title: Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement.
abstract: The histone variant H2A.Z is a genome-wide signature of nucleosomes proximal to eukaryotic regulatory DNA. Whereas the multisubunit chromatin remodeler SWR1 is known to catalyze ATP-dependent deposition of H2A.Z, the mechanism of SWR1 recruitment to S. cerevisiae promoters has been unclear. A sensitive assay for competitive binding of dinucleosome substrates revealed that SWR1 preferentially binds long nucleosome-free DNA and the adjoining nucleosome core particle, allowing discrimination of gene promoters over gene bodies. Analysis of mutants indicates that the conserved Swc2/YL1 subunit and the adenosine triphosphatase domain of Swr1 are mainly responsible for binding to substrate. SWR1 binding is enhanced on nucleosomes acetylated by the NuA4 histone acetyltransferase, but recognition of nucleosome-free and nucleosomal DNA is dominant over interaction with acetylated histones. Such hierarchical cooperation between DNA and histone signals expands the dynamic range of genetic switches, unifying classical gene regulation by DNA-binding factors with ATP-dependent nucleosome remodeling and posttranslational histone modifications.
authors.affiliation: Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: ranjana@mail.nih.gov.
authors.forename: Anand
authors.initials: A
authors.lastname: Ranjan
authors.forename: Gaku
authors.initials: G
authors.lastname: Mizuguchi
authors.forename: Peter C
authors.initials: PC
authors.lastname: FitzGerald
authors.forename: Debbie
authors.initials: D
authors.lastname: Wei
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.forename: Yingzi
authors.initials: Y
authors.lastname: Huang
authors.forename: Ed
authors.initials: E
authors.lastname: Luk
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Woodcock
authors.forename: Carl
authors.initials: C
authors.lastname: Wu
mesh_terms: D000107:Acetylation; D000251:Adenosine Triphosphatases / Q000378:metabolism; D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D051548:Histone Acetyltransferases / Q000378:metabolism; D006657:Histones / Q000378:metabolism*; D008969:Molecular Sequence Data; D046912:Multiprotein Complexes / Q000378:metabolism*; D009707:Nucleosomes / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D006657:Histones; C493530:Htz1 protein, S cerevisiae; D046912:Multiprotein Complexes; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D051548:Histone Acetyltransferases; D000251:Adenosine Triphosphatases; C481261:Swr1 protein, S cerevisiae
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