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

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. Subcellular RNA fractionation coupled with global mapping of uncapped and cleaved transcripts (subcellular GMUCT) to produce nucleoplasmic and cytoplasmic RNA-enriched degradomes was performed on early-stage flower buds of Arabidopsis WT and abh1 (abh1-8; Gregory et al 2008, Developmental Cell) plants in biological triplicate. In parallel, strand-specific mRNA sequencing was also performed on bulk RNA from WT and abh1 flower buds in biological triplicate.