The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs

Abstract RNA cleavage is essential for processing and regulating all classes of RNA. Current methods profiling genome-wide RNA cleavage are biased towards cytoplasmic events and ignore compartmentalized differences. Here, we couple subcellular RNA fractionation with degradome profiling to detect genome-wide nucleoplasm- and cytoplasm-enriched RNA cleavage in Arabidopsis thaliana. While messenger RNA (mRNA) cleavage dominated cytoplasmic fractions, we captured a diverse array of nucleoplasm-enriched RNA cleavage events. These included pre-mRNA cleavage and noncoding RNA processing, including for microRNAs, ribosomal RNAs, small nucleolar RNAs, enhancer-associated RNAs, and retrotransposon-derived RNA. Furthermore, our findings suggest that CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1 regulates mRNA surveillance within the perinuclear cytoplasm during the pioneer round of translation. Our data also emphasized its role in stabilizing nucleoplasmic RNAs (e.g. mRNA-associated antisense RNAs) and affecting cytoplasmic mRNA cleavage. Overall, our results highlight the diversity of compartmentalized RNA cleavage and reveal that the nuclear cap-binding complex has numerous functions in subcellular RNA processing and surveillance.

• Publication year

  2026

• Venue

  Nucleic Acids Research

• Publication date

  2026-01-05

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/nar/gkaf1467PMID 41495891PMCID 12774651
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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