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

ABSTRACT: 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 treatment with 5’-end enriched and full-length transcriptome sequencing of DCP2-deficinet 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 both wild type and dcp2 seedlings. Most caps localized near annotated transcription start sites, validating the accuracy of our approach. Loss of DCP2 led to a substantial accumulation of capped mRNAs, including 275 capped transcripts originating from previously unannotated loci. It also increased prevalence of multi-capped genes highlighting the role of DCP2-meidated decapping in removing unwanted transcripts. Integration of these data with degradome resources revealed that targets of co-translational and cytosolic XRN4-dependent decay, as well as of nonsense-mediated decay, were enriched among capped mRNAs specifically accumulated in dcp2. These findings support the impression that mRNA degradation in these decay pathways is mediated through decapping. In addition, this study provides valuable resource for transcript annotation and isoform-aware analysis of RNA turnover.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE315704 | GEO | 2026/08/19

REPOSITORIES: GEO