Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin

Cell

Volumn 96, Issue 4, 1999, Pages 575-585

  Shibahara, Kei Ichi ^a   Stillman, Bruce ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLINE; DNA;

ARTICLE; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; DNA REPLICATION; INHERITANCE; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN TARGETING;

EID: 0033582544     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)80661-3     Document Type: Article

References (69)

1. Almouzni, G., and Wolffe, A.P. (1993). Replication-coupled chromatin assembly is required for the repression of basal transcription in vivo. Genes Dev. 7, 2033-2047.
2. Aparicio, O.M., Billington, B.L., and Gottschling, D.E. (1991). Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66, 1279-1287.
3. Braunstein, M., Sobel, R.E., Allis, C.D., Turner, B.M., and Broach, U.R. (1996). Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol. 16, 4349-4356.
4. Bravo, R., and MacDonald-Bravo, H. (1987). Existence of two populations of cyclin/proliferating cell nuclear antigen during the cell cycle: association with DNA replication sites. J. Cell Biol. 705, 1549-1554.
5. Brown, D.D. (1984). The role of stable complexes that repress and activate eucaryotic genes. Cell 37, 359-365.
6. Bulger, M., Ito, T., Kamakaka, T.T., and Kadonana, J.T. (1995). Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histone-binding protein. Proc. Natl. Acad. Sci. USA 92, 11726-11730.
7. Burgers, P.M. (1991). Saccharomyces cerevisiae replication factor C: II. formation and activity of complexes with the proliferating cell nuclear antigen and with DNA polymerases δ and ε. J. Biol. Chem. 266, 22698-22706.
8. WAF1. Science 277, 1996-2000.
9. DePamphilis, M.L., and Wassarman, P.M. (1980). Replication of eukaryotic chromosomes: a close-up of the replication fork. Annu. Rev. Biochem. 49, 627-666.
10. Ekwall, K., Olsson, T., Turner, B.M., Cranston, G., and Allshire, R.C. (1997). Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres. Cell 91, 1021-1032.
11. Ellison, V., and Stillman, B. (1998). Reconstitution of recombinant human replication factor C (RFC) and identification of an RFC subcomplex processing DNA-dependent ATPase activity. J. Biol. Chem. 273, 5979-5987.
12. Enomoto, S., and Berman, J. (1998). Chromatain assembly factor I contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci. Genes Dev. 12, 219-232.
13. Enomoto, S., McCune-Zierath, P.D., Gerami-Nejad, M., Sanders, M.A., and Berman, J. (1997). RLF2, a subunit of yeast chromatin assembly factor-I, is required for telomeric chromatin function in vivo. Genes Dev. 11, 358-370.
14. Fien, K., and Stillman, B. (1992). Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading-strand DNA replication complex. Mol. Cell. Biol. 12, 155-163.
15. Fotedar, R., and Roberts, J.M. (1989). Multistep pathway for replication-dependent nucleosome assembly. Proc. Natl. Acad. Sci. USA 86, 6459-6463.
16. Gaillard, P.-H., Martini, E.M., Kaufman, P.D., Stillman, B., Moustacchi, E., and Almouzni, G. (1996). Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor 1. Cell 86, 887-896.
17. Gaillard, P.-H., Moggs, J.G., Roche, D.M., Quivy, J.-P., Becker, P.B., Wood, R.D., and Almouzni, G. (1997). Initiation and bidirectional propagation of chromatin assembly from a target site for nucleotide excision repair. EMBO J. 16, 6281-6289.
18. Gottschling, D.E., Aparicio, O.M., Billington, B.L., and Zakian, V.A. (1990). Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63, 751-762.
19. Grewal, S.I., Bonaduce, M.J., and Klar, A.J. (1998). Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast. Genetics 750, 563-576.
20. Grunstein, M. (1998). Yeast heterochromatin: regulation of its assembly and inheritance by histories. Cell 93, 325-328.
21. Hacker, K.J., and Alberts, B.M. (1994). The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairpin helix. A model for polymerase release following the termination of each Okazaki fragment. J. Biol. Chem. 269, 24221-24228.
22. Henderson, D.S., Banga, S.S., Grigliatti, T.A., and Boyd, J.B. (1994). Mutagen sensitivity and suppression of position-effect variegation result from mutations in mus209, the Drosophila gene encoding PCNA. EMBO 13, 1450-1459.
23. Herendeen, D.R., Kassavetis, G.A., Barry, J., Alberts, B.M., and Geiduschek, E.P. (1989). Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus. Science 245, 952-958.
24. Hübscher, U., Maga, G., and Podust, V.N. (1996). DNA replication accessory proteins. In DNA Replication in Eukaryotic Cells, M.L. DePamphilis, ed. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 525-544.
25. Ivanova, A.V., Bonaduce, M.J., Ivanov, S.V., and Klar, A.J. (1998). The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast. Nat. Genet. 19, 192-195.
26. Jonsson, Z.O., and Hübscher, U. (1997). Proliferating cell nuclear antigen: more than a clamp for DNA polymerases. Bioessays 19, 967-975.
27. Kamakaka, R.T., Bulger, M., Kaufman, P.D., Stillman, B., and Kadonaga, J.T. (1996). Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1. Mol. Cell. Biol. 16, 810-817.
28. Kaufman, P.D., Kobayashi, R., Kessler, N., and Stillman, B. (1995). The p150 and p60 subunits of chromatin assembly factor 1 : a molecular link between newly synthesized histones and DNA replication. Cell 81, 1105-1114.
29. Kaufman, P.D., Kobayashi, R., and Stillman, B. (1997). Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I. Genes Dev. 11, 345-357.
30. Kaufman, P.D., Cohen, J.L., and Osley, M.A. (1998). Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor I. Mol. Cell. Biol. 18, 4793-4806.
31. Kelman, Z., and Hurwitz, J. (1998). Protein-PCNA interactions: a DNA-scanning mechanism? Trends Biochem. Sci. 23, 236-238.
32. Klar, A.J., Ivanova, A.V., Dalgaard, U.Z., Bonaduce, M.J., and Grewal, S.I. (1998). Multiple epigenetic events regulate mating-type switching of fission yeast. Novartis Found. Symp. 274, 87-99.
33. Krishna, T.S., Kong, X.-P., Gary, S., Burgers, P.M., and Kuriyan, J. (1994). Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79, 1233-1243.
34. Krude, T. (1995). Chromatin assembly factor 1 (CAF-1) colocalizes with replication foci in HeLa cell nuclei. Exp. Cell Res. 220, 304-311.
35. Lee, S.-H., Kwong, A.D., Pan, Z.-Q., and Hurwitz, J. (1991). Studies on the activator 1 protein complex, an accessory factorfor proliferating cell nuclear antigen-dependent DNA polymerase 5. J. Biol. Chem. 266, 594-602.
36. Lewin, B. (1998). The mystique of epigenetics. Cell 93, 301-303.
37. Li, R., Hannon, G.J., Beach, D., and Stillman, B. (1996). Subcellular distribution of p21 and PCNA in normal and repair-deficient cells following DNA damage. Curr. Biol. 6, 189-199.
38. Martini, E., Roche, D.M., Marheineke, K., Verreault, A., and Almouzni, G. (1998). Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells. J. Cell Biol. 743, 563-575.
39. Miller, A.M., Sternglanz, R., and Nasmyth, K.A. (1984). The role of DNA replication in the repression of the yeast mating-type silent loci. Cold Spring Harb. Symp. Quant. Biol. 49, 105-113.
40. Monson, E.K., De Bruin, D., and Zakian, V.A. (1997). The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. Proc. Natl. Acad. Sci. USA 94, 13081-13086.
41. Nichols, A.F., and Sancar, A. (1992). Purification of PCNA as a nucleotide excision repair protein [corrected and republished with original paging, article originally printed in Nucleic Acids Res 1992 May 25;20(10):2441-2446]. Nucleic Acids Res. 20, 2441-2446.
42. Nossal, N.G. (1992). Protein-protein interactions at a DNA replication fork: bacteriophage T4 as a model. FASEB J. 6, 871-878.
43. Podust, V.N., and Hübscher, U. (1993). Lagging strand DNA synthesis by calf thymus DNA polymerases α, β, δ and ε in the presence of auxiliary proteins. Nucleic Acids Res. 27, 841-846.
44. Podust, L.M., Podust, V.N., Sogo, J.M., and Hübscher, U. (1995). Mammalian DNA polymerase auxiliary proteins: analysis of replication factor C-catalyzed proliferating cell nuclear antigen loading onto circular double-stranded DNA. Mol. Cell. Biol. 15, 3072-3081.
45. Prelich, G., Kostura, M., Marshak, D.R., Mathews, M.B., and Stillman, B. (1987a). The cell-cycle regulated proliferating cell nuclear antigen is required for SV40 DNA replication in vitro. Nature 326, 471-475.
46. Prelich, G.,Tan, C.K., Kostura, M., Mathews, M.B., So, A.G., Downey, K.M., and Stillman, B. (1987b). Functional identity of proliferating cell nuclear antigen and a DNA polymerase-delta auxiliary protein. Nature 326, 517-520.
47. Qian, Y.W., and Lee, E.Y. (1995). Dual retinoblastoma-binding proteins with properties related to a negative regulator of ras in yeast. J. Biol. Chem. 270, 25507-25513.
48. Qian, Z., Huang, H., Hong, J.Y., Burck, C.L., Johnston, S.D., Berman, J., Carol, A., and Liebman, S.W. (1998). Yeast Ty1 retrotransposition is stimulated by a synergistic interaction between mutations in chromatin assembly factor I and histone regulatory proteins. Mol. Cell. Biol. 18, 4783-4792.
49. Shivji, K.K., Kenny, M.K., and Wood, R.D. (1992). Proliferating cell nuclear antigen is required for DNA excision repair. Cell 69, 367-374.
50. Simon, R.H., and Felsenfeld, G. (1979). A new procedure for purifying histone pairs H2A+H2B and H3+H4 from chromatin using hydroxylapatite. Nucleic Acids Res. 6, 689-696.
51. Smith, S., and Stillman, B. (1989). Purification and characterization of CAF-1, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 58, 15-25.
52. Smith, S., and Stillman, B. (1991 a). Immunological characterization of chromatin assembly factor I, a human cell factor required for chromatin assembly during DNA replication in vitro. J. Biol. Chem. 266, 12041-12047.
53. Smith, S., and Stillman, B. (1991 b). Stepwise assembly of chromatin during DNA replication in vitro. EMBO J. 10, 971-980.
54. Stillman, B. (1986). Chromatin assembly during SV40 DNA replication in vitro. Cell 45, 555-565.
55. Stillman, B. (1994). Smart machines at the DNA replication fork. Cell 78, 725-728.
56. Stillman, B.W., and Gluzman, Y. (1985). Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells. Mol. Cell. Biol. 5, 2051-2060.
57. Stukenberg, P.T., Turner, J., and O'Donnell, M. (1994). An explanation for lagging strand replication: polymerase hopping among DNA sliding clamps. Cell 78, 877-887.
58. Svaren, J., and Chalkley, R. (1990). The structure and assembly of active chromatin. Trends Genet. 6, 52-56.
59. Tan, C.K., Castillo, C., So, A.G., and Downey, K.M. (1986). An auxiliary protein for DNA polymerase-5 from fetal calf thymus. J. Biol. Chem. 267, 12310-12316.
60. Tsurimoto, T., and Stillman, B. (1989). Purification of a cellular replication factor, RF-C, that is required for coordinated synthesis of leading and lagging strands during simian virus 40 DNA replication in vitro. Mol. Cell. Biol. 9, 609-619.
61. Tsurimoto, T., and Stillman, B. (1990). Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4. Proc. Natl. Acad. Sci. USA 87, 1023-1027.
62. Tsurimoto, T., and Stillman, B. (1991). Replication factors required for SV40 DNA replication in vitro: I. DNA structure-specific recognition of a primer-template junction by eukaryotic DNA polymerases and their accessory factors. J. Biol. Chem. 266, 1950-1960.
63. Tsurimoto, T., Melendy, T., and Stillman, B. (1990). Sequential initiation of lagging and leading strand synthesis by two DNA polymerase complexes at the SV40 DNA replication origin. Nature 346, 534-539.
64. Verreault, A., Kaufman, P.D., Kobayashi, R., and Stillman, B. (1996). Nucleosome assembly by a complex of CAF-1 and acetylated histories H3/H4. Cell 87, 95-104.
65. Waga, S., and Stillman, B. (1994). Anatomy of a DNA replication fork revealed by reconstitution of SV40 DNA replication in vitro. Nature 369, 207-212.
66. Waga, S., and Stillman, B. (1998). The DNA replication fork in eukaryotic cells. Annu. Rev. Biochem. 67, 721-751.
67. Weintraub, H. (1985). Assembly and propagation of repressed and derepressed chromosomal states. Cell 42, 705-711.
68. Woffle, A.P. (1991). Implications of DNA replication for eukaryotic gene expression. J. Cell Sci. 99, 201-206.
69. Yamamoto, Y., Girard, F., Bello, B., Affolter, M., and Gehring, W.J. (1997). The cramped gene of Drosophila is a member of the Polycomb-group, and interacts with mus209, the gene encoding proliferative cell nuclear antigen. Development 124, 3385-3394.