title: ChIP-on-chip analysis of DNA topoisomerases.
abstract: Here we describe an adapted ChIP-on-chip protocol for the analysis of DNA topoisomerase chromosomal binding in Saccharomyces cerevisiae cells. The ChIP-on-chip technique is based on the immunoprecipitation of crosslinked chromatin (ChIP, chromatin immunoprecipitation), followed by DNA amplification and hybridization to high-density oligonucleotide arrays (Chip). Comparison of the signal intensities of immunoprecipitated and control fractions provides a measurement of the protein-DNA association along entire genomes. ChIP-on-chip analysis of DNA topoisomerase binding to chromosomal DNA opens a window to the understanding of the in vivo contribution of these enzymes to the different DNA transactions taking place concomitantly within the context of the highly organized eukaryotic genome. Chromosomal binding profiles obtained from synchronized cells allow scoring the temporal and spatial restriction of these enzymes at different cell cycle stages. By using this approach, novel aspects of DNA topoisomerase function in chromosome metabolism might be unmasked.
authors.affiliation: Fondazione Italiana per la Ricerca sul Cancro, Institute of Molecular Oncology Foundation, Milan, Italy.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Bermejo
authors.forename: Yuki-Mori
authors.initials: YM
authors.lastname: Katou
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Shirahige
authors.forename: Marco
authors.initials: M
authors.lastname: Foiani
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000295:instrumentation / Q000379:methods; D015825:Chromosomes, Fungal / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D026942:DNA Topoisomerases / Q000378:metabolism*; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D004247:DNA; D026942:DNA Topoisomerases