title: Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.
abstract: Recent studies of the mechanisms involved in the regulation of gene expression in eukaryotic organisms depict a highly complex process requiring a coordinated rearrangement of numerous molecules to mediate DNA accessibility. Silencing in Saccharomyces cerevisiae involves the Sir family of proteins. Sir3p, originally described as repressing key areas of the yeast genome through interactions with the tails of histones H3 and H4, appears to have additional roles in that process, including involvement with a DNA binding component. Our in vitro studies focused on the characterization of Sir3p-nucleic acid interactions and their biological functions in Sir3p-mediated silencing using binding assays, EM imaging, and theoretical modeling. Our results suggest that the initial Sir3p recruitment is partially DNA-driven, highly cooperative, and dependent on nucleosomal features other than histone tails. The initial step appears to be rapidly followed by the spreading of silencing using linker DNA as a track.
authors.affiliation: Department of Biological Sciences and Cell Differentiation and Development Center, Marshall University, Huntington, West Virginia 25755, USA.
authors.forename: Nicholas L
authors.initials: NL
authors.lastname: Adkins
authors.forename: Steve J
authors.initials: SJ
authors.lastname: McBryant
authors.forename: Cotteka N
authors.initials: CN
authors.lastname: Johnson
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Leidy
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Woodcock
authors.forename: Charles H
authors.initials: CH
authors.lastname: Robert
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Hansen
authors.forename: Philippe T
authors.initials: PT
authors.lastname: Georgel
mesh_terms: D000465:Algorithms; D000818:Animals; D016367:Baculoviridae / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D001681:Biological Assay; D002843:Chromatin / Q000378:metabolism* / Q000648:ultrastructure; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D004275:DNA, Ribosomal / Q000302:isolation & purification; D004277:DNA, Single-Stranded / Q000378:metabolism; D020868:Gene Silencing; D016681:Genome, Fungal; D006657:Histones / Q000378:metabolism; D047331:Lytechinus / Q000737:chemistry; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae / Q000302:isolation & purification / Q000378:metabolism* / Q000648:ultrastructure; D018411:Spodoptera / Q000166:cytology; D013698:Templates, Genetic
chemical_list: D002843:Chromatin; D004271:DNA, Fungal; D004275:DNA, Ribosomal; D004277:DNA, Single-Stranded; D006657:Histones; D009707:Nucleosomes; C084122:SIR3 protein, S cerevisiae; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae