A simple biophysical model emulates budding yeast chromosome condensation

Elife. 2015 Apr 29;4:e05565. doi: 10.7554/eLife.05565.


Mitotic chromosomes were one of the first cell biological structures to be described, yet their molecular architecture remains poorly understood. We have devised a simple biophysical model of a 300 kb-long nucleosome chain, the size of a budding yeast chromosome, constrained by interactions between binding sites of the chromosomal condensin complex, a key component of interphase and mitotic chromosomes. Comparisons of computational and experimental (4C) interaction maps, and other biophysical features, allow us to predict a mode of condensin action. Stochastic condensin-mediated pairwise interactions along the nucleosome chain generate native-like chromosome features and recapitulate chromosome compaction and individualization during mitotic condensation. Higher order interactions between condensin binding sites explain the data less well. Our results suggest that basic assumptions about chromatin behavior go a long way to explain chromosome architecture and are able to generate a molecular model of what the inside of a chromosome is likely to look like.

Keywords: S. cerevisiae; chromosome architecture; chromosomes; computational biology; condensin; genes; mitosis; systems biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism
  • Binding Sites
  • Chromatin Assembly and Disassembly*
  • Chromosomes, Fungal / metabolism*
  • Chromosomes, Fungal / ultrastructure
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Gene Expression
  • Interphase
  • Mathematical Computing
  • Mitosis
  • Models, Biological*
  • Models, Molecular
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / genetics
  • Multiprotein Complexes / metabolism
  • Nucleosomes / metabolism*
  • Nucleosomes / ultrastructure
  • Protein Binding
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae / ultrastructure*
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Stochastic Processes


  • DNA-Binding Proteins
  • Multiprotein Complexes
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • condensin complexes
  • Adenosine Triphosphatases

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.