Replicating by the clock (original) (raw)

• Hand, R. Eucaryotic DNA: organization of the genome for replication. Cell 15, 317–325 (1978).
  Article CAS Google Scholar
• Holmquist, G. P. Role of replication time in the control of tissue specific gene expression. Am. J. Hum. Genet. 40, 151–173 (1987).
  CAS PubMed PubMed Central Google Scholar
• Gottesfeld, J. & Bloomer, L. S. Assembly of transcriptionally active 5S RNA gene chromatin in vitro. Cell 28, 781–791 (1982).
  Article CAS Google Scholar
• Brown, D. D. The role of stable complexes that repress and activate eucaryotic genes. Cell 37, 359–365 (1984).
  Article CAS Google Scholar
• Latt, S. A. Microfluorometric detection of deoxyribonucleic acid replication in human metaphase chromosomes. Proc. Natl Acad. Sci. USA 70, 3395–3399 (1973).
  Article CAS Google Scholar
• Drouin, R., Lemieux, N. & Richer, C. L. Analysis of DNA replication during S phase by means of dynamic chromosome banding at high resolution. Chromosoma 99, 272–280 (1990).
  Article Google Scholar
• Yunis, J. J. Mid-prophase human chromosomes. The attainment of 2000 bands. Hum. Genet. 56, 293–298 (1981).
  Article CAS Google Scholar
• Bernardi, G. Isochores and the evolutionary genomics of vertebrates. Gene 241, 3–17 (2000).
  Article CAS Google Scholar
• Tenzen, T. et al. Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex. Mol. Cell. Biol. 17, 4043–4050 (1997).
  Article CAS 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 Google Scholar
• Huberman, J. A. & Riggs, A. D. On the mechanism of DNA replication in mammalian chromosomes. J. Mol. Biol. 32, 327–341 (1968).
  Article CAS Google Scholar
• Hand, R. Regulation of DNA replication on subchromosomal units of mammalian cells. J. Cell Biol. 64, 89–97 (1975).
  Article CAS Google Scholar
• Raghuraman, M. K. et al. Replication dynamics of the yeast genome. Science 294, 115–121 (2001). The first report of a genome-wide replication timing map for a eukaryotic organism, the yeast Saccharomyces cerevisiae , which shows that there is no general correlation between gene expression and replication timing.
  Article CAS Google Scholar
• Goldman, M. A., Holmquist, G. P., Caston, L. A. & Nag, A. Replication timing of genes and middle repetitive sequences. Science 224, 686–692 (1984).
  Article CAS Google Scholar
• Schmidt, M. & Migeon, B. R. Asynchronous replication of homologous loci on human active and inactive X chromosome. Proc. Natl Acad. Sci. USA 87, 3685–3689 (1990).
  Article CAS Google Scholar
• Braunstein, D., Schulze, D., DelGiudice, T., Furst, A. & Schildkraut, C. L. The temporal order of replication of murine immunoglobulin heavy chain constant region sequences corresponds to their linear order in the genome. Nucleic Acids Res. 10, 6887–6902 (1982).
  Article CAS Google Scholar
• Gilbert, D. M. Temporal order of replication of Xenopus laevis 5S ribosomal RNA genes in somatic cells. Proc. Natl Acad. Sci. USA 83, 2924–2928 (1986).
  Article CAS Google Scholar
• Hansen, R. S., Canfield, T. K., Lamb, M. M., Gartler, S. M. & Laird, C. D. Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell 73, 1403–1409 (1993).
  Article CAS Google Scholar
• Schubeler, D. et al. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nature Genet. 32, 438–442 (2002). Genome-wide mapping that shows a strong correlation between replication timing and gene expression in Drosophila melanogaster.
  Article Google Scholar
• Selig, S., Okumura, K., Ward, D. C. & Cedar, H. Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J. 11, 1217–1225 (1992).
  Article CAS Google Scholar
• Gilbert, D. M. Replication timing and metazoan evolution. Nature Genet. 32, 336–337 (2002).
  Article CAS Google Scholar
• Reynolds, A. E., McCarroll, R. M., Newlon, C. S. & Fangman, W. L. Time of replication of ARS elements along yeast chromosome III. Mol. Cell. Biol. 9, 4488–4494 (1989).
  Article CAS Google Scholar
• Simon, I. et al. Developmental regulation of DNA replication timing at the human β globin locus. EMBO J. 20, 6150–6157 (2001).
  Article CAS Google Scholar
• Kerem, B. S., Goitein, R., Diamond, G., Cedar, H. & Marcus, M. Mapping of DNase-I sensitive regions on mitotic chromsomes. Cell 38, 493–499 (1984).
  Article CAS Google Scholar
• Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nature Rev. Genet. 2, 21–32 (2001).
  Article CAS Google Scholar
• Ferguson-Smith, A. C. & Surani, M. A. Imprinting and the epigenetic asymmetry between parental genomes. Science 293, 1086–1089 (2001).
  Article CAS Google Scholar
• Rand, E. & Cedar, H. Regulation of imprinting: a multi-tiered process. J. Cell. Biol. (in the press).
• Kitsberg, D., Selig, S., Keshet, I. & Cedar, H. Replication structure of the human β-globin gene domain. Nature 366, 588–590 (1993).
  Article CAS Google Scholar
• Knoll, J. H. M., Cheng, S. -D. & Lalande, M. Allele specificity of DNA replication timing in the Angelman/Prader–Willi syndrome imprinted chromosomal region. Nature Genet. 6, 41–46 (1994).
  Article CAS Google Scholar
• Simon, I. et al. Asynchronous replication of imprinted genes is established in the gametes and maintained during development. Nature 401, 929–932 (1999). Shows evidence that asynchronous replication timing in mammalian cells has the characteristics of a primary imprinting mark.
  Article CAS Google Scholar
• Shemer, R. et al. The imprinting of the Prader–Willi/Angelman syndrome domain. Nature Genet. 26, 440–443 (2000).
  Article CAS Google Scholar
• Gunaratne, P. H., Nakao, M., Ledbetter, D. H., Sutcliffe, J. S. & Chinault, A. C. Tissue-specific and allele-specific replication timing control in the imprinted human Prader–Willi syndrome region. Genes Dev. 9, 808–820 (1995).
  Article CAS Google Scholar
• Avner, P. & Heard, E. X-chromosome inactivation: counting, choice and initiation. Nature Rev. Genet. 2, 59–67 (2001).
  Article CAS Google Scholar
• Lock, L. F., Takagi, N. & Martin, G. R. Methylation of the HPRT gene on the inactive X occurs after chromosome inactivation. Cell 48, 39–46 (1987).
  Article CAS Google Scholar
• Chess, A., Simon, I., Cedar, H. & Axel, R. Allelic inactivation regulates olfactory receptor gene expression. Cell 78, 823–834 (1994).
  Article CAS Google Scholar
• Bix, M. & Locksley, R. M. Independent and epigenetic regulation of the interleukin-4 alleles in CD4+ T Cells. Science 281, 1352–1354 (1998).
  Article CAS Google Scholar
• Mostoslavsky, R. et al. Asynchronous replication and allelic exclusion in the immune system. Nature 414, 221–225 (2001).
  Article CAS Google Scholar
• Rajewsky, K. Clonal selection and learning in the antibody system. Nature 381, 751–758 (1996).
  Article CAS Google Scholar
• Goldmit, M., Schlissel, M., Cedar, H. & Bergman, Y. Differential accessibility at the κ chain locus plays a role in allelic exclusion. EMBO J. 21, 5255–5261 (2002).
  Article CAS Google Scholar
• Mostoslavsky, R. et al. κ chain monoallelic demethylation and the establishment of allelic exclusion. Genes Dev. 12, 1801–1811 (1998).
  Article CAS Google Scholar
• Mombaerts, P. How smell develops. Nature Neurosci. 4, 1192–1198 (2001).
  Article CAS Google Scholar
• Nathans, J. et al. Molecular genetics of human blue cone monochromacy. Science 245, 831–838 (1989).
  Article CAS Google Scholar
• Ermakova, O. V. et al. Evidence that a single replication fork proceeds from early to late replicating domains in the IgH locus in a non-B cell line. Mol. Cell 3, 321–330 (1999).
  Article CAS Google Scholar
• Raghuraman, M. K., Brewer, B. J. & Fangman, W. L. Cell cycle-dependent establishment of a late replication program. Science 276, 806–809 (1997). Shows that the replication timing profile is established by cis -acting elements during early G1 phase.
  Article CAS Google Scholar
• Ferguson, B. M. & Fangman, W. L. A position effect on the time of replication origin activation in yeast. Cell 68, 333–339 (1992). The first evidence that cis -acting sequences have a function in dictating the time of origin firing.
  Article CAS Google Scholar
• Ofir, R., Wong, A. C., McDermid, H. E., Skorecki, K. L. & Selig, S. Position effect of human telomeric repeats on replication timing. Proc. Natl Acad. Sci. USA 96, 11434–11439 (1999).
  Article CAS Google Scholar
• Cosgrove, A. J. et al. Ku complex controls the replication time of DNA in telomere regions. Genes Dev. 16, 2485–2490 (2002).
  Article CAS Google Scholar
• Stevenson, J. B. & Gottschling, D. E. Telomeric chromatin modulates replication timing near chromosome ends. Genes Dev. 13, 146–151 (1999).
  Article CAS Google Scholar
• Friedman, K. L. et al. Multiple determinanats controlling activation of yeast replication origins late in S phase. Genes Dev. 10, 1595–1607 (1996).
  Article CAS Google Scholar
• Kitsberg, D. et al. Allele-specific replication timing of imprinted gene regions. Nature 364, 459–463 (1993).
  Article CAS Google Scholar
• Aladjem, M. I. et al. Participation of human β-globin locus control region in initation of DNA replication. Science 270, 815–819 (1995).
  Article CAS Google Scholar
• Aladjem, M. I., Rodewald, L. W., Kolman, J. L. & Wahl, G. M. Genetic dissection of a mammalian replicator in the human β-globin locus. Science 281, 1005–1009 (1998).
  Article CAS Google Scholar
• Aladjem, M. I. et al. Replication initiation patterns in the β-globin loci of totipotent and differentiated murine cells: evidence for multiple initiation regions. Mol. Cell. Biol. 22, 442–452 (2002).
  Article CAS Google Scholar
• Kamath, S. & Leffak, M. Multiple sites of replication initiation in the human β-globin gene locus. Nucleic Acids Res. 29, 809–817 (2001).
  Article CAS Google Scholar
• Forrester, W. C. et al. A deletion of the human β-globin locus activation region causes a major alteration in chromatin structure and replication across the entire β-globin locus. Genes Dev. 4, 1637–1649 (1990).
  Article CAS Google Scholar
• Cimbora, D. M. et al. Long-distance control of origin choice and replication timing in the human β-globin locus are independent of the locus control region. Mol. Cell. Biol. 20, 5581–5591 (2000).
  Article CAS 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). The incubation in Xenopus egg extracts of mammalian nuclei isolated at different phases of the cell cycle showed that the organization of replication timing is established in early G1.
  Article CAS Google Scholar
• Gilbert, D. M. Nuclear position leaves its mark on replication timing. J. Cell Biol. 152, F11–F15 (2001).
  Article CAS Google Scholar
• Li, F. et al. The replication timing program of the Chinese hamster β-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase. J. Cell Biol. 154, 283–292 (2001).
  Article CAS Google Scholar
• Bridger, J. M., Boyle, S., Kill, I. R. & Bickmore, W. A. Re-modelling of nuclear architecture in quiescent and senescent human fibroblasts. Curr. Biol. 10, 149–152 (2000).
  Article CAS Google Scholar
• Heun, P., Laroche, T., Raghuraman, M. K. & Gasser, S. M. The positioning and dynamics of origins of replication in the budding yeast nucleus. J. Cell Biol. 152, 385–400 (2001).
  Article CAS Google Scholar
• Vogelauer, M., Rubbi, L., Lucas, I., Brewere, B. J. & Grunstein, M. Histone acetylation regulates the time of replication origin firing. Mol. Cell 10, 1223–1233 (2002). Shows that in yeast the histone acetylation status in the vicinity of origins can determine its replication time.
  Article CAS Google Scholar
• Kagotani, K. et al. Replication timing properties within the mouse distal chromosome 7 imprinting cluster. Biosci. Biotechnol. Biochem. 66, 1046–1051 (2002).
  Article CAS Google Scholar
• Hansen, R. S. et al. Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant. Hum. Mol. Genet. 9, 2575–2587 (2000).
  Article CAS Google Scholar
• Jablonka, E., Goitein, R., Marcus, M. & Cedar, H. DNA hypomethylation causes an increase in DNase-I sensitivity and an advance in the time of replication of the entire inactive X chromosome. Chromosoma 93, 152–156 (1985).
  Article CAS 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 Google Scholar
• Shirahige, K. et al. Regulation of DNA-replication origins during cell-cycle progression. Nature 395, 618–621 (1998).
  Article CAS 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 Google Scholar
• Paulovich, A. G. & Hartwell, L. H. A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage. Cell 82, 841–847 (1995).
  Article CAS Google Scholar
• Gilbert, D. M. Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 14, 377–383 (2002).
  Article CAS Google Scholar
• Zhang, J., Feng, X., Hashimshony, T., Keshet, I. & Cedar, H. The establishment of transcriptional competence in early and late S-phase. Nature 420, 198–202 (2002). Nuclear injection experiments showing that replicating DNA is automatically packaged in a repressed form during late S phase.
  Article CAS Google Scholar
• Jeppesen, P. & Turner, B. M. The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74, 281–289 (1993).
  Article CAS 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). This work shows that histone deacetylase HDAC2 localizes to replication foci exclusively during late S phase in mammalian cells. This could function as a mechanism for repressing late-replicating genes.
  Article CAS Google Scholar
• Grunstein, M. Histone acetylation in chromatin structure and transcription. Nature 389, 349–352 (1997).
  Article CAS Google Scholar
• Sobel, R. E., Cook, R. G., Perry, C. A., Annunziato, A. T. & Allis, C. D. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc. Natl Acad. Sci. USA 92, 1237–1247 (1995).
  Article CAS Google Scholar
• Razin, A. CpG methylation, chromatin structure and gene silencing — a three-way connection. EMBO J. 17, 4905–4908 (1998).
  Article CAS Google Scholar
• Surani, M. A., Barton, S. C. & Norris, M. L. Development of mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308, 548–550 (1984).
  Article CAS Google Scholar
• McGrath, J. & Solter, D. Complementation of mouse embryogenesis requires both maternal and paternal genomes. Cell 37, 179–183 (1984).
  Article CAS Google Scholar
• Schumacher, A. Mechanisms and brain specific consequences of genomic imprinting in Prader–Willi and Angelman syndrome. Gene Funct. Dis. 1, 1–19 (2001).
  Google Scholar
• Singh, N. et al. Coordination of the random asynchronous replication of autosomal loci. Nature Genet. (in the press).