Relating periodicity of nucleosome organization and gene regulation

Jun Wan, Jimmy Lin, Donald J Zack, Jiang Qian

Research output: Contribution to journalArticle

Abstract

Motivation: 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 genepromoters 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 ∼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.

Original languageEnglish (US)
Pages (from-to)1782-1788
Number of pages7
JournalBioinformatics
Volume25
Issue number14
DOIs
StatePublished - Jul 2009

Fingerprint

Gene Regulation
Nucleosomes
Periodicity
Gene expression
Gene Expression
Promoter
Genes
Autocorrelation
Genomics
Gene
Remodeling
Chromatin
DNA Sequence
Transcription
Positioning
Tend
DNA sequences
Chromatin Assembly and Disassembly
Transcription Initiation Site

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

Relating periodicity of nucleosome organization and gene regulation. / Wan, Jun; Lin, Jimmy; Zack, Donald J; Qian, Jiang.

In: Bioinformatics, Vol. 25, No. 14, 07.2009, p. 1782-1788.

Research output: Contribution to journalArticle

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