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. 1991 Oct;11(10):5346–5355. doi: 10.1128/mcb.11.10.5346

Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins.

D D Dubey 1, L R Davis 1, S A Greenfeder 1, L Y Ong 1, J G Zhu 1, J R Broach 1, C S Newlon 1, J A Huberman 1
PMCID: PMC361606  PMID: 1922050

Abstract

The silent mating-type loci of Saccharomyces cerevisiae, HML and HMR, are flanked by transcriptional silencers that have ARS activity (i.e., they function as replication origins when in plasmids). To test whether these ARS elements are chromosomal origins, we mapped origins near HML (close to the left telomere of chromosome III). Our results indicate that the HML-associated ARS elements either do not function as chromosomal replication origins or do so at a frequency below our detection level, suggesting that replication from a silencer-associated origin in each S phase is not essential for the maintenance of transcriptional repression at HML. Our results also imply that the ability of a DNA fragment to function as an ARS element in a plasmid does not ensure its ability to function as an efficient chromosomal replication origin. Telomere proximity is not responsible for inactivating these ARS elements, because they are not detectably functional as chromosomal origins even in genetically modified strains in which they are far from the telomere.

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Selected References

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  1. Abraham J., Nasmyth K. A., Strathern J. N., Klar A. J., Hicks J. B. Regulation of mating-type information in yeast. Negative control requiring sequences both 5' and 3' to the regulated region. J Mol Biol. 1984 Jul 5;176(3):307–331. doi: 10.1016/0022-2836(84)90492-3. [DOI] [PubMed] [Google Scholar]
  2. Baker T. A., Kornberg A. Transcriptional activation of initiation of replication from the E. coli chromosomal origin: an RNA-DNA hybrid near oriC. Cell. 1988 Oct 7;55(1):113–123. doi: 10.1016/0092-8674(88)90014-1. [DOI] [PubMed] [Google Scholar]
  3. Brand A. H., Micklem G., Nasmyth K. A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation. Cell. 1987 Dec 4;51(5):709–719. doi: 10.1016/0092-8674(87)90094-8. [DOI] [PubMed] [Google Scholar]
  4. Brewer B. J., Fangman W. L. A replication fork barrier at the 3' end of yeast ribosomal RNA genes. Cell. 1988 Nov 18;55(4):637–643. doi: 10.1016/0092-8674(88)90222-x. [DOI] [PubMed] [Google Scholar]
  5. Brewer B. J., Fangman W. L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 1987 Nov 6;51(3):463–471. doi: 10.1016/0092-8674(87)90642-8. [DOI] [PubMed] [Google Scholar]
  6. Broach J. R., Li Y. Y., Feldman J., Jayaram M., Abraham J., Nasmyth K. A., Hicks J. B. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1165–1173. doi: 10.1101/sqb.1983.047.01.132. [DOI] [PubMed] [Google Scholar]
  7. Chan C. S., Tye B. K. Organization of DNA sequences and replication origins at yeast telomeres. Cell. 1983 Jun;33(2):563–573. doi: 10.1016/0092-8674(83)90437-3. [DOI] [PubMed] [Google Scholar]
  8. DePamphilis M. L. Transcriptional elements as components of eukaryotic origins of DNA replication. Cell. 1988 Mar 11;52(5):635–638. doi: 10.1016/0092-8674(88)90398-4. [DOI] [PubMed] [Google Scholar]
  9. Devenish R. J., Newlon C. S. Isolation and characterization of yeast ring chromosome III by a method applicable to other circular DNAs. Gene. 1982 Jun;18(3):277–288. doi: 10.1016/0378-1119(82)90166-4. [DOI] [PubMed] [Google Scholar]
  10. Feldman J. B., Hicks J. B., Broach J. R. Identification of sites required for repression of a silent mating type locus in yeast. J Mol Biol. 1984 Oct 5;178(4):815–834. doi: 10.1016/0022-2836(84)90313-9. [DOI] [PubMed] [Google Scholar]
  11. Gahn T. A., Schildkraut C. L. The Epstein-Barr virus origin of plasmid replication, oriP, contains both the initiation and termination sites of DNA replication. Cell. 1989 Aug 11;58(3):527–535. doi: 10.1016/0092-8674(89)90433-9. [DOI] [PubMed] [Google Scholar]
  12. Goldman M. A., Holmquist G. P., Gray M. C., Caston L. A., Nag A. Replication timing of genes and middle repetitive sequences. Science. 1984 May 18;224(4650):686–692. doi: 10.1126/science.6719109. [DOI] [PubMed] [Google Scholar]
  13. Gottschling D. E., Aparicio O. M., Billington B. L., Zakian V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell. 1990 Nov 16;63(4):751–762. doi: 10.1016/0092-8674(90)90141-z. [DOI] [PubMed] [Google Scholar]
  14. Hartwell L. H., Mortimer R. K., Culotti J., Culotti M. Genetic Control of the Cell Division Cycle in Yeast: V. Genetic Analysis of cdc Mutants. Genetics. 1973 Jun;74(2):267–286. doi: 10.1093/genetics/74.2.267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hatton K. S., Dhar V., Brown E. H., Iqbal M. A., Stuart S., Didamo V. T., Schildkraut C. L. Replication program of active and inactive multigene families in mammalian cells. Mol Cell Biol. 1988 May;8(5):2149–2158. doi: 10.1128/mcb.8.5.2149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Herskowitz I. A regulatory hierarchy for cell specialization in yeast. Nature. 1989 Dec 14;342(6251):749–757. doi: 10.1038/342749a0. [DOI] [PubMed] [Google Scholar]
  17. Hicks J., Strathern J. N., Klar A. J. Transposable mating type genes in Saccharomyces cerevisiae. Nature. 1979 Nov 29;282(5738):478–473. doi: 10.1038/282478a0. [DOI] [PubMed] [Google Scholar]
  18. Huberman J. A., Spotila L. D., Nawotka K. A., el-Assouli S. M., Davis L. R. The in vivo replication origin of the yeast 2 microns plasmid. Cell. 1987 Nov 6;51(3):473–481. doi: 10.1016/0092-8674(87)90643-x. [DOI] [PubMed] [Google Scholar]
  19. Huberman J. A., Zhu J. G., Davis L. R., Newlon C. S. Close association of a DNA replication origin and an ARS element on chromosome III of the yeast, Saccharomyces cerevisiae. Nucleic Acids Res. 1988 Jul 25;16(14A):6373–6384. doi: 10.1093/nar/16.14.6373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ivy J. M., Klar A. J., Hicks J. B. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol Cell Biol. 1986 Feb;6(2):688–702. doi: 10.1128/mcb.6.2.688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jones E. W. Vacuolar proteases in yeast Saccharomyces cerevisiae. Methods Enzymol. 1990;185:372–386. doi: 10.1016/0076-6879(90)85033-k. [DOI] [PubMed] [Google Scholar]
  22. Kimmerly W. J., Rine J. 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. 1987 Dec;7(12):4225–4237. doi: 10.1128/mcb.7.12.4225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Klar A. J., Strathern J. N., Hicks J. B., Prudente D. Efficient production of a ring derivative of chromosome III by the mating-type switching mechanism in Saccharomyces cerevisiae. Mol Cell Biol. 1983 May;3(5):803–810. doi: 10.1128/mcb.3.5.803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Linskens M. H., Huberman J. A. Ambiguities in results obtained with 2D gel replicon mapping techniques. Nucleic Acids Res. 1990 Feb 11;18(3):647–652. doi: 10.1093/nar/18.3.647. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Linskens M. H., Huberman J. A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Nov;8(11):4927–4935. doi: 10.1128/mcb.8.11.4927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mahoney D. J., Broach J. R. The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers. Mol Cell Biol. 1989 Nov;9(11):4621–4630. doi: 10.1128/mcb.9.11.4621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Mahoney D. J., Marquardt R., Shei G. J., Rose A. B., Broach J. R. Mutations in the HML E silencer of Saccharomyces cerevisiae yield metastable inheritance of transcriptional repression. Genes Dev. 1991 Apr;5(4):605–615. doi: 10.1101/gad.5.4.605. [DOI] [PubMed] [Google Scholar]
  28. Marshall M., Mahoney D., Rose A., Hicks J. B., Broach J. R. Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol Cell Biol. 1987 Dec;7(12):4441–4452. doi: 10.1128/mcb.7.12.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Miller A. M., Nasmyth K. A. Role of DNA replication in the repression of silent mating type loci in yeast. Nature. 1984 Nov 15;312(5991):247–251. doi: 10.1038/312247a0. [DOI] [PubMed] [Google Scholar]
  30. Mortimer R. K., Johnston J. R. Genealogy of principal strains of the yeast genetic stock center. Genetics. 1986 May;113(1):35–43. doi: 10.1093/genetics/113.1.35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nawotka K. A., Huberman J. A. Two-dimensional gel electrophoretic method for mapping DNA replicons. Mol Cell Biol. 1988 Apr;8(4):1408–1413. doi: 10.1128/mcb.8.4.1408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Potashkin J. A., Huberman J. A. Characterization of DNA sequences associated with residual nuclei of Saccharomyces cerevisiae. Exp Cell Res. 1986 Jul;165(1):29–40. doi: 10.1016/0014-4827(86)90530-6. [DOI] [PubMed] [Google Scholar]
  33. 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. 1989 Oct;9(10):4488–4494. doi: 10.1128/mcb.9.10.4488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rine J., Herskowitz I. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics. 1987 May;116(1):9–22. doi: 10.1093/genetics/116.1.9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Snyder M., Sapolsky R. J., Davis R. W. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol Cell Biol. 1988 May;8(5):2184–2194. doi: 10.1128/mcb.8.5.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Strathern J. N., Newlon C. S., Herskowitz I., Hicks J. B. Isolation of a circular derivative of yeast chromosome III: implications for the mechanism of mating type interconversion. Cell. 1979 Oct;18(2):309–319. doi: 10.1016/0092-8674(79)90050-3. [DOI] [PubMed] [Google Scholar]
  37. Struhl K., Stinchcomb D. T., Scherer S., Davis R. W. High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1035–1039. doi: 10.1073/pnas.76.3.1035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Umek R. M., Linskens M. H., Kowalski D., Huberman J. A. New beginnings in studies of eukaryotic DNA replication origins. Biochim Biophys Acta. 1989 Jan 23;1007(1):1–14. doi: 10.1016/0167-4781(89)90123-1. [DOI] [PubMed] [Google Scholar]
  39. Yang L., Botchan M. Replication of bovine papillomavirus type 1 DNA initiates within an E2-responsive enhancer element. J Virol. 1990 Dec;64(12):5903–5911. doi: 10.1128/jvi.64.12.5903-5911.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Yoshikawa A., Isono K. Chromosome III of Saccharomyces cerevisiae: an ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes. Yeast. 1990 Sep-Oct;6(5):383–401. doi: 10.1002/yea.320060504. [DOI] [PubMed] [Google Scholar]

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