Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

Genome Biol. 2011 Nov 7;12(11):R111. doi: 10.1186/gb-2011-12-11-r111.


We propose a method to predict yeast transcription factor targets by integrating histone modification profiles with transcription factor binding motif information. It shows improved predictive power compared to a binding motif-only method. We find that transcription factors cluster into histone-sensitive and -insensitive classes. The target genes of histone-sensitive transcription factors have stronger histone modification signals than those of histone-insensitive ones. The two classes also differ in tendency to interact with histone modifiers, degree of connectivity in protein-protein interaction networks, position in the transcriptional regulation hierarchy, and in a number of additional features, indicating possible differences in their transcriptional regulation mechanisms.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Algorithms
  • Amino Acid Motifs
  • Binding Sites
  • Chromatin / genetics*
  • Chromatin Immunoprecipitation
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal*
  • Genome, Fungal*
  • Histones / genetics*
  • Models, Genetic
  • Protein Binding
  • Protein Interaction Mapping
  • Saccharomyces cerevisiae / genetics*
  • Transcription Factors / genetics*
  • Transcription, Genetic


  • Chromatin
  • Histones
  • Transcription Factors