Ribosomal DNA and the nucleolus in the context of genome organization

Chromosome Res. 2019 Mar;27(1-2):109-127. doi: 10.1007/s10577-018-9600-5. Epub 2019 Jan 17.


The nucleolus constitutes a prominent nuclear compartment, a membraneless organelle that was first documented in the 1830s. The fact that specific chromosomal regions were present in the nucleolus was recognized by Barbara McClintock in the 1930s, and these regions were termed nucleolar organizing regions, or NORs. The primary function of ribosomal DNA (rDNA) is to produce RNA components of ribosomes. Yet, ribosomal DNA also plays a pivotal role in nuclear organization by assembling the nucleolus. This review is focused on the rDNA and associated proteins in the context of genome organization. Recent advances in understanding chromatin organization suggest that chromosomes are organized into topological domains by a DNA loop extrusion process. We discuss the perspective that rDNA may also be organized in topological domains constrained by structural maintenance of chromosome protein complexes such as cohesin and condensin. Moreover, biophysical studies indicate that the nucleolar compartment may be formed by active processes as well as phase separation, a perspective that lends further insight into nucleolar organization. The application of the latest perspectives and technologies to this organelle help further elucidate its role in nuclear structure and function.

Keywords: Chromatin; Cohesin; Condensin; Genome organization; Nucleolus; Topoisomerase; UBF; rDNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism
  • Animals
  • Cell Cycle Proteins / metabolism
  • Cell Nucleolus / genetics*
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromosomal Proteins, Non-Histone / metabolism
  • DNA Topoisomerases / metabolism
  • DNA, Ribosomal / genetics*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Genome*
  • Genomics* / methods
  • Humans
  • Multiprotein Complexes / genetics
  • Multiprotein Complexes / metabolism
  • Pol1 Transcription Initiation Complex Proteins / metabolism


  • Cell Cycle Proteins
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • DNA, Ribosomal
  • DNA-Binding Proteins
  • Multiprotein Complexes
  • Pol1 Transcription Initiation Complex Proteins
  • cohesins
  • condensin complexes
  • transcription factor UBF
  • Adenosine Triphosphatases
  • DNA Topoisomerases