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

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.