title: reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells.
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.
authors.affiliation: Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Kinkley
authors.affiliation: Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
authors.forename: Johannes
authors.identifier: http://orcid.org/0000-0002-5380-4577
authors.initials: J
authors.lastname: Helmuth
authors.affiliation: Experimental Rheumatology, German Rheumatism Research Center Berlin, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Julia K
authors.initials: JK
authors.lastname: Polansky
authors.affiliation: Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
authors.forename: Ilona
authors.initials: I
authors.lastname: Dunkel
authors.affiliation: The Department of Genetics and Epigenetics, University of Saarland, Campus A2.4 66123 Saarbrücken, Germany.
authors.forename: Gilles
authors.initials: G
authors.lastname: Gasparoni
authors.affiliation: The Laboratory of Functional Genomics and Systems Biology, Max Delbruck Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Fröhler
authors.affiliation: The Laboratory of Functional Genomics and Systems Biology, Max Delbruck Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: The Department of Genetics and Epigenetics, University of Saarland, Campus A2.4 66123 Saarbrücken, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Walter
authors.affiliation: Experimental Rheumatology, German Rheumatism Research Center Berlin, Charitéplatz 1, 10117 Berlin, Germany.
authors.forename: Alf
authors.identifier: http://orcid.org/0000-0003-1518-5717
authors.initials: A
authors.lastname: Hamann
authors.affiliation: Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
authors.forename: Ho-Ryun
authors.identifier: http://orcid.org/0000-0002-4132-0911
authors.initials: HR
authors.lastname: Chung
mesh_terms: D001483:Base Sequence; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D044127:Epigenesis, Genetic; D015894:Genome, Human; D006657:Histones / Q000378:metabolism*; D006801:Humans; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; D008239:Lysine