Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus

Mol Cell. 2019 Dec 5;76(5):767-783.e11. doi: 10.1016/j.molcel.2019.08.014. Epub 2019 Sep 17.


Fibrillar centers (FCs) and dense fibrillar components (DFCs) are essential morphologically distinct sub-regions of mammalian cell nucleoli for rDNA transcription and pre-rRNA processing. Here, we report that a human nucleolus consists of several dozen FC/DFC units, each containing 2-3 transcriptionally active rDNAs at the FC/DFC border. Pre-rRNA processing factors, such as fibrillarin (FBL), form 18-24 clusters that further assemble into the DFC surrounding the FC. Mechanistically, the 5' end of nascent 47S pre-rRNA binds co-transcriptionally to the RNA-binding domain of FBL. FBL diffuses to the DFC, where local self-association via its glycine- and arginine-rich (GAR) domain forms phase-separated clusters to immobilize FBL-interacting pre-rRNA, thus promoting directional traffic of nascent pre-rRNA while facilitating pre-rRNA processing and DFC formation. These results unveil FC/DFC ultrastructures in nucleoli and suggest a conceptual framework for considering nascent RNA sorting using multivalent interactions of their binding proteins.

Keywords: Fibrillarin; RNA binding domain; RNA sorting; condensates; glycine- and arginine-rich; intrinsically disordered region; nucleolus; phase separation; ribosomal RNA; super-resolution microscopy.

Publication types

  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Active Transport, Cell Nucleus
  • Antigens, Nuclear / genetics
  • Antigens, Nuclear / metabolism
  • Cell Nucleolus / genetics
  • Cell Nucleolus / metabolism*
  • Cell Nucleolus / ultrastructure
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • Female
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA Precursors / ultrastructure
  • RNA Processing, Post-Transcriptional*
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / metabolism*
  • RNA, Ribosomal / ultrastructure


  • Antigens, Nuclear
  • Chromosomal Proteins, Non-Histone
  • RNA Precursors
  • RNA, Ribosomal
  • fibrillarin
  • nucleolar organizer region associated proteins