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  Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling

Perner, J., Lasserre, J., Kinkley, S., Vingron, M., & Chung, H.-R. (2014). Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling. Nucleic Acids Research (London), 42(22), 13689-13695. doi:10.1093/nar/gku1234.

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Item Permalink: https://hdl.handle.net/11858/00-001M-0000-0025-2127-8 Version Permalink: https://hdl.handle.net/11858/00-001M-0000-0025-6819-C
Genre: Journal Article

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© 2014 Oxford University Press
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 Creators:
Perner, Juliane1, Author           
Lasserre, Julia2, Author           
Kinkley, Sarah3, Author
Vingron, Martin4, Author           
Chung, Ho-Ryun5, Author           
Affiliations:
1IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479666              
2Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
3Max Planck Society, ou_persistent13              
4Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
5Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479658              

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 Abstract: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro. Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.

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Language(s): eng - English
 Dates: 2014-11-202014-12-16
 Publication Status: Issued
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 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gku1234
ISSN: 1362-4962 (Electronic)0305-1048 (Print)
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Title: Nucleic Acids Research (London)
  Other : Nucleic Acids Res
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 42 (22) Sequence Number: - Start / End Page: 13689 - 13695 Identifier: ISSN: 0305-1048
CoNE: https://pure.mpg.de/cone/journals/resource/110992357379342