title: Rif1 binds to G quadruplexes and suppresses replication over long distances.
abstract: Rif1 regulates replication timing and repair of double-strand DNA breaks. Using a chromatin immunoprecipitation-sequencing method, we identified 35 high-affinity Rif1-binding sites in fission yeast chromosomes. Binding sites tended to be located near dormant origins and to contain at least two copies of a conserved motif, CNWWGTGGGGG. Base substitution within these motifs resulted in complete loss of Rif1 binding and in activation of late-firing or dormant origins located up to 50 kb away. We show that Rif1-binding sites adopt G quadruplex-like structures in vitro, in a manner dependent on the conserved sequence and on other G tracts, and that purified Rif1 preferentially binds to this structure. These results suggest that Rif1 recognizes and binds G quadruplex-like structures at selected intergenic regions, thus generating local chromatin structures that may exert long-range suppressive effects on origin firing.
authors.affiliation: Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kanoh
authors.affiliation: Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
authors.forename: Seiji
authors.initials: S
authors.lastname: Matsumoto
authors.affiliation: Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
authors.forename: Rino
authors.initials: R
authors.lastname: Fukatsu
authors.affiliation: Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
authors.forename: Naoko
authors.initials: N
authors.lastname: Kakusho
authors.affiliation: Institute for Advanced Biosciences, Keio University, Yamagata, Japan.
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Kono
authors.affiliation: Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan.
authors.forename: Claire
authors.initials: C
authors.lastname: Renard-Guillet
authors.affiliation: Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Masuda
authors.affiliation: Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Iida
authors.affiliation: Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Nagasawa
authors.affiliation: Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan.
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Shirahige
authors.affiliation: Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
authors.forename: Hisao
authors.initials: H
authors.lastname: Masai
mesh_terms: D001665:Binding Sites; D004261:DNA Replication; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D054856:G-Quadruplexes; D008969:Molecular Sequence Data; D011485:Protein Binding; D012568:Schizosaccharomyces / Q000201:enzymology* / Q000502:physiology*; D029702:Schizosaccharomyces pombe Proteins / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D034501:Telomere-Binding Proteins / Q000378:metabolism*
chemical_list: D004271:DNA, Fungal; C570600:Rif1 protein, S pombe; D029702:Schizosaccharomyces pombe Proteins; D034501:Telomere-Binding Proteins