Nucleolar URB1 ensures 3' ETS rRNA removal to prevent exosome-surveillance
The nucleolus is the most prominent membrane-less condensate in the nucleus which comprises hundreds of proteins that play distinct roles in rapid ribosomal RNA (rRNA) transcription and efficient processing within Fibrillar Center/Dense Fibrillar Component (FC/DFC) units and ribosome assembly in Granular Component (GC)1. What the precise localization of most nucleolar proteins is and whether their specific localization contributes to the radial flux of pre-rRNA processing have remained elusive, owing to insufficient image resolution2-5. How these nucleolar proteins are functionally coordinated with the step-wise pre-rRNA processing requires a thorough investigation. Here, we screened 200 nucleolar candidate proteins with high-resolution, live-cell microscopy, and identified 12 proteins enriched to the periphery of DFC (PDFC). Among these proteins, URB1 (unhealthy ribosome biogenesis 1) is a static, nucleolar protein that ensures 3' end pre-rRNA anchoring and folding for U8 snoRNA recognition and subsequent 3' ETS (external transcribed spacer) removal at the DFC/PDFC boundary. URB1 depletion leads to disrupted PDFC, uncontrolled pre-rRNA movement, altered pre-rRNA conformation and 3' ETS retention. These aberrant 3' ETS-attached pre-rRNA intermediates activate exosome-dependent nucleolar surveillance, resulting in decreased 28S rRNA production, head malformations in zebrafish and retarded embryonic development in mice. Together, this study provides new insight into functional sub-nucleolar organization and identifies a physiologically essential step in rRNA maturation that requires the immobile protein URB1 in the phase-separated nucleolus.