title: Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains.
abstract: BACKGROUND
  It has been a long-term puzzle whether chromatin can be further divided into distinct gene expression domains. Because histone deacetylation affects chromatin structure, that in turn may affect the expression of nearby genes, histone deacetylation sites may act to partition chromatin into different gene expression domains. In this article, we explore the relationship between histone deacetylation sites and gene expression patterns on the genome scale using different data sources, including microarray data measuring gene expression levels, microarray data measuring histone deacetylation sites, and information on regulatory targets of transcription factors.
  
  
  RESULTS
  Using 269 Saccharomyces cerevisiae microarray datasets, histone deacetylation datasets, and regulatory targets of transcription factors assembled from the Yeast Proteome Database and ChIP-chip data, we found that histone deacetylation sites can reduce the level of co-expression of neighboring genes.
  
  
  CONCLUSIONS
  Histone deacetylation sites may serve as possible partition sites for chromatin domains and affect gene expression.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA. liang.chen@yale.edu
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D015870:Gene Expression; D005786:Gene Expression Regulation; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D006655:Histone Deacetylases / Q000378:metabolism; D006657:Histones / Q000737:chemistry / Q000378:metabolism*; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D029701:Saccharomyces cerevisiae Proteins; D006655:Histone Deacetylases