Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq

• Main Authors: Lei Ying, Song Jun S, Shin Hyunjin, Zhang Yong, Liu X Shirley
• Format: Article
• Language: English
• Published: BMC 2008-11-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/9/537

<p>Abstract</p> <p>Background</p> <p><it>In vivo </it>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>Our method provides an effective framework for studying nucleosome positioning and epigenetic marks in mammalian genomes. The algorithm is open source and available at <url>http://liulab.dfci.harvard.edu/NPS/</url>.</p>