High-Resolution Analysis of DNA Replication Domain Organization across an R/G-Band Boundary

REFERENCES

• Aghamohammadi, S. Z., and J. R. K. Savage. 1990. BrdU pulse/reverse staining protocols for investigating chromosome replication. Chromosoma (Berlin) 99:76–82.
   PubMedGoogle Scholar
• Bogenhagen, D., and D. A. Clayton. 1977. Mouse L cell mitochondrial DNA molecules are selected randomly for replication throughout the cell cycle. Cell 11:719–727.
   PubMed Web of Science ®Google Scholar
• Bull, P. C., and D. W. Cox. 1993. Long range restriction mapping of 13q14.3 focused on the Wilson disease region. Genomics 16:593–598.
   PubMedGoogle Scholar
• Bullrich, F., M. L. Veronese, S. Kitada, J. Jurlander, M. A. Caligiuri, J. C. Reed, and C. M. Croce. 1996. Minimal region of loss at 13q14 in B-cell chronic lymphocytic leukemia. Blood 88:3109–3115.
   PubMed Web of Science ®Google Scholar
• Craig, J. M., and W. A. Bickmore. 1993. Chromosome bands—flavours to savours. Bioessays 15:349–354.
   PubMedGoogle Scholar
• Cross, S. H., and A. P. Bird. 1995. CpG islands and genes. Curr. Opin. Genet. Dev. 5:309–314.
   PubMed Web of Science ®Google Scholar
• Davis, A. F., and D. A. Clayton. 1996. In situ localization of mitochondrial DNA replication in intact mammalian cells. J. Cell Biol. 135:883–893.
   PubMed Web of Science ®Google Scholar
• DePamphilis, M. I. 1993. Origins of DNA replication in metazoan chromosomes. J. Biol. Chem. 268:1–4.
   PubMed Web of Science ®Google Scholar
• Dhar, V., A. I. Skoultchi, and C. L. Schildkraut. 1989. Activation and repression of a beta-globin gene in cell hybrids is accompanied by a shift in its temporal replication. Mol. Cell. Biol. 9:3524–3532.
   PubMedGoogle Scholar
• Diviacco, S., P. Norio, L. Zentilin, S. Menzo, M. Clementi, G. Biamonti, S. Riva, A. Falaschi, and M. Giacca. 1992. A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates. Gene 122:313–320.
   PubMed Web of Science ®Google Scholar
• Drouin, R., J. P. Holmquist, and C.-L. Richer. 1994. High-resolution replication bands compared to morphologic G- and R-bands. Adv. Hum. Genet. 22:47–115.
   PubMedGoogle Scholar
• Epner, E., W. C. Forrester, and M. Groudine. 1988. Asynchronous DNA replication within the human þ-globin gene locus. Proc. Natl. Acad. Sci. USA 85:8081–8085.
   PubMedGoogle Scholar
• Eyre-Walker, A. 1992. Evidence that both G+C rich and G+C poor isochores are replicated early and late in the cell cycle. Nucleic Acids Res. 20:1497–1501.
   PubMed Web of Science ®Google Scholar
• Falaschi, A., M. Giacca, L. Zentilin, P. Norio, S. Diviacco, D. Dimitrova, S. Kumar, R. Tuteja, G. Biamonti, G. Perini, F. Weighardt, J. Brito, and S. Riva. 1993. Searching for replication origins in mammalian DNA. Gene 135:125–135.
   PubMedGoogle Scholar
• Fangman, W. L., and B. J. Brewer. 1992. A question of time: replication origins of eukaryotic chromosomes. Cell 71:363–366.
   PubMedGoogle Scholar
• Fetni, R., R. Drouin, C.-L. Richer, and N. Lemieux. 1996. Complementary replication R- and G-band patterns induced by cell blocking at the R-band/ G-band transition, a possible regulatory checkpoint within the S phase of the cell cycle. Cytogenet. Cell Genet. 75:172–179.
   PubMedGoogle Scholar
• Fukagawa, T., K. Sugaya, K. Matsumoto, K. Okumura, A. Ando, H. Inoko, and T. Ikemura. 1995. A boundary of long-range G+C% mosaic domains in the human MHC locus: pseudoautosomal boundary-like sequence exists near the boundary. Genomics 25:184–191.
   PubMed Web of Science ®Google Scholar
• Fukagawa, T., Y. Nakamura, K. Okumura, M. Nogami, A. Ando, H. Inoko, N. Saitou, and T. Ikemura. 1996. Human pseudoautosomal boundary-like sequences: expression and involvement in evolutionary formation of the present-day pseudoautosomal boundary of human sex chromosomes. Hum. Mol. Genet. 5:23–32.
   PubMedGoogle Scholar
• Gardiner, K. 1995. Human genome organization. Curr. Opin. Genet. Dev. 5:315–322.
   PubMedGoogle Scholar
• Gardiner, K. 1996. Base composition and gene distribution: critical patterns in mammalian genome organization. Trends Genet. 12:519–524.
   PubMedGoogle Scholar
• Gilbert, D. M., and S. N. Cohen. 1987. Bovine papilloma virus plasmids replicate randomly in mouse fibroblasts throughout S phase of the cell cycle. Cell 50:59–68.
   PubMedGoogle Scholar
• Glatt, K., H. Glatt, and M. Lalande. 1997. Structure and organization of GABRB3 and GABRA5. Genomics 41:63–69.
   PubMed Web of Science ®Google Scholar
• Hamlin, J. L. 1992. Mammalian origins of replication. Bioessays 14:651–659.
   PubMedGoogle Scholar
• Hamlin, J. L., and P. A. Dijkwel. 1995. On the nature of replication origins in higher eukaryotes. Curr. Opin. Genet. Dev. 5:153–161.
   PubMedGoogle Scholar
• Hand, R. 1975. Regulation of DNA replication on subchromosomal units of mammalian cells. J. Cell Biol. 64:89–97.
   PubMedGoogle Scholar
• Hansen, R. S., T. K. Canfield, M. M. Lamb, S. M. Gartler, and C. D. Laird. 1993. Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell 73:1403–1409.
   PubMed Web of Science ®Google Scholar
• Hansen, R. S., T. K. Canfield, and S. M. Gartler. 1995. Reverse replication timing for the XIST gene in human fibroblasts. Hum. Mol. Genet. 4:813–820.
   PubMedGoogle Scholar
• Hansen, R. S., T. K. Canfield, A. D. Fjeld, S. Mumm, C. D. Laird, and S. M. Gartler. 1997. A variable domain of delayed replication in FRAXA fragile X chromosomes: X inactivation-like spread of late replication. Proc. Natl. Acad. Sci. USA 94:4587–4592.
   PubMed Web of Science ®Google Scholar
• Hawthorn, L. A., and J. K. Cowell. 1995. Integration of the physical and genetic linkage map for human chromosome 13. Genomics 27:399–404.
   PubMedGoogle Scholar
• Hawthorn, L. A., T. Roberts, E. Verlind, R. F. Kooy, and J. K. Cowell. 1995. A yeast artificial chromosome contig that spans the RB1-D13S31 interval on human chromosome 13 and encompasses the frequently deleted region in B-cell chronic lymphocytic leukemia. Genomics 30:425–430.
   PubMedGoogle Scholar
• Holmquist, G. P. 1989. Evolution of chromosome bands: molecular ecology of noncoding DNA. J. Mol. Evol. 28:469–486.
   PubMedGoogle Scholar
• Holmquist, G. P. 1992. Chromosome bands, their chromatin flavors, and their functional features. Am. J. Hum. Genet. 51:17–37.
   PubMed Web of Science ®Google Scholar
• Houwen, R. H. J., S. E. Pautler, J. A. Barwell, K. Arden, J. A. Buchanan, C. D. James, W. K. Cavanee, C. H. C. M. Buys, J. K. Cowell, and D. W. Cox. 1991. Isolation and regional localization of 25 anonymous DNA probes on a chromosome 13 hybrid panel. Cytogenet. Cell Genet. 57:87–90.
   PubMedGoogle Scholar
• Huberman, J. A. 1995. Prokaryotic and eukaryotic replicons. Cell 82:535–542.
   PubMedGoogle Scholar
• Ioannou, P. A., C. T. Amemiya, J. Garnes, P. M. Kroisel, H. Shizuya, C. Chen, M. A. Batzer, and P. J. de Jong. 1994. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat. Genet. 6:84–89.
   PubMed Web of Science ®Google Scholar
• Kawame, H., S. M. Gartler, and R. S. Hansen. 1995. Allele-specific replication timing in imprinted domains: absence of asynchrony at several loci. Hum. Mol. Genet. 4:2287–2293.
   PubMedGoogle Scholar
• Kitsberg, D., S. Selig, I. Keshet, and H. Cedar. 1993. Replication structure of the human þ-globin gene domain. Nature 366:588–590.
   PubMed Web of Science ®Google Scholar
• Kitsberg, D., S. Selig, M. Brandeis, I. Simon, I. Keshet, D. J. Driscoll, R. D. Nicholls, and H. Cedar. 1993. Allele-specific replication timing of imprinted gene regions. Nature 364:459–463.
   PubMed Web of Science ®Google Scholar
• Kooy, R. F., A. Y. Van der Veen, E. Verlind, R. H. J. Houwen, H. Scheffer, and C. H. C. M. Buys. 1993. Physical localisation of the chromosomal marker D13S31 places the Wilson disease locus at the junction of bands q14.3 and q21.1 of chromosome 13. Hum. Genet. 91:504–506.
   PubMedGoogle Scholar
• Kooy, R. F., A. Wijngaard, E. Verlind, H. Scheffer, and C. H. C. M. Buys. 1995. An integrated map of human chromosome 13 allowing regional localization of genetic markers. Eur. J. Hum. Genet. 3:180–187.
   PubMedGoogle Scholar
• Lalande, M., T. P. Dryja, R. R. Schreck, J. Shipley, A. Flint, and S. A. Latt. 1984. Isolation of human chromosome 13-specific DNA sequences cloned from flow sorted chromosomes and potentially linked to the retinoblastoma locus. Cancer Genet. Cytogenet. 13:283–295.
   PubMed Web of Science ®Google Scholar
• Latt, S. A. 1976. Optical studies of metaphase chromosome organization. Annu. Rev. Biophys. Bioeng. 5:1–37.
   PubMedGoogle Scholar
• Lestou, V. S., M. De Braekeleer, S. Strehl, G. Ott, H. Gadner, and P. F. Ambros. 1993. Non-random integration of Epstein-Barr virus in lymphoblastoid cell lines. Genes Chromosomes Cancer 8:38–48.
   PubMedGoogle Scholar
• Petrukhin, K., S. G. Fischer, M. Piratsu, R. E. Tanzi, I. Chernov, M. Devoto, L. M. Brzustowicz, E. Cayanis, E. Vitale, J. J. Russo, D. Matseoane, B. Boukhgalter, W. Wasco, A. L. Figus, J. Loudianos, A. Cao, I. Sternlieb, O. Evgrafov, E. Parano, L. Pavone, D. Warburton, J. Ott, G. K. Penchaszadeh, I. H. Scheinberg, and T. C. Gilliam. 1993. Mapping, cloning and genetic characterization of the region containing the Wilson disease gene. Nat. Genet. 5:338–343.
   PubMed Web of Science ®Google Scholar
• Rivin, C. J., and W. L. Fangman. 1980. Replication fork rate and origin activation during the S phase of Saccharomyces cerevisiae. J. Cell Biol. 85:108–115.
   PubMedGoogle Scholar
• Saccone, S., A. De Sario, J. Wiegant, A. K. Raap, G. Della Valle, and G. Bernardi. 1993. Correlation between isochores and chromosomal bands in the human genome. Proc. Natl. Acad. Sci. USA 90:11929–11933.
   PubMed Web of Science ®Google Scholar
• Saccone, S., S. Caccio, J. Kusuda, L. Andreozzi, and G. Bernardi. 1996. Identification of the gene-richest bands in human chromosomes. Gene 174:85–94.
   PubMedGoogle Scholar
• Saitoh, Y., and U. K. Laemmli. 1994. Metaphase chromosome structure: bands arise from a differential folding path of the highly AT-rich scaffold. Cell 76:609–622.
   PubMed Web of Science ®Google Scholar
• Schweizer, D. 1981. Counterstain-enhanced chromosome banding. Hum. Genet. 57:1–14.
   PubMed Web of Science ®Google Scholar
• Selig, S., K. Okumura, D. C. Ward, and H. Cedar. 1992. Delineation of replication time zones by fluorescence in situ hybridization. EMBO J. 11:1217–1225.
   PubMed Web of Science ®Google Scholar
• Shizuya, H., B. Birren, U. J. Kim, V. Mancino, T. Slepak, Y. Tachiiri, and M. Simon. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor based vector. Proc. Natl. Acad. Sci. USA 89:8794–8797.
   PubMed Web of Science ®Google Scholar
• Sinnett, D., A. Flint, and M. Lalande. 1993. Determination of DNA replication kinetics in synchronized human cells using a PCR-based assay. Nucleic Acids Res. 21:3227–3232.
   PubMed Web of Science ®Google Scholar
• Sternberg, N. L. 1992. Cloning high molecular weight DNA fragments by the bacteriophage P1 system. Trends Genet. 8:11–16.
   PubMedGoogle Scholar
• Subramaniam, P. S., D. L. Nelson, and A. C. Chinault. 1996. Large domains of apparent delayed replication timing associated with triplet repeat expansion at FRAXA and FRAXE. Am. J. Hum. Genet. 59:407–416.
   PubMedGoogle Scholar
• Tenzen, T., T. Yamagata, T. Fukagawa, K. Sugaya, A. Ando, H. Inoko, T. Gojobori, A. Fujiyama, K. Okumura, and T. Ikemura. 1997. Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex. Mol. Cell. Biol. 17:4043–4050.
   PubMed Web of Science ®Google Scholar
• Vassilev, L., and G. Russev. 1988. Purification of nascent DNA chains by immunoprecipitation with anti-BrdU antibodies. Nucleic Acids Res. 16:10397.
   PubMedGoogle Scholar
• Vassilev, L. T., W. C. Burhans, and M. L. DePamphilis. 1990. Mapping an origin of DNA replication at a single-copy locus in exponentially proliferating mammalian cells. Mol. Cell. Biol. 10:4685–4689.
   PubMedGoogle Scholar
• Warburton, D., S. H. Shaw, T. C. Matise, S. Kalachikov, and S. Fischer. 1996. Report of the Third International Workshop on Human Chromosome 13 Mapping 1995. Cytogenet. Cell Genet. 75:85–110.
   PubMedGoogle Scholar
• White, A., J. Tomfohrde, E. Stewart, R. Barnes, D. Le Paslier, J. Weissenbach, L. Cavalli-Sforza, L. Farrer, and A. Bowcock. 1993. A 4.5-megabase yeast artificial chromosome contig from human chromosome 13q14.3 ordering 9 polymorphic microsatellites (22 sequence-tagged sites) tightly linked to the Wilson disease locus. Proc. Natl. Acad. Sci. USA 90:10105–10109.
   PubMedGoogle Scholar
• Yandell, D. W., and T. P. Dryja. 1989. Detection of DNA sequence polymorphisms by enzymatic amplification and direct genomic sequencing. Am. J. Hum. Genet. 45:547–555.
   PubMed Web of Science ®Google Scholar
• Zimmermann, K., and J. W. Mannhalter. 1996. Technical aspects of quantitative competitive PCR. BioTechniques 21:268–279.
   PubMed Web of Science ®Google Scholar
• Zoubak, S., O. Clay, and G. Bernardi. 1996. The gene distribution of the human genome. Gene 174:95–102.
   PubMedGoogle Scholar