Nucleolar Pol II interactome reveals TBPL1, PAF1, and Pol I at intergenic rDNA drive rRNA biogenesis

Nat Commun. 2024 Nov 6;15(1):9603. doi: 10.1038/s41467-024-54002-w.

Abstract

Ribosomal DNA (rDNA) repeats harbor ribosomal RNA (rRNA) genes and intergenic spacers (IGS). RNA polymerase (Pol) I transcribes rRNA genes yielding rRNA components of ribosomes. IGS-associated Pol II prevents Pol I from excessively synthesizing IGS non-coding RNAs (ncRNAs) that can disrupt nucleoli and rRNA production. Here, compartment-enriched proximity-dependent biotin identification (compBioID) revealed the TATA-less-promoter-binding TBPL1 and transcription-regulatory PAF1 with nucleolar Pol II. TBPL1 localizes to TCT motifs, driving Pol II and Pol I and maintaining its baseline ncRNA levels. PAF1 promotes Pol II elongation, preventing unscheduled R-loops that hyper-restrain IGS Pol I-associated ncRNAs. PAF1 or TBPL1 deficiency disrupts nucleolar organization and rRNA biogenesis. In PAF1-deficient cells, repressing unscheduled IGS R-loops rescues nucleolar organization and rRNA production. Depleting IGS Pol I-dependent ncRNAs is sufficient to compromise nucleoli. We present the nucleolar interactome of Pol II and show that its regulation by TBPL1 and PAF1 ensures IGS Pol I ncRNAs maintaining nucleolar structure and function.

MeSH terms

  • Cell Nucleolus* / metabolism
  • DNA, Intergenic / genetics
  • DNA, Ribosomal* / genetics
  • DNA, Ribosomal* / metabolism
  • HeLa Cells
  • Humans
  • Nuclear Proteins* / genetics
  • Nuclear Proteins* / metabolism
  • RNA Polymerase I* / genetics
  • RNA Polymerase I* / metabolism
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Ribosomal* / genetics
  • RNA, Ribosomal* / metabolism
  • RNA, Untranslated / genetics
  • RNA, Untranslated / metabolism
  • Transcription Factors* / genetics
  • Transcription Factors* / metabolism

Substances

  • RNA Polymerase I
  • RNA, Ribosomal
  • DNA, Ribosomal
  • Nuclear Proteins
  • Transcription Factors
  • PAF1 protein, human
  • RNA Polymerase II
  • RNA, Untranslated
  • DNA, Intergenic