalence of multi-capped genes, highlighting the role of DCP2-mediated decapping in removing unwanted transcripts. Integration with degradome resources revealed extensive convergence between DCP2-sensitive capped RNAs and substrates of co-translational, cytosolic XRN4-dependent decay, as well as nonsense-mediated decay pathways. Our results suggest that DCP2 shapes the steady-state 5′ cap landscape in vivo by limiting the accumulation of unstable and cryptic capped transcripts. Also, this study provides a valuable resource for transcript annotation and isoform-aware analysis of RNA turnover.