title: Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility.
abstract: Nucleosome position, density, and post-translational modification are widely accepted components of mechanisms regulating DNA transcription but still incompletely understood. We present a modified native ChIP-seq method combined with an analytical framework that allows MNase accessibility to be integrated with histone modification profiles. Application of this methodology to the primitive (CD34+) subset of normal human cord blood cells enabled genomic regions enriched in one versus two nucleosomes marked by histone 3 lysine 4 trimethylation (H3K4me3) and/or histone 3 lysine 27 trimethylation (H3K27me3) to be associated with their transcriptional and DNA methylation states. From this analysis, we defined four classes of promoter-specific profiles and demonstrated that a majority of bivalent marked promoters are heterogeneously marked at a single-cell level in this primitive cell type. Interestingly, extension of this approach to human embryonic stem cells revealed an altered relationship between chromatin modification state and nucleosome content at promoters, suggesting developmental stage-specific organization of histone methylation states.
authors.affiliation: Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Alireza
authors.initials: A
authors.lastname: Lorzadeh
authors.affiliation: Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada.
authors.forename: Misha
authors.initials: M
authors.lastname: Bilenky
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Colin
authors.initials: C
authors.lastname: Hammond
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: David J H F
authors.initials: DJHF
authors.lastname: Knapp
authors.affiliation: Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Luolan
authors.initials: L
authors.lastname: Li
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Paul H
authors.initials: PH
authors.lastname: Miller
authors.affiliation: Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Annaick
authors.initials: A
authors.lastname: Carles
authors.affiliation: Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada.
authors.forename: Alireza
authors.initials: A
authors.lastname: Heravi-Moussavi
authors.affiliation: Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada.
authors.forename: Sitanshu
authors.initials: S
authors.lastname: Gakkhar
authors.affiliation: Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Michelle
authors.initials: M
authors.lastname: Moksa
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
authors.forename: Connie J
authors.initials: CJ
authors.lastname: Eaves
authors.affiliation: Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Science Center, BC Cancer Agency Vancouver, BC V5Z 4S6, Canada. Electronic address: mhirst@bcgsc.ca.
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
mesh_terms: D018952:Antigens, CD34 / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D005312:Fetal Blood / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D000066449:Human Embryonic Stem Cells / Q000378:metabolism; D006801:Humans; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011499:Protein Processing, Post-Translational; D012313:RNA / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D018952:Antigens, CD34; D006657:Histones; D009707:Nucleosomes; D012313:RNA; D004247:DNA; D008836:Micrococcal Nuclease
keywords: ChIP-seq; bivalent promoter; cellular heterogeneity; epigenomics; histone modification; micrococcal nuclease; nucleosome density