Proteomic and genomic characterization of chromatin complexes at a boundary

Journal of Cell Biology

Volumn 169, Issue 1, 2005, Pages 35-47

  Tackett, Alan J ^a   Dilworth, David J ^b,c   Davey, Megan J ^a,d   O'Donnell, Michael ^a   Aitchison, John D ^b,c   Rout, Michael P ^a   Chait, Brian T ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c UNIVERSITY OF ALBERTA   (Canada)

^d UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA; HISTONE; PROTEIN SUBUNIT;

ARTICLE; CHROMATIN; CONTROLLED STUDY; EPIGENETICS; GENE EXPRESSION; GENOME; GENOMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

CHROMATIN; DNA REPLICATION; GENE EXPRESSION REGULATION, FUNGAL; GENE SILENCING; GENOME, FUNGAL; GENOMICS; HISTONES; MACROMOLECULAR SUBSTANCES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

SACCHAROMYCES CEREVISIAE;

EID: 17644367887     PISSN: 00219525     EISSN: None     Source Type: Journal    
DOI: 10.1083/jcb.200502104     Document Type: Article

References (70)

1. Aitchison, J.D., M.P. Rout, M. Marelli, G. Blobel, and R.W. Wozniak. 1995. Two novel related yeast nucleoporins Nup170p and Nup157p: complementation with the vertebrate homologue Nup155p and functional interactions with the yeast nuclear pore-membrane protein Pom152p. J. Cell Biol. 131:1133-1148.
2. Aitchison, J.D., G. Blobel, and M.P. Rout. 1996. Kap104p: a karyopherin involved in the nuclear transport of messenger RNA binding proteins. Science. 274:624-627.
3. Araki, H., R.K. Hamatake, A. Morrison, A.L. Johnson, L.H. Johnston, and A. Sugino. 1991. Cloning DPB3, the gene encoding the third subunit of DNA polymerase II of Saccharomyces cerevisiae. Nucleic Acids Res. 19:4867-4872.
4. Archambault, V., C.X. Li, A.J. Tackelt, R. Wasch, B.T. Chait, M.P. Rout, and F.R. Cross. 2003. Genetic and biochemical evaluation of the importance of Cdc6 in regulating mitotic exit. Mol. Biol. Cell. 14:4592-4604.
5. Archambault, V., E.J. Chang, B.J. Drapkin, F.R. Cross, B.T. Chait, and M.P. Rout. 2004. Targeted proteomic study of the cyclin-cdk module. Mol. Cell. 14:699-711.
6. Becker, P.B., and W. Horz. 2002. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:247-273.
7. Bi, X., and J.R. Broach. 2001. Chromosomal boundaries in S. cerevisiae. Curr. Opin. Genet. Dev. 11:199-204.
8. Bi, X., M. Braunstein, G.J. Shei, and J.R. Broach. 1999. The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing. Proc. Natl. Acad. Sci. USA. 96:11934-11939.
9. Braunstein, M., R.E. Sobel, C.D. Allis, B.M. Turner, and J.R. Broach. 1996. Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol. 16:4349-4356.
10. Burgess-Beusse, B., C. Farrell, M. Gaszner, M. Litt, V. Mutskov, F. Recillas-Targa, M. Simpson, A. West, and G. Felsenfeld. 2002. The insulation of genes from external enhancers and silencing chromatin. Proc. Natl. Acad. Sci. USA. 99:16433-16437.
11. Chilkova, O., B.H. Jonsson, and E. Johansson. 2003. The quaternary structure of DNA polymerase epsilon from Saccharomyces cerevisiae. J. Biol. Chem. 278:14082-14086.
12. Dhillon, N., and R.T. Kamakaka. 2002. Breaking through to the other side: silencers and barriers. Curr. Opin. Genet. Dev. 12:188-192.
13. Donze, D., and R.T. Kamakaka. 2001. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20:520-531.
14. Donze, D., C.R. Adams, J. Rine, and R.T. Kamakaka. 1999. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13: 698-708.
15. Dua, R., D.L. Levy, and J.L. Campbell. 1998. Role of the putative zinc finger domain of Saccharomyces cerevisiae DNA polymerase epsilon in DNA replication and the S/M checkpoint pathway. J. Biol. Chem. 273:30046-30055.
16. Dua, R., S. Edwards, D.L. Levy, and J.L. Campbell. 2000. Subunit interactions within the Saccharomyces cerevisiae DNA polymerase epsilon (pol epsilon) complex. Demonstration of a dimeric pol epsilon. J. Biol. Chem. 275:28816-28825.
17. Edwards, S., C.M. Li, D.L. Levy, J. Brown, P.M. Snow, and J.L. Campbell. 2003. 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. 23:2733-2748.
18. Fazzio, T.G., and T. Tsukiyama. 2003. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Mol. Cell. 12:1333-1340.
19. Fischle, W., Y. Wang, and C.D. Allis. 2003. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15:172-183.
20. Frohlich, K.U. 2001. An AAA family tree. J. Cell Sci. 114:1601-1602.
21. Gavin, A.C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, C.M. Crucial, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:141-147.
22. Goto, T., P. Laipis, and J.C. Wang. 1984. The purification and characterization of DNA topoisomerases I and II of the yeast Saccharomyces cerevisiae. J. Biol. Chem. 259:10422-10429.
23. Haber, J.E. 1998. Mating-type gene switching in Saccharomyces cerevisiae. Annu. Rev. Genet. 32:561-599.
24. Halme, A., S. Bumgarner, C. Styles, and G.R. Fink. 2004. Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast. Cell. 116:405-415.
25. Hamatake, R.K., H. Hasegawa, A.B. Clark, K. Bebenek, T.A. Kunkel, and A. Sugino. 1990. Purification and characterization of DNA polymerase II from the yeast Saccharomyces cerevisiae. Identification of the catalytic core and a possible holoenzyme form of the enzyme. J. Biol. Chem. 265:4072-4083.
26. Hanna, J.S., E.S. Kroll, V. Lundblad, and P.A. Spencer. 2001. Saccharomyces cerevisiae CTF18 and CTF4 are required for sister chromatid cohesion. Mol. Cell. Biol. 21:3144-3158.
27. Ho, Y., A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:180-183.
28. Howe, L., D. Auston, P. Grant, S. John, R.G. Cook, J.L. Workman, and L. Pillus. 2001. Histone H3 specific acetyltransferases are essential for cell cycle progression. Genes Dev. 15:3144-3154.
29. Hubscher, U., G. Maga, and S. Spadari. 2002. Eukaryotic DNA polymerases. Annu. Rev. Biochem. 71:133-163.
30. Iida, T., and H. Araki. 2004. Noncompetitive counteractions of DNA polymerase epsilon and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae. Mol. Cell. Biol. 24:217-227.
31. Ishii, K., and U.K. Laemmli. 2003. Structural and dynamic functions establish chromatin domains. Mol. Cell. 11:237-248.
32. Jenuwein, T., and C.D. Allis. 2001. Translating the histone code. Science. 293:1074-1080.
33. Jeruzalmi, D., M. O'Donnell, and J. Kuriyan. 2002. Clamp loaders and sliding clamps. Curr. Opin. Struct. Biol. 12:217-224.
34. John, S., L. Howe, S.T. Tafrov, P.A. Grant, R. Sternglanz, and J.L. Workman. 2000. The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev. 14:1196-1208.
35. Kalkum, M., G.J. Lyon, and B.T. Chait. 2003. Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry. Proc. Natl. Acad. Sci. USA. 100:2795-2800.
36. Kassabov, S.R., N.M. Henry, M. Zofall, T. Tsukiyama, and B. Bartholomew. 2002. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22:7524-7534.
37. Kent, N.A., N. Karabetsou, P.K. Politis, and J. Mellor. 2001. In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev. 15:619-626.
38. Krutchinsky, A.N., W. Zhang, and B.T. Chait. 2000. Rapidly switchable matrix-assisted laser desorption/ionization and electrospray quadrupole-time-of-flight mass spectrometry for protein identification. J. Am. Soc. Mass Spectrom. 11:493-504.
39. Krutchinsky, A.N., M. Kalkum, and B.T. Chait, 2001. Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. Anal. Chem. 73:5066-5077.
40. Kurdistani, S.K., S. Tavazoie, and M. Grunstein. 2004. Mapping global histone acetylation patterns to gene expression. Cell. 117:721-733.
41. Labrador, M., and V.G. Corces. 2002. Setting the boundaries of chromatin domains and nuclear organization. Cell. 111:151-154.
42. Laloraya, S., V. Guacci, and D, Koshland. 2000, Chromosomal addresses of the cohesin component Mcd1p. J Cell Biol. 151:1047-1056.
43. Lieb, J.D., X. Liu, D. Botstein, and P.O. Brown, 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:327-334.
44. Mayer, M.L., S.P. Gygi, R. Aebersold, and P. Mieter, 2001. Identification of RFC(Ctf18p, Ctf8p, Dcc 1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mol. Cell, 7:959-970.
45. McConnell, A.D., M.E. Gelbart, and T. Tsukiyama. 2004. Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Mol. Cell. Biol. 24:2605-2613.
46. Meneghini, M.D., M. Wu, and H.D. Madhani. 2003. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell. 112:725-736,
47. Mizuguchi, G., X. Shen, J. Landry, W.H. Wu, S. Sen, and C. Wu, 2004. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 303:343-348.
48. Myer, V.E., and R.A. Young. 1998. RNA polymerase II holoenzymes and sub-complexes. J. Biol. Chem. 273:27757-27760
49. Navas, T.A., Z. Zhou, and S.J. Elledge. 1995. DNA polymerase epsilon links the DNA replication machinery to the S phase checkpoint. Cell. 80:29-39.
50. Ohya, T., S. Maki, Y. Kawasaki, and A. Sugino. 2000. Structure and function of the fourth subunit (Dpb4p) of DNA polymerase epsilon in Saccharomyces cerevisiae. Nucleic Acids Res. 28:3846-3852.
51. Ohya, T., Y. Kawasaki, S. Hiraga, S. Kanbara, K. Nakajo, N. Nakashima, A. Suzuki, and A. Sugino. 2002. The DNA polymerase domain of pol(epsilon) is required for rapid, efficient, and highly accurate chromosomal DNA replication, telomere length maintenance, and normal cell senescence in Saccharomyces cerevisiae. J. Biol. Chem. 277:28099-28108.
52. Oki, M., L. Valenzuela, T. Chiba, T. Ito, and R.T. Kamakaka. 2004. Barrier proteins remodel and modify chromatin to restrict silenced domains. Mol. Cell Biol. 24:1956-1967.
53. Osborn, A.J., S.J. Elledge, and L. Zou. 2002. Checking on the fork: the DNA-replication stress-response pathway. Trends Cell Biol. 12:509-516.
54. Qiu, C., K, Sawada, X. Zhang, and X. Cheng. 2002. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol. 9:217-224.
55. Rachidi, N., M.J. Martinez, P. Barre, and B. Blondin. 2000. Saccharomyces cerevisiae PAU genes are induced by anaerobiosis. Mol. Microbiol. 35:1421-1430.
56. Ren, B., F., Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, et al. 2000. Genome-wide location and function of DNA binding proteins. Science. 290:2306-2309.
57. Rout, M.P., G. Blobel, and J.D. Aitchison, 1997. A distinct nuclear import pathway used by ribosomal proteins. Cell. 89:715-725.
58. Rout, M.P., J.D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, and B.T. Chait. 2000. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148:635-651.
59. Rusche, L.N., A.L. Kirchmaier, and J. Rine. 2003, The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Anna. Rev. Biochem. 72:481-516.
60. Smith, C.M., Z.W. Haimberger, C.O. Johnson, A.J. Wolf, P.R. Gafken, Z. Zhang, M.R. Parthun, and D.E. Gottschling. 2002. Heritable chromatin structure: mapping "memory" in histones H3 and H4. Proc. Natl. Acad. Sci. USA. 99:16454-16461.
61. Smith, C.M., P.R. Gafken, Z. Zhang, D.E. Gottschling, J.B. Smith, and D.L. Smith. 2003. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4. Anal. Biochem, 316:23-33.
62. Smith, J.J., M. Marelli, R.H. Christmas, F.J. Vizeacoumar, D.J. Dilworth, T. Ideker, T. Galitski, K. Dimitrov, R.A. Rachubinski, and J.D. Aitchison. 2002. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J. Cell Biol. 158:259-271.
63. Stec, I., S.B. Nagl, G.J. van Ommen, and J.T. den Dunnen. 2000. The PWWP domain: a potential protein-protein interaction domain in nuclear proteins influencing differentiation? FEBS Lett. 473:1-5.
64. Strahl-Bolsinger, S., A. Hecht, K. Luo, and M. Grunstein. 1997. Sir2 and Sir4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83-93.
65. Suka, N., K. Luo, and M. Grunstein. 2002. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine 16 and spreading of heterochromatin. Nat. Genet. 32:378-383.
66. van Leeuwen, F., P.R. Gafken, and D.E. Gottschling. 2002. Dotl p modulates silencing in yeast by methylation of the nucleosome core. Cell. 109:745-756.
67. Vermaak, D., K. Ahmad, and S. Henikoff. 2003. Maintenance of chromatin states: an open-and-shut case. Curr. Opin. Cell Biol. 15:266-274.
68. Verstrepen, K.J., T.B. Reynolds, and G.R. Fink. 2004. Origins of variation in the fungal cell surface. Nat Rev Microbiol, 2:533-540.
69. Waterborg, J.H. 2000. Steady-state levels of histone acetylation in Saccharomyces cerevisiae. J. Biol. Chem. 275:13007-13011.
70. Zhang, Z., M.K. Hayashi, O. Merkel, B. Stillman, and R.M. Xu. 2002. Structure and function of the BAH-containing domain of Ore lp in epigenetic silencing. EMBO J. 21:4600-4611.