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

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

Author information

  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, 44 Binney St, Boston, MA 02115, USA.

Abstract

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 http://liulab.dfci.harvard.edu/NPS/.

PMID:
19014516
[PubMed - indexed for MEDLINE]
PMCID:
PMC2596141
Free PMC Article

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