Nucleolar endonuclease MBLAC2 orchestrates co-transcriptional ribosomal RNA processing and global transcriptional output

The metallo-β-lactamase (MBL)-domain superfamily includes multiple nucleases that process distinct transcript classes. We show that human MBLAC2 acts as a ribosomal (r)RNA quality control factor, being nucleolar specific, chromatin-associated and required for co-transcriptional pre-rRNA processing. Notably MBLAC2 is functionally distinct from other MBL containing proteins, being required for maintenance of nucleolar architecture, cell cycle progression and proliferative fitness. Selective MBLAC2 depletion causes accumulation of pre-rRNA intermediates that lead to perturbed RNA polymerase (Pol) I-associated RNA homeostasis and nucleolar stress signalling. Nascent RNA profiling with long-read nanopore sequencing reveals extended and aberrant pre-rRNA species, consistent with defective processing and transcript release. Remarkably disruption of rRNA processing reduces global Pol II transcriptional output, even though the Pol II nuclear distribution remains unchanged across genomic compartments. Altogether, we define MBLAC2 as the nucleolar branch of an MBL-domain RNA surveillance network that couples rRNA quality control with transcriptional homeostasis.