title: Single-molecule tools elucidate H2A.Z nucleosome composition.
abstract: Although distinct epigenetic marks correlate with different chromatin states, how they are integrated within single nucleosomes to generate combinatorial signals remains largely unknown. We report the successful implementation of single molecule tools constituting fluorescence correlation spectroscopy (FCS), pulse interleave excitation-based Förster resonance energy transfer (PIE-FRET) and fluorescence lifetime imaging-based FRET (FLIM-FRET) to elucidate the composition of single nucleosomes containing histone variant H2A.Z (Htz1p in yeast) in vitro and in vivo. We demonstrate that yeast nucleosomes containing Htz1p are primarily composed of H4 K12ac and H3 K4me3 but not H3 K36me3 and that these patterns are conserved in mammalian cells. Quantification of epigenetic modifications in nucleosomes will provide a new dimension to epigenetics research and lead to a better understanding of how these patterns contribute to the targeting of chromatin-binding proteins and chromatin structure during gene regulation.
authors.affiliation: Department of Agricultural and Biological Engineering, Purdue University Center for Cancer Research, 225 South University Street, West Lafayette, IN 47907,  USA.
authors.forename: Jiji
authors.initials: J
authors.lastname: Chen
authors.forename: Andrew
authors.initials: A
authors.lastname: Miller
authors.forename: Ann L
authors.initials: AL
authors.lastname: Kirchmaier
authors.forename: Joseph M K
authors.initials: JM
authors.lastname: Irudayaraj
mesh_terms: D000107:Acetylation; D002460:Cell Line; D044127:Epigenesis, Genetic; D057890:Epigenomics; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D006657:Histones / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008745:Methylation; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013050:Spectrometry, Fluorescence / Q000379:methods*
chemical_list: D006657:Histones; C493530:Htz1 protein, S cerevisiae; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; C077020:histone H2A.F-Z