Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq

BMC Genomics. 2008 Nov 13;9:537. doi: 10.1186/1471-2164-9-537.


Background: In vivo positioning and covalent modifications of nucleosomes play an important role in epigenetic regulation, but genome-wide studies of positioned nucleosomes and their modifications in human still remain limited.

Results: This paper describes a novel computational framework to efficiently identify positioned nucleosomes and their histone modification profiles from nucleosome-resolution histone modification ChIP-Seq data. We applied the algorithm to histone methylation ChIP-Seq data in human CD4+ T cells and identified over 438,000 positioned nucleosomes, which appear predominantly at functionally important regions such as genes, promoters, DNase I hypersensitive regions, and transcription factor binding sites. Our analysis shows the identified nucleosomes play a key role in epigenetic gene regulation within those functionally important regions via their positioning and histone modifications.

Conclusion: Our method provides an effective framework for studying nucleosome positioning and epigenetic marks in mammalian genomes. The algorithm is open source and available at

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • CD4-Positive T-Lymphocytes / metabolism
  • Computational Biology / methods*
  • Epigenesis, Genetic*
  • Gene Expression Regulation*
  • Genome, Human*
  • Histones / metabolism
  • Humans
  • Methylation
  • Nucleosomes / genetics*
  • Software


  • Histones
  • Nucleosomes