title: Analysis of chromatin composition of repetitive sequences: the ChIP-Chop assay.
abstract: Chromatin immunoprecipitation (ChIP) is a powerful method that allows to probe specific protein-DNA interactions in vivo and to estimate the occupancy of proteins at specific sites of the genome. However, the traditional ChIP assay is not able to distinguish whether repeats that share identical sequences display a different composition of associated factors and, consequently, different functions. The ChIP-chop method provides a useful application to analyze the interaction of proteins with repetitive sequences based on their CpG methylation content. The detailed ChIP-chop protocol that serves to determine the chromatin composition of active and silent ribosomal RNA (rRNA) genes, repeats that share identical sequences but display distinct functions and chromatin compositions, is reported here.
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Santoro
mesh_terms: D000818:Animals; D001483:Base Sequence; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*
chemical_list: D002843:Chromatin; D004275:DNA, Ribosomal