title: Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq.
abstract: Specific DNA-protein interactions are the basis for many important cellular mechanisms like the regulation of gene expression or replication. Knowledge about the precise genomic locations of DNA-protein interactions is important because it provides insight into the regulation of these processes. Recently, we have adapted an approach that combines micrococcal nuclease (MNase) digestion of chromatin with chromatin immunoprecipitation in Trypanosoma brucei. Here, we describe in detail how this method can be used to map the genome-wide distribution of nucleosomes or other DNA-binding proteins at high resolution in T. brucei.
authors.affiliation: Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Straße 2 / Bau D15, 97080 Würzburg, Germany.
authors.forename: Carolin
authors.initials: C
authors.lastname: Wedel
authors.affiliation: Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Straße 2 / Bau D15, 97080 Würzburg, Germany. Electronic address: nicolai.siegel@uni-wuerzburg.de.
authors.forename: T Nicolai
authors.initials: TN
authors.lastname: Siegel
mesh_terms: D000911:Antibodies, Monoclonal / Q000276:immunology; D000913:Antibodies, Protozoan / Q000276:immunology; D000918:Antibody Specificity; D002843:Chromatin / Q000235:genetics* / Q000648:ultrastructure; D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000592:standards; D002874:Chromosome Mapping / Q000379:methods; D053938:DNA Fragmentation; D017931:DNA Primers / Q000737:chemistry; D016054:DNA, Protozoan / Q000737:chemistry / Q000302:isolation & purification; D004268:DNA-Binding Proteins / Q000378:metabolism; D000939:Epitopes / Q000276:immunology; D055106:Genome-Wide Association Study; D008836:Micrococcal Nuclease / Q000378:metabolism*; D008856:Microscopy, Fluorescence; D009707:Nucleosomes / Q000235:genetics / Q000648:ultrastructure; D010539:Permeability; D016133:Polymerase Chain Reaction; D015800:Protozoan Proteins / Q000235:genetics / Q000276:immunology; D013010:Sonication; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000276:immunology / Q000648:ultrastructure
chemical_list: D000911:Antibodies, Monoclonal; D000913:Antibodies, Protozoan; D002843:Chromatin; D017931:DNA Primers; D016054:DNA, Protozoan; D004268:DNA-Binding Proteins; D000939:Epitopes; D009707:Nucleosomes; D015800:Protozoan Proteins; D008836:Micrococcal Nuclease
keywords: ChIP; Chromatin; Micrococcal nuclease; Nucleosome