2
Views
2
CrossRef citations to date
0
Altmetric
DNA Dynamics and Chromosome Structure

The Chromatin Structure of Saccharomyces cerevisiae Autonomously Replicating Sequences Changes during the Cell Division Cycle

, &
Pages 5301-5311 | Published online: 31 Mar 2023

References

  • Amati, B. B., and S. M. Gasser. 1988. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54:967-978.
  • Bloom, K. S., and J. Carbon. 1982. Yeast centromere DNA is in a unique and highly ordered structure in chromosomes and small circular minichromosomes. Cell 29:305-317.
  • Bouton, A. H., and M. M. Smith. 1986. Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids. Mol. Cell. Biol. 6:2354-2363.
  • Bouton, A. H., V. S. Stirling, and M. M. Smith. 1987. Analysis of DNA sequences homologous with the ARS core consensus in Saccharomyces cerevisiae. Yeast 3:107-115.
  • Brand, A. H., G. Micklem, and K. Nasmyth. 1987. A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation. Cell 51:709-719.
  • Brewer, B. J., and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463-471.
  • Broach, J., Y. Li, J. Feldman, M. Jayaram, J. Abraham, K. A. Nasmyth, and J. B. Hicks. 1982. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harbor Symp. Quant. Biol. 47:1165-1173.
  • Buchman, A. R., W. J. Kimmerly, J. Rine, and R. D. Kornberg. 1988. Two DNA binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:210-225.
  • Celniker, S. E., K. Sweder, F. Srienc, J. E. Bailey, and J. L. Campbell. 1984. Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Mol. Cell. Biol. 4:2455-2466.
  • Cereghini, S., and M. Yaniv. 1984. Assembly of transfected DNA into chromatin: structural changes in the origin-promoter-enhancer region upon replication. EMBO J. 3:1243-1253.
  • Corliss, D. A., and W. E. White, Jr. 1981. Fluorescence of yeast vitally stained with ethidium bromide and propidium iodide. J. Histochem. Cytochem. 29:45-48.
  • Dijkwel, P. A., L. H. F. Mullenders, and F. Wanka. 1979. Analysis of the attachment of replication DNA to a nuclear matrix in mammalian interphase nuclei. Nucleic Acids Res. 6:219-230.
  • Dijkwel, P. A., P. W. Wenink, and J. Poddighe. 1986. Permanent attachment of replication origins to the nuclear matrix in BHK cells. Nucleic Acids Res. 14:3241-3249.
  • Eissenberg, J. C., I. L. Cartwright, G. H. Thomas, and S. C. R. Elgin. 1985. Selected topics in chromatin structure. Annu. Rev. Genet. 19:485-536.
  • Fagrelius, T. J., and D. M. Livingston. 1984. Location of DNase I sensitive cleavage sites in the yeast 2μ plasmid DNA chromosome. J. Mol. Biol. 173:1-13.
  • Fangman, W. L., R. H. Hice, and E. Chlebowicz-Sledziewska. 1983. ARS replication during the yeast S phase. Cell 32:831-838.
  • Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6-13.
  • Ferguson, B. M., B. J. Brewer, A. E. Reynolds, and W. L. Fangman. 1991. A yeast origin of replication is activated late in S phase. Cell 65:507-515.
  • Fraser, R. S. S., and A. Barnes. 1983. Theoretical analysis of a method for determining the pattern of macromolecular synthesis during the cell cycle. J. Cell Sci. 62:187-207.
  • Gross, D. S., and W. T. Garrard. 1988. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57:159-197.
  • Hartwell, L. H. 1973. Three additional genes required for deoxyribonucleic acid synthesis in Saccharomyces cerevisiae. J. Bacteriol. 115:966-974.
  • Hereford, L. M., and L. H. Hartwell. 1974. Sequential gene function in the initiation of Saccharomyces cerevisiae DNA synthesis. J. Mol. Biol. 84:445-461.
  • Hereford, L. M., and M. A. Osley. 1981. Cell-cycle regulation of yeast histone mRNA. Cell 24:367-375.
  • Hofmann, J. F.-X., and S. M. Gasser. 1991. Identification and purification of a protein that binds the yeast ARS consensus sequence. Cell 64:951-960.
  • Holmes, S. G., and M. M. Smith. 1989. Interaction of the H4 autonomously replicating sequence core consensus with its 3′ flanking domain. Mol. Cell. Biol. 9:5464-5472.
  • Hsiao, C. L., and J. Carbon. 1979. High frequency transformation of yeast by plasmids containing the cloned ARG4 gene. Proc. Natl. Acad. Sci. USA 76:3829-3833.
  • Huberman, J. A., L. D. Spotila, K. A. Nawotka, S. M. El-Assouli, and L. R. Davis. 1987. The in vivo replication origin of the yeast two micron plasmid. Cell 51:473-481.
  • Huberman, J. A., J. Zhu, L. R. Davis, and C. S. Newlon. 1988. Close association of a DNA replication origin and an ARS element on chromosome III of the yeast, Saccharomyces cerevisiae. Nucleic Acids Res. 16:6373-6383.
  • Jackson, D. A., and P. R. Cook. 1986. Replication occurs at a nucleoskeleton. EMBO J. 5:1403-1410.
  • Jacobs, C. W., A. E. M. Adams, P. J. Szaniszlo, and J. R. Pringle. 1988. Functions of microtubules in the Saccharomyces cerevisiae cell cycle. J. Cell Biol. 107:1409-1426.
  • Jakobovits, E. B., S. Bratosin, and Y. Aloni. 1980. A nucleo-some-free region in SV40 minichromosomes. Nature (London) 285:263-265.
  • Kearsey, S. 1983. Analysis of sequences conferring autonomous replication in baker’s yeast. EMBO J. 2:1571-1575.
  • Kearsey, S. 1984. Structural requirements for the function of a yeast chromosomal replicator. Cell 37:299-307.
  • Kolakowski, L. F., Jr., M. Schloesser, and B. S. Cooperman. 1988. Cloning, molecular characterization, and chromosome localization of the inorganic pyrophosphatase (PPA) gene from S. cerevisiae. Nucleic Acids Res. 23:10441-10452.
  • Linskens, M. H. K., and J. A. Huberman. 1988. Organization of replication in the rDNA of Saccharomyces cerevisiae. Mol. Cell. Biol. 8:4927-4935.
  • Livingston, D. M. 1982. A sequence of the yeast 2μm plasmid chromosome near the origin of replication is exposed to restriction endonuclease digestion. J. Mol. Biol. 160:397-410.
  • Lohr, D., and G. Ide. 1979. Comparison of the structure and transcriptional capability of growing phase and stationary yeast chromatin: a model for reversible gene activation. Nucleic Acids Res. 6:1909-1927.
  • Lohr, D., and T. Torchia. 1988. Structure of the chromosomal copy of yeast ARS1. Biochemistry 27:3961-3965.
  • Long, C. M., C. M. Brajkovich, and J. F. Scott. 1985. Alternative model for chromatin organization of the Saccharomyces cerevisiae chromosomal DNA plasmid TRP1 RI circle (YARp1). Mol. Cell. Biol. 5:3124-3130.
  • Nedospasov, S. A., and G. P. Georgiev. 1980. Non random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem. Biophys. Res. Commun. 92:532-539.
  • Nelder, J. A., and R. Mead. 1965. A simplex method for function minimization. Comput. J. 7:308-313.
  • Newlon, C. S. 1988. Yeast chromosome replication and segregation. Microbiol. Rev. 52:568-601.
  • Newlon, C. S., R. J. Devenish, P. A. Suci, and C. J. Roffis. 1981. Replication origins used in vivo in yeast. ICN-UCLA Symp. Mol. Cell. Biol. 22:501-516.
  • Palen, T. E., and T. R. Cech. 1984. Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of Tetrahymena. Cell 36:933-942.
  • Palzkill, T. G., and C. S. Newlon. 1988. A yeast replication origin consists of multiple copies of a small conserved sequence. Cell 53:441-450.
  • Pardoll, D. M., B. Vogelstein, and C. S. Coffey. 1980. A fixed site of DNA replication in eukaryotic cells. Cell 19:527-536.
  • Press, W. H., B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. 1988. Numerical recipes in C. Cambridge University Press, Cambridge.
  • Pringle, J. R., and L. H. Hartwell. 1981. The Saccharomyces cerevisiae cell cycle, p. 97-142. In J. N. Strathem, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
  • Razin, S. V., M. G. Kekelidze, E. M. Lukanidin, K. Scherrer, and G. P. Georgiev. 1986. Replication origins are attached to the nuclear skeleton. Nucleic Acids Res. 14:8189-8207.
  • Saffer, L. D., and O. L. Miller, Jr. 1986. Electron microscopic study of Saccharomyces cerevisiae rDNA chromatin replication. Mol. Cell. Biol. 6:1148-1157.
  • Saragosti, S., G. Moyne, and M. Yaniv. 1980. Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell 20:65-73.
  • Shore, D., D. J. Stillman, A. H. Brand, and K. A. Nasmyth. 1987. Identification of silencer binding proteins from yeast: possible roles in SIR control and DNA replication. EMBO J. 6:461-467.
  • Simpson, R. 1990. Nucleosome positioning can affect the function of a cis acting DNA element in vivo. Nature (London) 343:387-389.
  • Slater, M. L., S. O. Sharrow, and J. J. Gart. 1977. Cell cycle of Saccharomyces cerevisiae in populations growing at different rates. Proc. Natl. Acad. Sci. USA 74:3850-3854.
  • Smith, H. C., E. Puvion, L. A. Buchholtz, and R. Berezney. 1984. Spatial distribution of DNA loop attachment and replicational sites in the nuclear matrix. J. Cell Biol. 99:1794-1802.
  • Smith, M. M., and K. Murray. 1983. Yeast H3 and H4 histone messenger RNAs are transcribed from two non-allelic gene sets. J. Mol. Biol. 169:641-661.
  • Smith, M. M., and V. B. Stirling. 1988. Histone H3 and H4 gene deletions in Saccharomyces cerevisiae. J. Cell Biol. 106:557-566.
  • Snyder, M., A. R. Buchman, and R. W. Davis. 1986. Bent DNA at a yeast autonomously replicating sequence. Nature (London) 324:87-89.
  • Snyder, M., R. J. Sapolsky, and R. W. Davis. 1988. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:2184-2194.
  • Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503-517.
  • Spradling, A., and T. Orr-Weaver. 1987. Regulation of DNA replication during Drosophila development. Annu. Rev. Genet. 21:373-403.
  • Srienc, F., J. E. Bailey, and J. L. Campbell. 1985. Effect of ARS1 mutations on chromosome stability in Saccharomyces cerevisiae. Mol. Cell. Biol. 5:1676-1684.
  • Stinchcomb, D. T., C. Mann, E. Selker, and R. W. Davis. 1981. DNA sequences that allow the replication and segregation of yeast chromosomes. ICN-UCLA Symp. Mol. Cell. Biol. 22:473-488.
  • Stinchcomb, D. T., K. Struhl, and R. W. Davis. 1979. Isolation and characterisation of a yeast chromosomal replicator. Nature (London) 282:39-43.
  • Struhl, K., D. T. Stinchcomb, S. Scherer, and R. W. Davis. 1979. High-frequency transformation of yeast: autonomous replica tion of hybrid DNA molecules. Proc. Natl. Acad. Sci. USA 76:1035-1039.
  • Thoma, F. 1986. Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin. J. Mol. Biol. 190:177-190.
  • Thoma, F., L. W. Bergman, and R. T. Simpson. 1984. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol. Biol. 177:715-733.
  • Thoma, F., and R. T. Simpson. 1985. Local protein-DNA interactions may determine nucleosome positions on yeast plasmids. Nature (London) 315:250-252.
  • Umek, R. M., and D. Kowalski. 1988. The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell 52:559-567.
  • Umek, R. M., and D. Kowalski. 1990. Thermal energy suppresses mutational defects in DNA unwinding at a yeast replication origin. Proc. Natl. Acad. Sci. 87:2486-2490.
  • Umek, R. M., M. H. K. Linskens, D. Kowalski, and J. A. Huberman. 1989. New beginnings in studies of eukaryotic DNA replication origins. Biochim. Biophys. Acta 1007:1-14.
  • Van der Velden, H. M. W., G. van Willigen, R. H. W. Wetzels, and F. Wanka. 1984. Attachment of origins of replication to the nuclear matrix and chromosomal scaffold. FEBS Lett. 171:13-16.
  • Veit, B. E., and W. L. Fangman. 1985. Chromatin organization of the Saccharomyces cerevisiae 2μm plasmid depends on plasmid-encoded products. Mol. Cell. Biol. 5:2190-2196.
  • Williams, J. S., T. T. Eckdahl, and J. N. Anderson. 1988. Bent DNA functions as a replication enhancer in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:2763-2769.
  • Williamson, D., and D. Fennell. 1975. The use of fluorescent DNA-binding agent for detecting and separating yeast mitochondrial DNA. Methods Cell Biol. 20:335-351.
  • Wu, C. 1980. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature (London) 286:854-860.
  • Zakian, V. A., B. J. Brewer, and W. L. Fangman. 1979. Replication of each copy of the yeast 2 micron plasmid occurs during the S phase. Cell 17:923-934.
  • Zakian, V. A., and J. F. Scott. 1982. Construction, replication, and chromatin structure of TRP1 RI circle, a multiple-copy synthetic plasmid derived from Saccharomyces cerevisiae chromosomal DNA. Mol. Cell. Biol. 2:221-232.

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.