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  reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells

Kinkley, S., Helmuth, J., Polansky, J. K., Dunkel, I., Gasparoni, G., Fröhler, S., et al. (2016). reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells. Nature Communications, 7: 7:12514. doi:10.1038/ncomms12514.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-6142-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-6143-1
Genre: Journal Article

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 Creators:
Kinkley, Sarah1, Author              
Helmuth, Johannes1, Author              
Polansky, Julia K. , Author
Dunkel, Ilona1, Author              
Gasparoni, Gilles , Author
Fröhler, Sebastian, Author
Chen, Wei, Author
Walter, Jörn, Author
Hamann, Alf, Author
Chung, Ho-Ryun2, Author              
Affiliations:
1Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479658              
2Epigenomics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479658              

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 Abstract: The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4(+) memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP-seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action.

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Language(s): eng - English
 Dates: 2016-08-17
 Publication Status: Published online
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 Identifiers: DOI: 10.1038/ncomms12514
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Title: Nature Communications
  Abbreviation : Nat. Commun.
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 7 Sequence Number: 7:12514 Start / End Page: - Identifier: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723