Two DNA-Binding Factors Recognize Specific Sequences at Silencers, Upstream Activating Sequences, Autonomously Replicating Sequences, and Telomeres in Saccharomyces cerevisiae

Literature Cited

• Abraham, J., K. A. Nasmyth, J. N. Strathern, A. J. S. Klar, and J. B. Hicks. 1984. Regulation of mating type information in yeast. J. Mol. Biol. 176:307-331.
   PubMedGoogle Scholar
• Astell, C. R., L. Ahlstrom-Jonesson, M. Smith, K. Tatehell, K. A. Nasmyth, and B. D. Hall. 1981. The sequence of the DNAs coding for the mating type loci of Saccharomyces cerevisiae. Cell 27:15-23.
   PubMed Web of Science ®Google Scholar
• Barnes, D. A., and J. Thorner. 1986. Genetic manipulation of Saccharomyces cerevisiae by use of the LYS2 gene. Mol. Cell. Biol. 6:2828-2838.
   PubMedGoogle Scholar
• Beggs, J. D. 1978. Transformation of yeast by a replicating hybrid plasmid. Nature (London) 275:104-109.
   PubMed Web of Science ®Google Scholar
• Beggs, J. D. 1981. Multiple-copy yeast plasmid vectors, p. 383-389. In D. Von Wettstein, J. Frus, M. Kielland-Brandt, and A. Stenderup (ed.), Molecular genetics in yeast: proceedings of the Alfred Benzon symposium 16. State Mutual Book & Periodical Service, Ltd., New York.
   Google Scholar
• Berman, J., C. Y. Tachibana, and B.-K. Tye. 1986. Identification of a telomere-binding activity from yeast. Proc. Natl. Acad. Sci. USA 83:3713-3717.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
   PubMed Web of Science ®Google Scholar
• Bram, R. J., and R. D. Kornberg. 1985. Specific protein binding to far upstream activating sequences in polymerase II promoters. Proc. Natl. Acad. Sci. USA 82:43-47.
   PubMedGoogle Scholar
• Bram, R. J., and R. D. Kornberg. 1987. Isolation of a Saccharomyces cerevisiae centromere DNA-binding protein, its human homolog, and its possible role as a transcription factor. Mol. Cell. Biol. 7:403-409.
   PubMedGoogle Scholar
• Bram, R. J., N. F. Lue, and R. D. Kornberg. 1986. A GAL family of upstream activating sequences in yeast: roles in both induction and repression of transcription. EMBO J. 5:603-608.
   PubMedGoogle Scholar
• Brand, A. H., L. Breeden, J. Abraham, R. Sternglanz, and K. Nasmyth. 1985. Characterization of a “silencer” in yeast: a DNA sequence with properties opposite to those of a transcriptional enhancer. Cell 41:41-48.
   PubMed Web of Science ®Google Scholar
• Broach, J. R., Y.-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.
   Google Scholar
• Button, L. L., and C. R. Astell. 1986. The Saccharomyces cerevisiae chromosome III left telomere has a type X, but not a Y′ ARS region. Mol. Cell. Biol. 6:1352-1356.
   PubMedGoogle Scholar
• Campbell, J. L. 1983. Yeast DNA replication in vitro and in vivo, p. 109-155. In J. Setlow and A. Hollander (ed.), Genetic engineering, vol. 5. Plenum Press, New York.
   Google Scholar
• Carthew, R. W., L. A. Chodosh, and P. A. Sharp. 1985. An RNA polymerase II transcription factor binds to an upstream element of the adenovirus major late promoter. Cell 43:439-448.
   PubMed Web of Science ®Google Scholar
• Celiniker, 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.
   PubMedGoogle Scholar
• Devereux, J., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
   PubMed Web of Science ®Google Scholar
• de Villiers, J., W. Schaffner, C. Tyndall, S. Lupten, and R. Kamen. 1984. Polyoma virus DNA replication requires an enhancer. Nature (London) 312:242-246.
   PubMed Web of Science ®Google Scholar
• Dove, W. F., H. Inokuchi, and W. F. Stevens. 1971. Replication control on phage lambda, p. 747-771. In A. D. Hershey (ed.), The bacteriophage lambda. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Dunn, B., P. Szauter, M. L. Pardue, and J. Szostak. 1984. Transfer of yeast telomeres to linear plasmids by recombination. Cell 39:191-201.
   PubMed Web of Science ®Google Scholar
• Echols, H. 1986. Multiple DNA-protein interactions governing high-precision DNA transactions. Science 233:1050-1056.
   PubMed Web of Science ®Google Scholar
• Ephrussi, A., G. Church, S. Tonegawa, and W. Gilbert. 1985. B-lineage specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science 227:134-140.
   PubMed Web of Science ®Google Scholar
• Feldman, J. B., J. B. Hicks, and J. R. Broach. 1984. Identification of sites required for repression of a silent mating type locus in yeast. J. Mol. Biol. 178:815-834.
   PubMed Web of Science ®Google Scholar
• Fried, M., and D. M. Crothers. 1981. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9:6505-6525.
   PubMed Web of Science ®Google Scholar
• Garner, M. M., and A. Revzin. 1981. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the E. coli lactose operon regulatory system. Nucleic Acids Res. 9:3047-3060.
   PubMed Web of Science ®Google Scholar
• Gilmour, D. S., and J. T. Lis. 1985. In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Mol. Cell. Biol. 5:2009-2018.
   PubMed Web of Science ®Google Scholar
• Haber, J. E., and J. P. George. 1979. A mutation that permits the expression of normally silent copies of mating type information in Saccharomyces cerevisiae. Genetics 93:13-35.
   PubMedGoogle Scholar
• Harashima, S., Y. Nogi, and Y. Oshima. 1974. The genetic system controlling homothallism in Saccharomyces yeasts. Genetics 77:639-650.
   PubMed Web of Science ®Google Scholar
• Hartley, J. L., and J. E. Donelson. 1980. Nucleotide sequence of the yeast plasmid. Nature (London) 286:860-865.
   PubMed Web of Science ®Google Scholar
• Hay, R. T. 1985. Origin of adenovirus DNA replication: role of the nuclear factor I binding site in vivo. J. Mol. Biol. 186:129-136.
   PubMedGoogle Scholar
• Hereford, L., S. Bromley, and M. Osley. 1982. Periodic transcription of yeast histone genes. Cell 30:305-310.
   PubMedGoogle Scholar
• Herskowitz, I., and Y. Oshima. 1981. Control of cell type in Saccharomyces cerevisiae: mating type and mating-type inter-conversion, p. 181-209. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces cerevisiae: life cycle and inheritance. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Hertz, G. Z., and J. E. Mertz. 1986. Bidirectional promoter elements of simian virus 40 are required for efficient replication of viral DNA. Mol. Cell. Biol. 6:3513-3522.
   PubMed Web of Science ®Google Scholar
• Hicks, J. B., and I. Herskowitz. 1976. Interconversion of yeast mating types. I. Direct observations of the action of the homothallism (HO) gene. Genetics 83:373-393.
   PubMedGoogle Scholar
• Hieter, P., C. Mann, M. Snyder, and R. W. Davis. 1985. Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss. Cell 40:381-392.
   PubMedGoogle Scholar
• Huet, J., P. Cottrelle, M. Cool, M.-L. Vignais, D. Thiele, C. Merck, J.-M. Buhler, A. Sentenac, and P. Fromageot. 1985. A general upstream binding factor for genes of the yeast translation apparatus. EMBO J. 4:3539-3547.
   PubMedGoogle Scholar
• Itoh, T., and J. Tomizawa. 1978. Initiation of replication of plasmid ColE1 DNA by RNA polymerase, ribonuclease H, and DNA polymerase I. Cold Spring Harbor Symp. Quant. Biol. 43:409-417.
   Google Scholar
• Ivy, J. M., A. M. Klar, and J. B. Hicks. 1986. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 6:688-702.
   PubMed Web of Science ®Google Scholar
• Jayaram, M., Y.-Y. Li, and J. R. Broach. 1983. The yeast plasmid 2μ circle encodes components required for its high copy propagation. Cell 34:95-104.
   PubMed Web of Science ®Google Scholar
• Jayaram, M., A. Sutton, and J. R. Broach. 1985. Properties of REP3: a cis-acting locus required for stable propagation of the Saccharomyces cerevisiae plasmid 2μm circle. Mol. Cell. Biol. 5:2466-2475.
   PubMedGoogle Scholar
• Johnston, M., and R. W. Davis. 1984. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol. Cell. Biol. 4:1440-1448.
   PubMed Web of Science ®Google Scholar
• Jones, K. A., J. T. Kadonaga, P. J. Rosenfeld, T. J. Kelly, and R. Tjian. 1987. A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication. Cell 48:79-89.
   PubMed Web of Science ®Google Scholar
• Kikuchi, Y. 1983. Yeast plasmid requires a cis-acting locus and two plasmid proteins for stable maintenance. Cell 35:487-493.
   PubMed Web of Science ®Google Scholar
• Kimmerly, W. J., and J. Rine. 1987. Replication and segregation of plasmids containing cis-acting regulatory sites of silent mating-type genes in Saccharomyces cerevisiae are controlled by the SIR genes. Mol. Cell. Biol. 7:4225-4237.
   PubMedGoogle Scholar
• Klar, A. J. S., S. Fogel, and K. Macleod. 1979. MAR1, a regulator of HMa and HMα loci in Saccharomyces cerevisiae. Genetics 93:37-50.
   PubMedGoogle Scholar
• Klar, A. J. S., J. Mclndoo, J. N. Strathern, and J. B. Hicks. 1980. Evidence for a physical interaction between the transposed and substituted sequences during mating type transposition in yeast. Cell 22:291-298.
   PubMedGoogle Scholar
• Klar, A. J. S., J. N. Strathern, J. R. Broach, and J. B. Hicks. 1981. Regulation of transcription in expressed and unexpressed mating type cassettes of yeast. Nature (London) 289:239-244.
   PubMed Web of Science ®Google Scholar
• Klar, A. J. S., J. N. Strathern, and J. A. Abraham. 1984. Involvement of double-stranded chromosomal breaks for mating type switching in Saccharomyces cerevisiae. Cold Spring Harbor Symp. Quant. Biol. 49:77-82.
   PubMedGoogle Scholar
• Kostriken, R., J. N. Strathern, A. J. S. Klar, J. B. Hicks, and F. Heffron. 1983. A site-specific endonuclease essential for mating type switching in Saccharomyces cerevisiae. Cell 35:167-174.
   PubMed Web of Science ®Google Scholar
• Laughon, A., and R. Gesteland. 1982. Isolation and preliminary characterization of the GAL4 gene, a positive regulator of transcription in yeast. Proc. Natl. Acad. Sci. USA 79:6827-6831.
   PubMed Web of Science ®Google Scholar
• Leer, R. J., M. M. C. van Raamsdonsk-Duon, W. H. Mager, and R. Planta. 1985. Conserved sequences upstream of yeast ribosomal protein genes. Curr. Genet. 9:273-277.
   PubMedGoogle Scholar
• Li, J. J., K. W. C. Peden, R. A. F. Dixon, and T. Kelly. 1986. Functional organization of the simian virus 40 origin of DNA replication. Mol. Cell. Biol. 6:1117-1128.
   PubMed Web of Science ®Google Scholar
• Lorch, Y., and R. D. Romberg. 1985. A region flanking the GAL7 gene and a binding site for GAL4 protein as upstream activating sequences in yeast. J. Mol. Biol. 186:821-824.
   PubMed Web of Science ®Google Scholar
• Lue, N. F., D. I. Chasman, A. R. Buchman, and R. D. Kornberg. 1987. Interaction of GAL4 and GAL80 gene regulatory proteins in vitro. Mol. Cell. Biol. 7:3446-3451.
   PubMedGoogle Scholar
• Lnskey, M. L., and M. R. Botchan. 1986. Transient replication of bovine papillomavirus type 1 plasmids: cis and trans requirements. Proc. Natl. Acad. Sci. USA 83:3609-3613.
   PubMedGoogle Scholar
• Maniatas, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Martin, K., L. Huo, and R. F. Schleif. 1986. The DNA loop model for ara repression: ara C protein occupies the proposed loop sites in vivo and repression negative mutations lie in these same sites. Proc. Natl. Acad. Sci. USA 83:3654-3658.
   PubMed Web of Science ®Google Scholar
• Miller, A., and K. A. Nasmyth. 1984. Role of DNA replication in the repression of silent mating type loci in yeast. Nature (London) 312:247-251.
   PubMedGoogle Scholar
• Nagata, K., R. A. Guggenheimer, T. Enomoto, J. H. Lichy, and J. Hurwitz. 1982. Adenovirus DNA replication in vitro: identification of a host factor that stimulates synthesis of the preterminal protein-dCMP complex. Proc. Natl. Acad. Sci. USA 80:6177-6181.
   Google Scholar
• Nasmyth, K., and K. Tatchell. 1980. The structure of transpos-able yeast mating type loci. Cell 19:753-764.
   PubMed Web of Science ®Google Scholar
• Needleman, S. B., and C. D. Wunsch. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453.
   PubMed Web of Science ®Google Scholar
• Ptashne, M. 1986. Gene regulation by proteins acting nearby and at a distance. Nature (London) 322:697-701.
   PubMed Web of Science ®Google Scholar
• Ratzkin, B., and J. Carbon. 1977. Functional expression of cloned yeast DNA in E. coli. Proc. Natl. Acad. Sci. USA 74:487-491.
   PubMed Web of Science ®Google Scholar
• Rawlins, D. R., P. J. Rosenfeld, R. J. Wides, M. D. Challberg, and T. J. Kelly. 1984. Structure and function of the adenovirus origin of replication. Cell 37:309-319.
   PubMed Web of Science ®Google Scholar
• Rine, J., and I. Herskowitz. 1987. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:9-22.
   PubMed Web of Science ®Google Scholar
• Rine, J., J. N. Strathern, J. B. Hicks, and I. Herskowitz. 1979. A suppressor of mating type locus mutations in Saccharomyces cerevisiae: evidence for identification of cryptic mating type loci. Genetics 93:877-901.
   PubMed Web of Science ®Google Scholar
• Rose, M., P. Grisafi, and D. Botstein. 1984. Structure and function of the yeast URA3 gene: expression in Escherichia coli. Gene 29:113-124.
   PubMedGoogle Scholar
• Rotenberg, M. O., and J. L. Woolford. 1986. Tripartite upstream promoter element essential for expression of Saccharomyces cerevisiae ribosomal protein genes. Mol. Cell. Biol. 6:674-687.
   PubMedGoogle Scholar
• Sawadogo, M., and R. G. Roeder. 1985. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 43:165-175.
   PubMed Web of Science ®Google Scholar
• Schneil, R. A., and J. Rine. 1986. A position effect on the expression of a tRNA gene mediated by the SIR genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 6:494-501.
   PubMedGoogle Scholar
• Shampay, J., J. W. Szostak, and E. H. Blackburn. 1984. DNA sequences of telomeres maintained in yeast. Nature (London) 310:154-157.
   PubMed Web of Science ®Google Scholar
• Shore, D., M. Squire, and K. A. Nasmyth. 1984. Characterization of two genes required for position effect control of mating type. EMBO J. 3:2817-2823.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Siliciano, P. G., and K. Tatchell. 1984. Transcription and regulatory signals at the mating type locus on yeast. Cell 37:969-978.
   PubMed Web of Science ®Google Scholar
• Snyder, M., A. R. Buchman, and R. W. Davis. 1986. Bent DNA at a yeast autonomously replicating sequence. Nature (London) 324:87-89.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Stinchcomb, D. T., K. Struhl, and R. W. Davis. 1979. Isolation and characterization of a yeast chromosomal replicator. Nature (London) 282:39-43.
   PubMed Web of Science ®Google Scholar
• St. John, T. P., and R. W. Davis. 1981. The organization and transcription of the galactose cluster of Saccharomyces. J. Mol. Biol. 152:285-315.
   PubMedGoogle Scholar
• Strathern, J. N., and I. Herskowitz. 1979. Asymmetry and directionality in production of new cell types during clonal growth: the switching pattern of homothallic yeast. Cell 17:371-381.
   PubMed Web of Science ®Google Scholar
• Struhl, K. 1985. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc. Natl. Acad. Sci. USA 82:8419-8423.
   PubMed Web of Science ®Google Scholar
• Struhl, K. 1985. Nucleotide sequence and transcriptional mapping of the yeast pet56-his3-ded1 gene region. Nucleic Acids Res. 13:8587-8601.
   PubMedGoogle Scholar
• Struhl, K., D. T. Stinchcomb, S. Scherer, and R. W. Davis. 1979. High frequency transformation of yeast: autonomous replication of hybrid DNA molecules. Proc. Natl. Acad. Sci. USA 76:1035-1039.
   PubMed Web of Science ®Google Scholar
• Sutton, A., and J. R. Broach. 1985. Signals for transcription in the Saccharomyces cerevisiae plasmid 2μm circle. Mol. Cell. Biol. 5:2770-2780.
   PubMedGoogle Scholar
• Torchia, T. E., R. W. Hamilton, C. L. Cano, and J. E. Hopper. 1984. Disruption of regulatory gene GAL80 in Saccharomyces cerevisiae: effects on carbon-controlled regulation of the galactose/melibiose pathway genes. Mol. Cell. Biol. 4:1521-1527.
   PubMed Web of Science ®Google Scholar
• Tschumper, G., and J. Carbon. 1980. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene 10:157-166.
   PubMed Web of Science ®Google Scholar
• Tschumper, G., and J. Carbon. 1982. Delta sequences and double symmetry in a yeast chromosomal replicator region. J. Mol. Biol. 156:293-307.
   PubMedGoogle Scholar
• Walmsley, R. W., C. S. M. Chan, B.-K. Tye, and T. D. Petes. 1984. Unusual DNA sequences associated with the ends of yeast chromosomes. Nature (London) 310:157-160.
   PubMed Web of Science ®Google Scholar
• Wouldt, L. P., A. B. Smit, W. H. Mager, and R. Planta. 1986. Conserved sequence elements upstream of the gene encoding yeast ribosomal protein L25 are involved in transcriptional activation. EMBO J. 5:1037-1040.
   PubMedGoogle Scholar