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  Inferring nucleosome positions with their histone mark annotation from ChIP data

Mammana, A., Vingron, M., & Chung, H.-R. (2013). Inferring nucleosome positions with their histone mark annotation from ChIP data. Bioinformatics, 29(20), 2547-2554. doi:10.1093/bioinformatics/btt449.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-7C23-7 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-7C24-5
Genre: Journal Article

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Mammana, Alessandro1, Author              
Vingron, Martin2, Author              
Chung, Ho-Ryun1, Author              
Affiliations:
1Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr. 73, 14195 Berlin, Germany, ou_1479658              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr, 73, 14195 Berlin, Germany, ou_1479639              

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 Abstract: MOTIVATION: The nucleosome is the basic repeating unit of chromatin. It contains two copies each of the four core histones H2A, H2B, H3 and H4 and about 147 bp of DNA. The residues of the histone proteins are subject to numerous post-translational modifications, such as methylation or acetylation. Chromatin immunoprecipitiation followed by sequencing (ChIP-seq) is a technique that provides genome-wide occupancy data of these modified histone proteins, and it requires appropriate computational methods. RESULTS: We present NucHunter, an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes. NucHunter annotates each of these nucleosomes with the intensities of the histone modifications. We demonstrate that these annotations can be used to infer nucleosomal states with distinct correlations to underlying genomic features and chromatin-related processes, such as transcriptional start sites, enhancers, elongation by RNA polymerase II and chromatin-mediated repression. Thus, NucHunter is a versatile tool that can be used to predict positioned nucleosomes from a panel of histone modification ChIP-seq experiments and infer distinct histone modification patterns associated to different chromatin states. AVAILABILITY: The software is available at http://epigen.molgen.mpg.de/nuchunter/. CONTACT: chung@molgen.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Language(s): eng - English
 Dates: 2013-08-262013-10-15
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1093/bioinformatics/btt449
ISSN: 1367-4811 (Electronic)1367-4803 (Print)
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 29 (20) Sequence Number: - Start / End Page: 2547 - 2554 Identifier: ISSN: 1367-4803
CoNE: /journals/resource/954926969991