The specificity and topology of chromatin interaction pathways in yeast

Mol Cell. 2011 May 20;42(4):536-49. doi: 10.1016/j.molcel.2011.03.026.


Packaging of DNA into chromatin has a profound impact on gene expression. To understand how changes in chromatin influence transcription, we analyzed 165 mutants of chromatin machinery components in Saccharomyces cerevisiae. mRNA expression patterns change in 80% of mutants, always with specific effects, even for loss of widespread histone marks. The data are assembled into a network of chromatin interaction pathways. The network is function based, has a branched, interconnected topology, and lacks strict one-to-one relationships between complexes. Chromatin pathways are not separate entities for different gene sets, but share many components. The study evaluates which interactions are important for which genes and predicts additional interactions, for example between Paf1C and Set3C, as well as a role for Mediator in subtelomeric silencing. The results indicate the presence of gene-dependent effects that go beyond context-dependent binding of chromatin factors and provide a framework for understanding how specificity is achieved through regulating chromatin.

MeSH terms

  • Chromatin / metabolism*
  • Gene Expression Regulation, Fungal
  • Gene Silencing
  • Histone Deacetylases / metabolism
  • Histones / metabolism
  • Mediator Complex / metabolism
  • Metabolic Networks and Pathways
  • Nuclear Proteins / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Telomere / metabolism
  • Transcription, Genetic


  • Chromatin
  • Histones
  • Mediator Complex
  • Nuclear Proteins
  • PAF1 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Set3 protein, S cerevisiae
  • Histone Deacetylases

Associated data

  • GEO/GSE25909