title: Inferring nucleosome positions with their histone mark annotation from ChIP data.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The software is available at http://epigen.molgen.mpg.de/nuchunter/.
authors: Otto-Warburg-Laboratories, Epigenomics and Computational Molecular Biology, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.
authors: Alessandro
authors: A
authors: Mammana
authors: Martin
authors: M
authors: Vingron
authors: Ho-Ryun
authors: HR
authors: Chung
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism*; D006801:Humans; D020407:Internet; D020014:K562 Cells; D009707:Nucleosomes / Q000737:chemistry*; D012441:Saccharomyces cerevisiae; D012984:Software
chemical_list: D006657:Histones; D009707:Nucleosomes
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