title: Chromatin Endogenous Cleavage (ChEC) as a Method to Quantify Protein Interaction with Genomic DNA in Saccharomyces cerevisiae.
abstract: Chromatin endogenous cleavage (ChEC) is a technique which allows to monitor protein-DNA interaction in the nucleus of eukaryotic cells. In addition to mapping of genomic interaction sites ChEC may also yield quantitative information about the occupancy of proteins at their genomic target regions. Here, we provide a protocol for ChEC experiments in S. cerevisiae, downstream DNA analysis and quantification of ChEC-mediated degradation. The potential of the method is exemplified in ChEC experiments with RNA polymerase I and the yeast homolog of linker histone H1.
authors.affiliation: Lehrstuhl Biochemie III, Biochemie-Zentrum Regensburg (BZR), Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany.
authors.forename: Virginia
authors.initials: V
authors.lastname: Babl
authors.affiliation: Lehrstuhl Biochemie III, Biochemie-Zentrum Regensburg (BZR), Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Stöckl
authors.affiliation: Lehrstuhl Biochemie III, Biochemie-Zentrum Regensburg (BZR), Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany. herbert.tschochner@ur.de.
authors.forename: Herbert
authors.initials: H
authors.lastname: Tschochner
authors.affiliation: Lehrstuhl Biochemie III, Biochemie-Zentrum Regensburg (BZR), Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany. philipp.milkereit@ur.de.
authors.forename: Philipp
authors.initials: P
authors.lastname: Milkereit
authors.affiliation: Lehrstuhl Biochemie III, Biochemie-Zentrum Regensburg (BZR), Universität Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany. joachim.griesenbeck@ur.de.
authors.forename: Joachim
authors.initials: J
authors.lastname: Griesenbeck
mesh_terms: D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D008967:Molecular Biology / Q000379:methods*; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D009707:Nucleosomes; D004247:DNA
keywords: ChEC; ChIP; Chromatin; Exponential phase; Histone H1; Protein-DNA interaction; RNA polymerase I; Stationary phase