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

ABSTRACT: RNA cleavage is essential for processing and regulating all classes of RNA. Current methods to profile 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 nucleoplasmic and cytoplasmic RNA cleavage in Arabidopsis thaliana. While mRNA cleavage dominated cytoplasmic fractions, we captured a diverse array of nucleoplasm-enriched RNA cleavage events. This included pre-mRNA cleavage and non-coding RNA processing, including microRNAs, ribosomal RNAs, small nucleolar RNAs, enhancer-associated RNAs, and retrotransposon-derived RNAs. Furthermore, we revealed that CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1 regulates RNA surveillance at the nuclear periphery during the pioneer round of translation. Our data also emphasized its role in stabilizing nucleoplasmic RNAs (e.g. mRNA-associated anti-sense 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE291993 | GEO | 2025/05/09

REPOSITORIES: GEO

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