title: Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome.
abstract: Functional interactions between gene regulatory factors and chromatin architecture have been difficult to directly assess. Here, we use micrococcal nuclease (MNase) footprinting to probe the functions of two chromatin-remodeling complexes. By simultaneously quantifying alterations in small MNase footprints over the binding sites of 30 regulatory factors in mouse embryonic stem cells (ESCs), we provide evidence that esBAF and Mbd3/NuRD modulate the binding of several regulatory proteins. In addition, we find that nucleosome occupancy is reduced at specific loci in favor of subnucleosomes upon depletion of esBAF, including sites of histone H2A.Z localization. Consistent with these data, we demonstrate that esBAF is required for normal H2A.Z localization in ESCs, suggesting esBAF either stabilizes H2A.Z-containing nucleosomes or promotes subnucleosome to nucleosome conversion by facilitating H2A.Z deposition. Therefore, integrative examination of MNase footprints reveals insights into nucleosome dynamics and functional interactions between chromatin structure and key gene-regulatory factors.
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Hainer
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: thomas.fazzio@umassmed.edu.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Fazzio
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D001665:Binding Sites; D042002:Chromatin Assembly and Disassembly; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D003851:Deoxyribonucleases / Q000737:chemistry; D004622:Embryo, Mammalian; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D016678:Genome; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000378:metabolism; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex / Q000235:genetics / Q000378:metabolism; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism* / Q000648:ultrastructure; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism* / Q000648:ultrastructure; D061251:Primary Cell Culture; D011485:Protein Binding; D023302:Protein Footprinting; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C501960:Banf1 protein, mouse; D004268:DNA-Binding Proteins; D006657:Histones; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors; C492013:Mbd3 protein, mouse; D009687:Nuclear Proteins; D009707:Nucleosomes; D014157:Transcription Factors; D003851:Deoxyribonucleases; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex