NVL2-interacting protein CWF19L2 is required for debranching of intron-derived lariat RNAs

NVL2 is a chaperone-like AAA-ATPase involved in pre-ribosomal particles maturation and pre-rRNA processing during ribosome biogenesis. Here, we identified a nuclear protein CWF19L2, with C-terminal homology to yeast spliceosomal Cwf19 and mammalian CWF19L1, as a novel NVL2-interacting protein. Cryo-EM-based structural studies have indicated the loading of CWF19L2 into the intron lariat spliceosome (ILS) at the late-stage spliceosome cycle. Co-immunoprecipitation analysis gave a consistent result, showing interactions of CWF19L2 with the ILS components, lariat RNA debranching enzyme DBR1, and NVL2-interacting exonuclease complex MTR4-RNA exosome in cells. RNA debranching assays using a pre-mRNA splicing reporter minigene or detection of endogenous lariat RNA using reverse transcription PCR showed CWF19L2 is required for debranching as potently as DBR1. Super-resolution immunofluorescence imaging showed distinct but closely associated localization of CWF19L2 to DBR1 and CWF19L1. These results suggest a critical role for CWF19L2 in debranching lariat RNAs for clearance of intron-derived RNAs from the nucleus.