title: Relating periodicity of nucleosome organization and gene regulation.
abstract: BACKGROUND
  The relationship between nucleosome positioning and gene regulation is fundamental yet complex. Previous studies on genomic nucleosome positions have revealed a correlation between nucleosome occupancy on promoters and gene expression levels. Many of these studies focused on individual nucleosomes, especially those proximal to transcription start sites. To study the collective effect of multiple nucleosomes on the gene expression, we developed a mathematical approach based on autocorrelation to relate genomic nucleosome organization to gene regulation.
  
  
  RESULTS
  We found that nucleosome organization in gene promoters can be well described by autocorrelation transformation. Some promoters show obvious periods in their nucleosome organization, while others have no clear periodicity. The genes with periodic nucleosome organization in promoters tend to be lower expressed than the genes without periodic nucleosome organization. These suggest that regular organization of nucleosomes plays a critical role in gene regulation. To quantitatively associate nucleosome organization and gene expression, we predicted gene expression solely based on nucleosome status and found that nucleosome status accounts for approximately 25% of the observed gene expression variability. Furthermore, we explored the underlying forces that maintain the periodicity in nucleosome organization, namely intrinsic (i.e. DNA sequence) and extrinsic forces (i.e. chromatin remodeling factors). We found that the extrinsic factors play a critical role in maintaining the periodic nucleosome organization.
authors.affiliation: Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Wan
authors.forename: Jimmy
authors.initials: J
authors.lastname: Lin
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Zack
authors.forename: Jiang
authors.initials: J
authors.lastname: Qian
mesh_terms: D002843:Chromatin / Q000378:metabolism; D016000:Cluster Analysis; D005786:Gene Expression Regulation; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors