ATP-dependent chromatin remodeling shapes the DNA replication landscape (original) (raw)

• Becker, P.B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273 (2002).
  Article CAS PubMed Google Scholar
• Smith, C.L. & Peterson, C.L. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65, 115–148 (2005).
  Article CAS PubMed Google Scholar
• Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475–487 (2002).
  Article CAS PubMed Google Scholar
• Varga-Weisz, P. Chromatin remodeling factors and DNA replication. Prog. Mol. Subcell. Biol. 38, 1–30 (2005).
  Article CAS PubMed Google Scholar
• Ataian, Y. & Krebs, J.E. Five repair pathways in one context: chromatin modification during DNA repair. Biochem. Cell Biol. 84, 490–504 (2006).
  Article CAS PubMed Google Scholar
• Jaskelioff, M., Van Komen, S., Krebs, J.E., Sung, P. & Peterson, C.L. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem. 278, 9212–9218 (2003).
  Article CAS PubMed Google Scholar
• van Attikum, H. & Gasser, S.M. ATP-dependent chromatin remodeling and DNA double-strand break repair. Cell Cycle 4, 1011–1014 (2005).
  Article CAS PubMed Google Scholar
• Eisen, J.A., Sweder, K.S. & Hanawalt, P.C. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23, 2715–2723 (1995).
  Article CAS PubMed PubMed Central Google Scholar
• Flaus, A., Martin, D.M., Barton, G.J. & Owen-Hughes, T. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res. 34, 2887–2905 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Fazzio, T.G. & Tsukiyama, T. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Mol. Cell 12, 1333–1340 (2003).
  Article CAS PubMed Google Scholar
• Whitehouse, I. & Tsukiyama, T. Antagonistic forces that position nucleosomes in vivo. Nat. Struct. Mol. Biol. 13, 633–640 (2006).
  Article CAS PubMed Google Scholar
• Papamichos-Chronakis, M., Krebs, J.E. & Peterson, C.L. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. Genes Dev. 20, 2437–2449 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Tong, A.H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364–2368 (2001).
  Article CAS PubMed Google Scholar
• Shen, X., Mizuguchi, G., Hamiche, A. & Wu, C. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406, 541–544 (2000).
  Article CAS PubMed Google Scholar
• Morrison, A.J. et al. INO80 and γ-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell 119, 767–775 (2004).
  Article CAS PubMed Google Scholar
• Raghuraman, M.K. et al. Replication dynamics of the yeast genome. Science 294, 115–121 (2001).
  Article CAS PubMed Google Scholar
• McCarroll, R.M. & Fangman, W.L. Time of replication of yeast centromeres and telomeres. Cell 54, 505–513 (1988).
  Article CAS PubMed Google Scholar
• Alvino, G.M. et al. Replication in hydroxyurea: it's a matter of time. Mol. Cell. Biol. 27, 6396–6406 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Yabuki, N., Terashima, H. & Kitada, K. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7, 781–789 (2002).
  Article CAS PubMed Google Scholar
• Feng, W. et al. Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nat. Cell Biol. 8, 148–155 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Wyrick, J.J. et al. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294, 2357–2360 (2001).
  Article CAS PubMed Google Scholar
• Nieduszynski, C.A., Knox, Y. & Donaldson, A.D. Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 20, 1874–1879 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Santocanale, C. & Diffley, J.F.A. Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. Nature 395, 615–618 (1998).
  Article CAS PubMed Google Scholar
• Shirahige, K. et al. Regulation of DNA-replication origins during cell-cycle progression. Nature 395, 618–621 (1998).
  Article CAS PubMed Google Scholar
• Tercero, J.A. & Diffley, J.F. Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 412, 553–557 (2001).
  Article CAS PubMed Google Scholar
• Fazzio, T.G. et al. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21, 6450–6460 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Chang, M., Bellaoui, M., Boone, C. & Brown, G.W. A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc. Natl. Acad. Sci. USA 99, 16934–16939 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Sugino, A. Yeast DNA polymerases and their role at the replication fork. Trends Biochem. Sci. 20, 319–323 (1995).
  Article CAS PubMed Google Scholar
• Burgers, P.M. Eukaryotic DNA polymerases in DNA replication and DNA repair. Chromosoma 107, 218–227 (1998).
  Article CAS PubMed Google Scholar
• Papamichos-Chronakis, M. & Peterson, C.L. The Ino80 chromatin-remodeling enzyme regulates replisome function and stability. Nat. Struct. Mol. Biol. 15, 338–345 (2008).
  Article CAS PubMed Google Scholar
• Donaldson, A.D. et al. CLB5-dependent activation of late replication origins in S. cerevisiae. Mol. Cell 2, 173–182 (1998).
  Article CAS PubMed Google Scholar
• Falbo, K.B. & Shen, X. Chromatin remodeling in DNA replication. J. Cell. Biochem. 97, 684–689 (2006).
  Article CAS PubMed Google Scholar
• Ye, X. et al. Defective S phase chromatin assembly causes DNA damage, activation of the S phase checkpoint, and S phase arrest. Mol. Cell 11, 341–351 (2003).
  Article CAS PubMed Google Scholar
• Collins, N. et al. An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nat. Genet. 32, 627–632 (2002).
  Article CAS PubMed Google Scholar
• Bozhenok, L., Wade, P.A. & Varga-Weisz, P. WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J. 21, 2231–2241 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Poot, R.A. et al. The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci. Nat. Cell Biol. 6, 1236–1244 (2004).
  Article CAS PubMed Google Scholar
• Li, J., Santoro, R., Koberna, K. & Grummt, I. The chromatin remodeling complex NoRC controls replication timing of rRNA genes. EMBO J. 24, 120–127 (2005).
  Article PubMed Google Scholar
• Thomas, B.J. & Rothstein, R. The genetic control of direct-repeat recombination in Saccharomyces: the effect of Rad52 and Rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene. Genetics 123, 725–738 (1989).
  CAS PubMed PubMed Central Google Scholar
• Zhao, X., Muller, E.G. & Rothstein, R. A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Mol. Cell 2, 329–340 (1998).
  Article CAS PubMed Google Scholar
• Guldener, U., Heck, S., Fielder, T., Beinhauer, J. & Hegemann, J.H. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24, 2519–2524 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Goldstein, A.L. & McCusker, J.H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15, 1541–1553 (1999).
  Article CAS PubMed Google Scholar
• Lindstrom, K.C., Vary, J.C. Jr, Parthun, M.R., Delrow, J. & Tsukiyama, T. Isw1 functions in parallel with the NuA4 and Swr1 complexes in stress-induced gene repression. Mol. Cell. Biol. 26, 6117–6129 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Gelbart, M.E., Bachman, N., Delrow, J., Boeke, J.D. & Tsukiyama, T. Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant. Genes Dev. 19, 942–954 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Nieduszynski, C.A., Hiraga, S., Ak, P., Benham, C.J. & Donaldson, A.D. OriDB: a DNA replication origin database. Nucleic Acids Res. 35, D40–D46 (2007).
  Article CAS PubMed Google Scholar