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bioRxiv · 10.64898/2026.03.04.709597

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

Shukla, N.·Schon, M. A.·Raxwal, V. K.·Nodine, M. D.·Riha, K.
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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-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 both wild type and dcp2 seedlings. Most caps were 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-mediated 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 suggest that mRNA degradation in these decay pathways is mediated through decapping. In addition, this study provides a valuable resource for transcript annotation and isoform-aware analysis of RNA turnover. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/709597v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@3569a2org.highwire.dtl.DTLVardef@aa2ca3org.highwire.dtl.DTLVardef@58a27forg.highwire.dtl.DTLVardef@1147350_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Shukla, N., Schon, M. A., Raxwal, V. K., Nodine, M. D., Riha, K.. 2026-03-06. Genome-wide mapping of DCP2-dependent 5' cap footprints in Arabidopsis thaliana. https://doi.org/10.64898/2026.03.04.709597

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