7
Views
67
CrossRef citations to date
0
Altmetric
Research Article

Precise Switching of DNA Replication Timing in the GC Content Transition Area in the Human Major Histocompatibility Complex

, , , , , , , , & show all
Pages 4043-4050 | Received 10 Feb 1997, Accepted 09 Apr 1997, Published online: 29 Mar 2023

REFERENCES

  • Aota, S., and T. Ikemura. 1986. Diversity in G+C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res. 14:6345–6355.
  • Baran, N., A. Lapidot, and H. Manor. 1991. Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts. Proc. Natl. Acad. Sci. USA 88:507–511.
  • Bernardi, G. 1989. The isochore organization of the human genome. Annu. Rev. Genet. 23:637–661.
  • Bernardi, G. 1993. The isochore organization of the human genome and its evolutionary history—a review. Gene 135:57–66.
  • Bernardi, G., B. Olofsson, J. Filipski, M. Zerial, J. Salinas, G. Cuny, M. Meunier-Rotival, and F. Rodier. 1985. The mosaic genome of warm-blooded vertebrates. Science 228:953–958.
  • Biamonti, G., G. Perini, F. Weighardt, S. Riva, M. Giacca, P. Norio, L. Zentilin, S. Diviacco, D. Dimitrova, and A. Falaschi. 1992. A human DNA replication origin: localization and transcriptional characterization. Chromosoma 102:S24–S31.
  • Bodnar, J. W., C. J. Jones, D. H. Coombs, G. D. Pearson, and D. C. Ward. 1983. Proteins tightly bound to HeLa cell DNA at nuclear matrix attachment sites. Mol. Cell. Biol. 3:1567–1579.
  • Brinton, B. T., M. S. Caddle, and N. H. Heintz. 1991. Position and orientation-dependent effects of a eukaryotic Z-triplex DNA motif on episomal DNA replication in COS-7 cells. J. Biol. Chem. 266:5153–5161.
  • Brotherton, T., D. Zenk, S. Kahanic, and J. Reneker. 1991. Avian nuclear matrix proteins bind very tightly to cellular DNA of the b-globin gene enhancer in a tissue-specific fashion. Biochemistry 30:5845–5850.
  • Campbell, R. D., and J. Trowsdale. 1993. Map of the human MHC. Immunol. Today 14:349–352.
  • Contreas, G., M. Giacca, and A. Falaschi. 1992. Purification of BrdUrd-substituted DNA by immunoaffinity chromatography with anti-BrdUrd antibodies. BioTechniques 12:824–825.
  • Craig, J. M., and W. A. Bickmore. 1993. Chromosome bands—flavours to savour. BioEssays 15:349–354.
  • Cress, A. E., and K. M. Kurath. 1988. Identification of attachment proteins for DNA in Chinese hamster ovary cells. J. Biol. Chem. 263:19678–19683.
  • Dayn, A., G. M. Samadashwily, and S. M. Mirkin. 1992. Intramolecular DNA triplexes: unusual sequence requirements and influence on DNA polymerization. Proc. Natl. Acad. Sci. USA 89:11406–11410.
  • 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.
  • Drouin, R., G. P. Holmquist, and C.-L. Richer. 1994. High-resolution replication bands compared with morphologic G- and R-bands. Adv. Hum. Genet. 22:47–115.
  • Ellis, N., and P. N. Goodfellow. 1989. The mammalian pseudoautosomal region. Trends Genet. 5:406–410.
  • Ellis, N., P. Yen, K. Neiswanger, L. J. Shapiro, and P. N. Goodfellow. 1990. Evolution of the pseudoautosomal boundary in Old World monkeys and great apes. Cell 63:977–986.
  • Ellis, N. A., P. J. Goodfellow, B. Pym, M. Smith, M. Palmer, A.-M. Frischauf, and P. N. Goodfellow. 1989. The pseudoautosomal boundary in man is defined by an Alu repeat sequence inserted on the Y chromosome. Nature 337:81–84.
  • 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.
  • 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.
  • 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.
  • Gardiner, K., B. Aissani, and G. Bernardi. 1990. A compositional map of human chromosome 21. EMBO J. 9:1853–1858.
  • Gilliland, G., S. Perrin, K. Blanchard, and H. F. Bunn. 1990. Analysis of cytokine mRNA and DNA: detection and quantitation by competitive polymerase chain reaction. Proc. Natl. Acad. Sci. USA 87:2725–2729.
  • Goldman, M. A., G. P. Holmquist, M. C. Gray, L. A. Caston, and A. Nag. 1984. Replication timing of genes and middle repetitive sequences. Science 224:686–692.
  • Hidaka, M., M. Akiyama, and T. Horiuchi. 1988. A consensus sequence of three DNA replication terminus sites on the E. coli chromosome is highly homologous to the terR sites of the R6K plasmid. Cell 55:467–475.
  • Holmquist, G., M. Gray, T. Porter, and J. Jordan. 1982. Characterization of Giemsa dark- and light-band DNA. Cell 31:121–129.
  • Holmquist, G. P. 1989. Evolution of chromosome bands: molecular ecology of noncoding DNA. J. Mol. Evol. 28:469–486.
  • Holmquist, G. P. 1992. Chromosome bands, their chromatin flavors, and their functional features. Am. J. Hum. Genet. 51:17–37.
  • Huberman, J. A., and A. D. Riggs. 1968. On the mechanism of DNA replication in mammalian chromosomes. J. Mol. Biol. 32:327–341.
  • Ikemura, T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:13–34.
  • Ikemura, T., and S. Aota. 1988. Global variation in G+C content along vertebrate genome DNA: possible correlation with chromosome band structures. J. Mol. Biol. 203:1–13.
  • Ikemura, T., and K. Wada. 1991. Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res. 19:4333–4339.
  • Ikemura, T., K. Wada, and S. Aota. 1990. Giant G+C% mosaic structures of the human genome found by arrangement of GenBank human DNA sequences according to genetic positions. Genomics 8:207–216.
  • Jackson, D. A., P. Dickinson, and P. R. Cook. 1990. The size of chromatin loops in HeLa cells. EMBO J. 9:567–571.
  • Jackson, D. A., J. Yuan, and P. R. Cook. 1988. A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. J. Cell Sci. 90:365–378.
  • Jurka, J. 1990. Novel families of interspersed repetitive elements from the human genome. Nucleic Acids Res. 18:137–141.
  • Klevecz, R. R., B. A. Keniston, and L. L. Deaven. 1975. The temporal structure of S phase. Cell 5:195–203.
  • Kobayashi, T., M. Hidaka, M. Nishizawa, and T. Horiuchi. 1992. Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae. Mol. Gen. Genet. 233:355–362.
  • Little, R. D., T. H. K. Platt, and C. L. Schildkraut. 1993. Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol. 13:6600–6613.
  • Matsumoto, K., M. Arai, N. Ishihara, A. Ando, H. Inoko, and T. Ikemura. 1992. Cluster of fibronectin type III repeats found in the human major histocompatibility complex class III region shows the highest homology with the repeats in an extracellular matrix protein, tenascin. Genomics 12:485–491.
  • Nakamura, H., T. Morita, and C. Sato. 1986. Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp. Cell Res. 165:291–297.
  • Okumura, K. Unpublished data.
  • Pedrali-Noy, G., S. Spadari, A. Miller-Faurés, A. O. A. Miller, J. Kruppa, and G. Koch. 1980. Synchronization of HeLa cell cultures by inhibition of DNA polymerase α with aphidicolin. Nucleic Acids Res. 8:377–387.
  • Pilia, G., R. D. Little, B. Aïssani, G. Bernardi, and D. Schlessinger. 1993. Isochores and CpG islands in YAC contigs in human Xq26.1-qter. Genomics 17:456–462.
  • Rao, B. S. 1994. Pausing of simian virus 40 DNA replication fork movement in vivo by (dG-dA)n z (dT-dC)n tracts. Gene 140:233–237.
  • Razin, S. V., V. V. Chernokhvostov, A. V. Roodyn, I. B. Zbarsky, and G. P. Georgiev. 1981. Proteins tightly bound to DNA in the regions of DNA attachment to the skeletal structures of interphase nuclei and metaphase chromosomes. Cell 27:65–73.
  • Saccone, S., A. De Sario, J. Wiegant, A. K. Raap, G. Della Valle, and G. Bernardi. 1993. Correlations between isochores and chromosomal bands in the human genome. Proc. Natl. Acad. Sci. USA 90:11929–11933.
  • Schirmbeck, R., and W. Deppert. 1991. Structural topography of simian virus 40 DNA replication. J. Virol. 65:2578–2588.
  • Senger, G., J. Ragoussis, J. Trowsdale, and D. Sheer. 1993. Fine mapping of the human MHC class II region within chromosome band 6p21 and evaluation of probe ordering using interphase fluorescence in situ hybridization. Cytogenet. Cell Genet. 64:49–53.
  • Sharp, P. M., and A. T. Lloyd. 1993. Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. Nucleic Acids Res. 21:179–183.
  • Siebert, P. D., and J. W. Larrick. 1992. Competitive PCR. Nature 359:557–558.
  • Spack, E. G., E. D. Lewis, B. Paradowski, R. T. Schimke, and P. P. Jones. 1992. Temporal order of DNA replication in the H-2 major histocompatibility complex of the mouse. Mol. Cell. Biol. 12:5174–5188.
  • Spring, B., C. Fonatsch, C. Müller, G. Pawelec, J. Kompf, P. Wernet, and A. Ziegler. 1985. Refinement of HLA gene mapping with induced B-cell line mutants. Immunogenetics 21:277–291.
  • Sugaya, K., T. Fukagawa, K. Matsumoto, K. Mita, E. Takahashi, A. Ando, H. Inoko, and T. Ikemura. 1994. Three genes in the human MHC class III region near the junction with the class II: gene for receptor of advanced glycosylation end products, PBX2 homeobox gene and a Notch homolog, human counterpart of mouse mammary tumor gene int-3. Genomics 23:408–419.
  • Sugaya, K., S. Sasanuma, J. Nohata, T. Kimura, T. Fukagawa, Y. Nakamura, A. Ando, H. Inoko, T. Ikemura, and K. Mita. Gene organization of human NOTCH4 and (CTG)n polymorphism in this human counterpart gene of mouse proto-oncogene Int3. Gene, in press.
  • Tribioli, C., G. Biamonti, M. Giacca, M. Colonna, S. Riva, and A. Falaschi. 1987. Characterization of human DNA sequences synthesized at the onset of S-phase. Nucleic Acids Res. 15:10211–10232.
  • Yoon, Y., J. A. Sanchez, C. Brun, and J. A. Huberman. 1995. Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis. Mol. Cell. Biol. 15:2482–2489.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.