Replication timing and epigenetic reprogramming of gene expression: a two-way relationship? (original) (raw)

• Aladjem, M. I. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nature Rev. Genet. 8, 588–600 (2007).
  Article CAS PubMed Google Scholar
• Collins, N. et al. An ACF1–ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nature Genet. 32, 627–632 (2002).
  Article CAS PubMed Google Scholar
• Groth, A., Rocha, W., Verreault, A. & Almouzni, G. Chromatin challenges during DNA replication and repair. Cell 128, 721–733 (2007).
  Article CAS PubMed Google Scholar
• Huvet, M. et al. Human gene organization driven by the coordination of replication and transcription. Genome Res. 17, 1278–1285 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Wintersberger, E. Why is there late replication? Chromosoma 109, 300–307 (2000).
  Article CAS PubMed Google Scholar
• Farkash-Amar, S. et al. Global organization of replication time zones of the mouse genome. Genome Res. 18, 1562–1570 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Hiratani, I. et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 6, e245 (2008).
  Article PubMed PubMed Central Google Scholar
• McNairn, A. J. & Gilbert, D. M. Epigenomic replication: linking epigenetics to DNA replication. Bioessays 25, 647–656 (2003).
  Article CAS PubMed Google Scholar
• Cedar, H. & Bergman, Y. Choreography of Ig allelic exclusion. Curr. Opin. Immunol. 20, 308–317 (2008).
  Article CAS PubMed Google Scholar
• Horsthemke, B., Surani, A., James, T. & Ohlsson, R. The mechanisms of genomic imprinting. Results Probl. Cell Differ. 25, 91–118 (1999).
  Article CAS PubMed Google Scholar
• Pant, V. et al. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. Genes Dev. 17, 586–590 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Bergstrom, R., Whitehead, J., Kurukuti, S. & Ohlsson, R. CTCF regulates asynchronous replication of the imprinted H19/Igf2 domain. Cell Cycle 6, 450–454 (2007).
  Article PubMed Google Scholar
• Tremblay, K. D., Duran, K. L. & Bartolomei, M. S. A 5′ 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol. Cell Biol. 17, 4322–4329 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Kanduri, C. et al. Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr. Biol. 10, 853–856 (2000).
  Article CAS PubMed Google Scholar
• Dimitrova, D. S. & Gilbert, D. M. The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol. Cell 4, 983–993 (1999).
  Article CAS PubMed Google Scholar
• Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B. J. & Grunstein, M. Histone acetylation regulates the time of replication origin firing. Mol. Cell 10, 1223–1233 (2002).
  Article CAS PubMed Google Scholar
• Bell, S. P., Kobayashi, R. & Stillman, B. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science 262, 1844–1849 (1993).
  Article CAS PubMed Google Scholar
• DePamphilis, M. L. et al. Regulating the licensing of DNA replication origins in metazoa. Curr. Opin. Cell Biol. 18, 231–239 (2006).
  Article CAS PubMed Google Scholar
• Sasaki, T. & Gilbert, D. M. The many faces of the origin recognition complex. Curr. Opin. Cell Biol. 19, 337–343 (2007).
  Article CAS PubMed Google Scholar
• DePamphilis, M. L. The 'ORC cycle': a novel pathway for regulating eukaryotic DNA replication. Gene 310, 1–15 (2003).
  Article CAS PubMed Google Scholar
• Cadoret, J. C. et al. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc. Natl Acad. Sci. USA 105, 15837–15842 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Zellner, E., Herrmann, T., Schulz, C. & Grummt, F. Site-specific interaction of the murine pre-replicative complex with origin DNA: assembly and disassembly during cell cycle transit and differentiation. Nucleic Acids Res. 35, 6701–6713 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Tabancay, A. P. Jr & Forsburg, S. L. Eukaryotic DNA replication in a chromatin context. Curr. Top. Dev. Biol. 76, 129–184 (2006).
  Article CAS PubMed Google Scholar
• Danis, E. et al. Specification of a DNA replication origin by a transcription complex. Nature Cell Biol. 6, 721–730 (2004).
  Article CAS PubMed Google Scholar
• Kan, J. et al. ORC mediates histone 3 lysine 4 methylation through cooperation with SPP1 in Saccharomyces cerevisiae. J. Biol. Chem. 9 Oct 2008 (doi:10.1074/jbc.C800182200).
  Article CAS PubMed PubMed Central Google Scholar
• Miotto, B. & Struhl, K. HBO1 histone acetylase is a coactivator of the replication licensing factor Cdt1. Genes Dev. 22, 2633–2638 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Goren, A., Tabib, A., Hecht, M. & Cedar, H. DNA replication timing of the human β-globin domain is controlled by histone modification at the origin. Genes Dev. 22, 1319–1324 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Zhou, J. et al. Cell cycle regulation of chromatin at an origin of DNA replication. EMBO J. 24, 1406–1417 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Zhou, J., Chau, C., Deng, Z., Stedman, W. & Lieberman, P. M. Epigenetic control of replication origins. Cell Cycle 4, 889–892 (2005).
  Article CAS PubMed Google Scholar
• Perry, P. et al. A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction. Cell Cycle 3, 1645–1650 (2004).
  Article CAS PubMed Google Scholar
• Zhang, J., Xu, F., Hashimshony, T., Keshet, I. & Cedar, H. Establishment of transcriptional competence in early and late S phase. Nature 420, 198–202 (2002).
  Article CAS PubMed Google Scholar
• Zhang, Z., Shibahara, K. & Stillman, B. PCNA connects DNA replication to epigenetic inheritance in yeast. Nature 408, 221–225 (2000).
  Article CAS PubMed Google Scholar
• Moldovan, G. L., Pfander, B. & Jentsch, S. PCNA, the maestro of the replication fork. Cell 129, 665–679 (2007).
  Article CAS PubMed Google Scholar
• Rountree, M. R., Bachman, K. E. & Baylin, S. B. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nature Genet. 25, 269–277 (2000).
  Article CAS PubMed Google Scholar
• Esteve, P. O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Wu, R., Terry, A. V., Singh, P. B. & Gilbert, D. M. Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol. Biol. Cell 16, 2872–2881 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Jorgensen, H. F. et al. The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells. Genome Biol. 8, R169 (2007).
  Article PubMed PubMed Central Google Scholar
• Kupper, K. et al. Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116, 285–306 (2007).
  Article PubMed PubMed Central Google Scholar
• Pombo, A. & Branco, M. R. Functional organisation of the genome during interphase. Curr. Opin. Genet. Dev. 17, 451–455 (2007).
  Article CAS PubMed Google Scholar
• Cremer, M. et al. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 9, 541–567 (2001).
  Article CAS PubMed Google Scholar
• Conti, C. et al. Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. Mol. Biol. Cell 18, 3059–3067 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Izumi, M., Yatagai, F. & Hanaoka, F. Localization of human Mcm10 is spatially and temporally regulated during the S phase. J. Biol. Chem. 279, 32569–32577 (2004).
  Article CAS PubMed Google Scholar
• Taddei, A., Hediger, F., Neumann, F. R. & Gasser, S. M. The function of nuclear architecture: a genetic approach. Annu. Rev. Genet. 38, 305–345 (2004).
  Article CAS PubMed Google Scholar
• Hancock, R. A new look at the nuclear matrix. Chromosoma 109, 219–225 (2000).
  Article CAS PubMed Google Scholar
• Courbet, S. et al. Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 455, 557–560 (2008).
  Article CAS PubMed Google Scholar
• Lemaitre, J. M., Danis, E., Pasero, P., Vassetzky, Y. & Mechali, M. Mitotic remodeling of the replicon and chromosome structure. Cell 123, 787–801 (2005).
  Article CAS PubMed Google Scholar
• Buongiorno-Nardelli, M., Micheli, G., Carri, M. T. & Marilley, M. A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298, 100–102 (1982).
  Article CAS PubMed Google Scholar
• Fisher, D. & Mechali, M. Vertebrate HoxB gene expression requires DNA replication. EMBO J. 22, 3737–3748 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Sproul, D., Gilbert, N. & Bickmore, W. A. The role of chromatin structure in regulating the expression of clustered genes. Nature Rev. Genet. 6, 775–781 (2005).
  Article CAS PubMed Google Scholar
• Johmura, Y., Osada, S., Nishizuka, M. & Imagawa, M. FAD24 acts in concert with histone acetyltransferase HBO1 to promote adipogenesis by controlling DNA replication. J. Biol. Chem. 283, 2265–2274 (2008).
  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
• Pasero, P., Bensimon, A. & Schwob, E. Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. Genes Dev. 16, 2479–2484 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Petermann, E. et al. Chk1 requirement for high global rates of replication fork progression during normal vertebrate S phase. Mol. Cell Biol. 26, 3319–3326 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Shechter, D., Costanzo, V. & Gautier, J. ATR and ATM regulate the timing of DNA replication origin firing. Nature Cell Biol. 6, 648–655 (2004).
  Article CAS PubMed Google Scholar
• Siddiqui, K. & Stillman, B. ATP-dependent assembly of the human origin recognition complex. J. Biol. Chem. 282, 32370–32383 (2007).
  Article CAS PubMed Google Scholar
• Cuvier, O., Stanojcic, S., Lemaitre, J. M. & Mechali, M. A topoisomerase II-dependent mechanism for resetting replicons at the S–M-phase transition. Genes Dev. 22, 860–865 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Labit, H., Perewoska, I., Germe, T., Hyrien, O. & Marheineke, K. DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts. Nucleic Acids Res. 36, 5623–5634 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Egli, D., Rosains, J., Birkhoff, G. & Eggan, K. Developmental reprogramming after chromosome transfer into mitotic mouse zygotes. Nature 447, 679–685 (2007).
  Article CAS PubMed Google Scholar
• Kloc, A., Zaratiegui, M., Nora, E. & Martienssen, R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18, 490–495 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Chen, E. S. et al. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451, 734–737 (2008).
  Article CAS PubMed Google Scholar
• Karnani, N., Taylor, C., Malhotra, A. & Dutta, A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res. 17, 865–876 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Gimelbrant, A., Hutchinson, J. N., Thompson, B. R. & Chess, A. Widespread monoallelic expression on human autosomes. Science 318, 1136–1140 (2007).
  Article CAS PubMed Google Scholar
• Kelly, B. L. & Locksley, R. M. Coordinate regulation of the IL-4, IL-13, and IL-5 cytokine cluster in Th2 clones revealed by allelic expression patterns. J. Immunol. 165, 2982–2986 (2000).
  Article CAS PubMed Google Scholar
• State, M. W. et al. Epigenetic abnormalities associated with a chromosome 18(q21–q22) inversion and a Gilles de la Tourette syndrome phenotype. Proc. Natl Acad. Sci. USA 100, 4684–4689 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• D'Antoni, S. et al. Altered replication timing of the HIRA/Tuple1 locus in the DiGeorge and Velocardiofacial syndromes. Gene 333, 111–119 (2004).
  Article CAS PubMed Google Scholar
• Watanabe, Y., Shibata, K., Sugimura, H. & Maekawa, M. p53-dependent change in replication timing of the human genome. Biochem. Biophys. Res. Commun. 364, 289–293 (2007).
  Article CAS PubMed Google Scholar
• McGarvey, K. M. et al. Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res. 66, 3541–3549 (2006).
  Article CAS PubMed Google Scholar
• Watanabe, Y. et al. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum. Mol. Genet. 11, 13–21 (2002).
  Article CAS PubMed Google Scholar
• Watanabe, Y., Ikemura, T. & Sugimura, H. Amplicons on human chromosome 11q are located in the early/late-switch regions of replication timing. Genomics 84, 796–805 (2004).
  Article CAS PubMed Google Scholar
• Sclafani, R. A. & Holzen, T. M. Cell cycle regulation of DNA replication. Annu. Rev. Genet. 41, 237–280 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Hasan, S., Hassa, P. O., Imhof, R. & Hottiger, M. O. Transcription coactivator p300 binds PCNA and may have a role in DNA repair synthesis. Nature 410, 387–391 (2001).
  Article CAS PubMed Google Scholar
• Jorgensen, S. et al. The histone methyltransferase SET8 is required for S-phase progression. J. Cell Biol. 179, 1337–1345 (2007).
  Article PubMed PubMed Central Google Scholar