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. 2004 Jun;167(2):579–591. doi: 10.1534/genetics.103.024851

The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae.

Bernhard Suter 1, Amy Tong 1, Michael Chang 1, Lisa Yu 1, Grant W Brown 1, Charles Boone 1, Jasper Rine 1
PMCID: PMC1470908  PMID: 15238513

Abstract

Mutations in genes encoding the origin recognition complex (ORC) of Saccharomyces cerevisiae affect initiation of DNA replication and transcriptional repression at the silent mating-type loci. To explore the function of ORC in more detail, a screen for genetic interactions was undertaken using large-scale synthetic lethal analysis. Combination of orc2-1 and orc5-1 alleles with the complete set of haploid deletion mutants revealed synthetic lethal/sick phenotypes with genes involved in DNA replication, chromatin structure, checkpoints, DNA repair and recombination, and other genes that were unexpected on the basis of previous studies of ORC. Many of these genetic interactions are shared with other genes that are involved in initiation of DNA replication. Strong synthetic interactions were demonstrated with null mutations in genes that contribute to sister chromatid cohesion. A genetic interaction between orc5-1 and the cohesin mutant scc1-73 suggested that ORC function contributes to sister chromatid cohesion. Thus, comprehensive screening for genetic interactions with a replication gene revealed a connection between initiation of DNA replication and sister chromatid cohesion. Further experiments linked sister chromatid cohesion genes to silencing at mating-type loci and telomeres.

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Selected References

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  1. Bailis Julie M., Bernard Pascal, Antonelli Richard, Allshire Robin C., Forsburg Susan L. Hsk1-Dfp1 is required for heterochromatin-mediated cohesion at centromeres. Nat Cell Biol. 2003 Nov 16;5(12):1111–1116. doi: 10.1038/ncb1069. [DOI] [PubMed] [Google Scholar]
  2. Bell S. P., Mitchell J., Leber J., Kobayashi R., Stillman B. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell. 1995 Nov 17;83(4):563–568. doi: 10.1016/0092-8674(95)90096-9. [DOI] [PubMed] [Google Scholar]
  3. Bell Stephen P., Dutta Anindya. DNA replication in eukaryotic cells. Annu Rev Biochem. 2001 Nov 9;71:333–374. doi: 10.1146/annurev.biochem.71.110601.135425. [DOI] [PubMed] [Google Scholar]
  4. Bernard P., Maure J. F., Partridge J. F., Genier S., Javerzat J. P., Allshire R. C. Requirement of heterochromatin for cohesion at centromeres. Science. 2001 Oct 11;294(5551):2539–2542. doi: 10.1126/science.1064027. [DOI] [PubMed] [Google Scholar]
  5. Blat Y., Kleckner N. Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell. 1999 Jul 23;98(2):249–259. doi: 10.1016/s0092-8674(00)81019-3. [DOI] [PubMed] [Google Scholar]
  6. Carson D. R., Christman M. F. Evidence that replication fork components catalyze establishment of cohesion between sister chromatids. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8270–8275. doi: 10.1073/pnas.131022798. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chang Michael, Bellaoui Mohammed, Boone Charles, Brown Grant W. A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci U S A. 2002 Dec 13;99(26):16934–16939. doi: 10.1073/pnas.262669299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Costanzo M. C., Crawford M. E., Hirschman J. E., Kranz J. E., Olsen P., Robertson L. S., Skrzypek M. S., Braun B. R., Hopkins K. L., Kondu P. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 2001 Jan 1;29(1):75–79. doi: 10.1093/nar/29.1.75. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dillin A., Rine J. Separable functions of ORC5 in replication initiation and silencing in Saccharomyces cerevisiae. Genetics. 1997 Nov;147(3):1053–1062. doi: 10.1093/genetics/147.3.1053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Donze D., Adams C. R., Rine J., Kamakaka R. T. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 1999 Mar 15;13(6):698–708. doi: 10.1101/gad.13.6.698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Edwards Shaune, Li Caroline M., Levy Daniel L., Brown Jessica, Snow Peter M., Campbell Judith L. Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma interact physically and functionally, suggesting a role for polymerase epsilon in sister chromatid cohesion. Mol Cell Biol. 2003 Apr;23(8):2733–2748. doi: 10.1128/MCB.23.8.2733-2748.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ehrenhofer-Murray A. E., Gossen M., Pak D. T., Botchan M. R., Rine J. Separation of origin recognition complex functions by cross-species complementation. Science. 1995 Dec 8;270(5242):1671–1674. doi: 10.1126/science.270.5242.1671. [DOI] [PubMed] [Google Scholar]
  13. Ehrenhofer-Murray A. E., Kamakaka R. T., Rine J. A role for the replication proteins PCNA, RF-C, polymerase epsilon and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae. Genetics. 1999 Nov;153(3):1171–1182. doi: 10.1093/genetics/153.3.1171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Foss M., McNally F. J., Laurenson P., Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838–1844. doi: 10.1126/science.8266071. [DOI] [PubMed] [Google Scholar]
  15. Fox C. A., Loo S., Dillin A., Rine J. The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication. Genes Dev. 1995 Apr 15;9(8):911–924. doi: 10.1101/gad.9.8.911. [DOI] [PubMed] [Google Scholar]
  16. Guacci V., Koshland D., Strunnikov A. A direct link between sister chromatid cohesion and chromosome condensation revealed through the analysis of MCD1 in S. cerevisiae. Cell. 1997 Oct 3;91(1):47–57. doi: 10.1016/s0092-8674(01)80008-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Guarente L. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 1993 Oct;9(10):362–366. doi: 10.1016/0168-9525(93)90042-g. [DOI] [PubMed] [Google Scholar]
  18. Hagstrom Kirsten A., Meyer Barbara J. Condensin and cohesin: more than chromosome compactor and glue. Nat Rev Genet. 2003 Jul;4(7):520–534. doi: 10.1038/nrg1110. [DOI] [PubMed] [Google Scholar]
  19. Hanna J. S., Kroll E. S., Lundblad V., Spencer F. A. Saccharomyces cerevisiae CTF18 and CTF4 are required for sister chromatid cohesion. Mol Cell Biol. 2001 May;21(9):3144–3158. doi: 10.1128/MCB.21.9.3144-3158.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hartman J. L., 4th, Garvik B., Hartwell L. Principles for the buffering of genetic variation. Science. 2001 Feb 9;291(5506):1001–1004. doi: 10.1126/science.291.5506.1001. [DOI] [PubMed] [Google Scholar]
  21. Hartwell L. H., Smith D. Altered fidelity of mitotic chromosome transmission in cell cycle mutants of S. cerevisiae. Genetics. 1985 Jul;110(3):381–395. doi: 10.1093/genetics/110.3.381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. He X., Asthana S., Sorger P. K. Transient sister chromatid separation and elastic deformation of chromosomes during mitosis in budding yeast. Cell. 2000 Jun 23;101(7):763–775. doi: 10.1016/s0092-8674(00)80888-0. [DOI] [PubMed] [Google Scholar]
  23. Hodges P. E., McKee A. H., Davis B. P., Payne W. E., Garrels J. I. The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res. 1999 Jan 1;27(1):69–73. doi: 10.1093/nar/27.1.69. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Hogan E., Koshland D. Addition of extra origins of replication to a minichromosome suppresses its mitotic loss in cdc6 and cdc14 mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):3098–3102. doi: 10.1073/pnas.89.7.3098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Katou Yuki, Kanoh Yutaka, Bando Masashige, Noguchi Hideki, Tanaka Hirokazu, Ashikari Toshihiko, Sugimoto Katsunori, Shirahige Katsuhiko. S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature. 2003 Aug 28;424(6952):1078–1083. doi: 10.1038/nature01900. [DOI] [PubMed] [Google Scholar]
  26. Kaufman P. D., Cohen J. L., Osley M. A. Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor I. Mol Cell Biol. 1998 Aug;18(8):4793–4806. doi: 10.1128/mcb.18.8.4793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kenna Margaret A., Skibbens Robert V. Mechanical link between cohesion establishment and DNA replication: Ctf7p/Eco1p, a cohesion establishment factor, associates with three different replication factor C complexes. Mol Cell Biol. 2003 Apr;23(8):2999–3007. doi: 10.1128/MCB.23.8.2999-3007.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kirchmaier A. L., Rine J. DNA replication-independent silencing in S. cerevisiae. Science. 2001 Jan 26;291(5504):646–650. doi: 10.1126/science.291.5504.646. [DOI] [PubMed] [Google Scholar]
  29. Kroll E. S., Hyland K. M., Hieter P., Li J. J. Establishing genetic interactions by a synthetic dosage lethality phenotype. Genetics. 1996 May;143(1):95–102. doi: 10.1093/genetics/143.1.95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Laloraya S., Guacci V., Koshland D. Chromosomal addresses of the cohesin component Mcd1p. J Cell Biol. 2000 Nov 27;151(5):1047–1056. doi: 10.1083/jcb.151.5.1047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lau Anna, Blitzblau Hannah, Bell Stephen P. Cell-cycle control of the establishment of mating-type silencing in S. cerevisiae. Genes Dev. 2002 Nov 15;16(22):2935–2945. doi: 10.1101/gad.764102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lew Daniel J., Burke Daniel J. The spindle assembly and spindle position checkpoints. Annu Rev Genet. 2003;37:251–282. doi: 10.1146/annurev.genet.37.042203.120656. [DOI] [PubMed] [Google Scholar]
  33. Li Y. C., Cheng T. H., Gartenberg M. R. Establishment of transcriptional silencing in the absence of DNA replication. Science. 2001 Jan 26;291(5504):650–653. doi: 10.1126/science.291.5504.650. [DOI] [PubMed] [Google Scholar]
  34. Liang C., Weinreich M., Stillman B. ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genome. Cell. 1995 Jun 2;81(5):667–676. doi: 10.1016/0092-8674(95)90528-6. [DOI] [PubMed] [Google Scholar]
  35. Loo S., Fox C. A., Rine J., Kobayashi R., Stillman B., Bell S. The origin recognition complex in silencing, cell cycle progression, and DNA replication. Mol Biol Cell. 1995 Jun;6(6):741–756. doi: 10.1091/mbc.6.6.741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Mayer M. L., Gygi S. P., Aebersold R., Hieter P. Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mol Cell. 2001 May;7(5):959–970. doi: 10.1016/s1097-2765(01)00254-4. [DOI] [PubMed] [Google Scholar]
  37. Mayer Melanie L., Pot Isabelle, Chang Michael, Xu Hong, Aneliunas Victoria, Kwok Teresa, Newitt Rick, Aebersold Ruedi, Boone Charles, Brown Grant W. Identification of protein complexes required for efficient sister chromatid cohesion. Mol Biol Cell. 2004 Jan 23;15(4):1736–1745. doi: 10.1091/mbc.E03-08-0619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Meneghini Marc D., Wu Michelle, Madhani Hiten D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell. 2003 Mar 7;112(5):725–736. doi: 10.1016/s0092-8674(03)00123-5. [DOI] [PubMed] [Google Scholar]
  39. Michaelis C., Ciosk R., Nasmyth K. Cohesins: chromosomal proteins that prevent premature separation of sister chromatids. Cell. 1997 Oct 3;91(1):35–45. doi: 10.1016/s0092-8674(01)80007-6. [DOI] [PubMed] [Google Scholar]
  40. Miles J., Formosa T. Evidence that POB1, a Saccharomyces cerevisiae protein that binds to DNA polymerase alpha, acts in DNA metabolism in vivo. Mol Cell Biol. 1992 Dec;12(12):5724–5735. doi: 10.1128/mcb.12.12.5724. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Naiki T., Kondo T., Nakada D., Matsumoto K., Sugimoto K. Chl12 (Ctf18) forms a novel replication factor C-related complex and functions redundantly with Rad24 in the DNA replication checkpoint pathway. Mol Cell Biol. 2001 Sep;21(17):5838–5845. doi: 10.1128/MCB.21.17.5838-5845.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Osborn Alexander J., Elledge Stephen J. Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. Genes Dev. 2003 Jul 15;17(14):1755–1767. doi: 10.1101/gad.1098303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Page B. D., Snyder M. CIK1: a developmentally regulated spindle pole body-associated protein important for microtubule functions in Saccharomyces cerevisiae. Genes Dev. 1992 Aug;6(8):1414–1429. doi: 10.1101/gad.6.8.1414. [DOI] [PubMed] [Google Scholar]
  45. Schwartz K., Richards K., Botstein D. BIM1 encodes a microtubule-binding protein in yeast. Mol Biol Cell. 1997 Dec;8(12):2677–2691. doi: 10.1091/mbc.8.12.2677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Sharp J. A., Fouts E. T., Krawitz D. C., Kaufman P. D. Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr Biol. 2001 Apr 3;11(7):463–473. doi: 10.1016/s0960-9822(01)00140-3. [DOI] [PubMed] [Google Scholar]
  47. Shibahara K., Stillman B. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell. 1999 Feb 19;96(4):575–585. doi: 10.1016/s0092-8674(00)80661-3. [DOI] [PubMed] [Google Scholar]
  48. Shimada Kenji, Pasero Philippe, Gasser Susan M. ORC and the intra-S-phase checkpoint: a threshold regulates Rad53p activation in S phase. Genes Dev. 2002 Dec 15;16(24):3236–3252. doi: 10.1101/gad.239802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Sjögren C., Nasmyth K. Sister chromatid cohesion is required for postreplicative double-strand break repair in Saccharomyces cerevisiae. Curr Biol. 2001 Jun 26;11(12):991–995. doi: 10.1016/s0960-9822(01)00271-8. [DOI] [PubMed] [Google Scholar]
  50. Skibbens R. V., Corson L. B., Koshland D., Hieter P. Ctf7p is essential for sister chromatid cohesion and links mitotic chromosome structure to the DNA replication machinery. Genes Dev. 1999 Feb 1;13(3):307–319. doi: 10.1101/gad.13.3.307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Sussel L., Vannier D., Shore D. Epigenetic switching of transcriptional states: cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Jul;13(7):3919–3928. doi: 10.1128/mcb.13.7.3919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Takeda T., Ogino K., Tatebayashi K., Ikeda H., Arai Ki, Masai H. Regulation of initiation of S phase, replication checkpoint signaling, and maintenance of mitotic chromosome structures during S phase by Hsk1 kinase in the fission yeast. Mol Biol Cell. 2001 May;12(5):1257–1274. doi: 10.1091/mbc.12.5.1257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Tharun S., He W., Mayes A. E., Lennertz P., Beggs J. D., Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature. 2000 Mar 30;404(6777):515–518. doi: 10.1038/35006676. [DOI] [PubMed] [Google Scholar]
  54. Tong A. H., Evangelista M., Parsons A. B., Xu H., Bader G. D., Pagé N., Robinson M., Raghibizadeh S., Hogue C. W., Bussey H. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001 Dec 14;294(5550):2364–2368. doi: 10.1126/science.1065810. [DOI] [PubMed] [Google Scholar]
  55. Tong Amy Hin Yan, Lesage Guillaume, Bader Gary D., Ding Huiming, Xu Hong, Xin Xiaofeng, Young James, Berriz Gabriel F., Brost Renee L., Chang Michael. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6;303(5659):808–813. doi: 10.1126/science.1091317. [DOI] [PubMed] [Google Scholar]
  56. Tyler J. K., Adams C. R., Chen S. R., Kobayashi R., Kamakaka R. T., Kadonaga J. T. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature. 1999 Dec 2;402(6761):555–560. doi: 10.1038/990147. [DOI] [PubMed] [Google Scholar]
  57. Tóth A., Ciosk R., Uhlmann F., Galova M., Schleiffer A., Nasmyth K. Yeast cohesin complex requires a conserved protein, Eco1p(Ctf7), to establish cohesion between sister chromatids during DNA replication. Genes Dev. 1999 Feb 1;13(3):320–333. doi: 10.1101/gad.13.3.320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Uhlmann F., Lottspeich F., Nasmyth K. Sister-chromatid separation at anaphase onset is promoted by cleavage of the cohesin subunit Scc1. Nature. 1999 Jul 1;400(6739):37–42. doi: 10.1038/21831. [DOI] [PubMed] [Google Scholar]
  59. Wang Z., Castaño I. B., De Las Peñas A., Adams C., Christman M. F. Pol kappa: A DNA polymerase required for sister chromatid cohesion. Science. 2000 Aug 4;289(5480):774–779. doi: 10.1126/science.289.5480.774. [DOI] [PubMed] [Google Scholar]
  60. Warren Cheryl D., Eckley D. Mark, Lee Marina S., Hanna Joseph S., Hughes Adam, Peyser Brian, Jie Chunfa, Irizarry Rafael, Spencer Forrest A. S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion. Mol Biol Cell. 2004 Jan 23;15(4):1724–1735. doi: 10.1091/mbc.E03-09-0637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Xie J., Pierce M., Gailus-Durner V., Wagner M., Winter E., Vershon A. K. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J. 1999 Nov 15;18(22):6448–6454. doi: 10.1093/emboj/18.22.6448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Zhang Z., Shibahara K., Stillman B. PCNA connects DNA replication to epigenetic inheritance in yeast. Nature. 2000 Nov 9;408(6809):221–225. doi: 10.1038/35041601. [DOI] [PubMed] [Google Scholar]
  63. Zou L., Mitchell J., Stillman B. CDC45, a novel yeast gene that functions with the origin recognition complex and Mcm proteins in initiation of DNA replication. Mol Cell Biol. 1997 Feb;17(2):553–563. doi: 10.1128/mcb.17.2.553. [DOI] [PMC free article] [PubMed] [Google Scholar]

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