Rif1 binds to G quadruplexes and suppresses replication over long distances

• DOI: 10.1038/nsmb.3102
• Publication Date: 2015-10-05T15:02:03Z
• Authors: Yutaka Kanoh; Seiji Matsumoto; Rino Fukatsu; Naoko Kakusho; Nobuaki Kono; Claire Renard-Gui...; Koji Masuda; Keisuke Iida; Kazuo Nagasawa; Katsuhiko Shirahige; Hisao Masai
• Keywords: DNA Replication; G-Quadruplexes; 0303 health sciences; 03 medical and health sciences; Binding Sites; Molecular Sequence Data; Schizosaccharomyces; Telomere-Binding Proteins; Schizosaccharomyces pombe Proteins; Sequence Analysis, DNA; DNA, Fungal; Protein Binding

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.