Host Cell Factor and an Uncharacterized SANT Domain Protein Are Stable Components of ATAC, a Novel dAda2A/dGcn5-Containing Histone Acetyltransferase Complex in Drosophila

REFERENCES

• Barlev, N. A., A. V. Emelyanov, P. Castagnino, P. Zegerman, A. J. Bannister, M. A. Sepulveda, F. Robert, L. Tora, T. Kouzarides, B. K. Birshtein, and S. L. Berger. 2003. A novel human Ada2 homologue functions with Gcn5 or Brg1 to coactivate transcription. Mol. Cell. Biol. 23:6944–6957.
   PubMedGoogle Scholar
• Boyer, L. A., M. R. Langer, K. A. Crowley, S. Tan, J. M. Denu, and C. L. Peterson. 2002. Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Mol. Cell 10:935–942.
   PubMed Web of Science ®Google Scholar
• Boyer, L. A., R. R. Latek, and C. L. Peterson. 2004. The SANT domain: a unique histone-tail-binding module? Nat. Rev. Mol. Cell Biol. 5:158–163.
   PubMed Web of Science ®Google Scholar
• Brown, C. E., L. Howe, K. Sousa, S. C. Alley, M. J. Carrozza, S. Tan, and J. L. Workman. 2001. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science 292:2333–2337.
   PubMed Web of Science ®Google Scholar
• Brownell, J. E., J. Zhou, T. Ranalli, R. Kobayashi, D. G. Edmondson, S. Y. Roth, and C. D. Allis. 1996. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84:843–851.
   PubMed Web of Science ®Google Scholar
• Bunch, T. A., Y. Grinblat, and L. S. Goldstein. 1988. Characterization and use of the Drosophila metallothionein promoter in cultured Drosophila melanogaster cells. Nucleic Acids Res. 16:1043–1061.
   PubMed Web of Science ®Google Scholar
• Carrozza, M. J., R. T. Utley, J. L. Workman, and J. Cote. 2003. The diverse functions of histone acetyltransferase complexes. Trends Genet. 19:321–329.
   PubMed Web of Science ®Google Scholar
• Eberharter, A., S. John, P. A. Grant, R. T. Utley, and J. L. Workman. 1998. Identification and analysis of yeast nucleosomal histone acetyltransferase complexes. Methods 15:315–321.
   PubMed Web of Science ®Google Scholar
• Fischle, W., Y. Wang, and C. D. Allis. 2003. Histone and chromatin cross-talk. Curr. Opin. Cell Biol. 15:172–183.
   PubMed Web of Science ®Google Scholar
• Flaus, A., and T. Owen-Hughes. 2004. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14:165–173.
   PubMedGoogle Scholar
• Grant, P. A., and S. L. Berger. 1999. Histone acetyltransferase complexes. Semin. Cell Dev. Biol. 10:169–177.
   PubMed Web of Science ®Google Scholar
• Grant, P. A., D. E. Sterner, L. J. Duggan, J. L. Workman, and S. L. Berger. 1998. The SAGA unfolds: convergence of transcription regulators in chromatin-modifying complexes. Trends Cell Biol. 8:193–197.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Howe, L., C. E. Brown, T. Lechner, and J. L. Workman. 1999. Histone acetyltransferase complexes and their link to transcription. Crit. Rev. Eukaryot. Gene Expr. 9:231–243.
   PubMedGoogle Scholar
• Julien, E., and W. Herr. 2003. Proteolytic processing is necessary to separate and ensure proper cell growth and cytokinesis functions of HCF-1. EMBO J. 22:2360–2369.
   PubMed Web of Science ®Google Scholar
• Kikuchi, H., Y. Takami, and T. Nakayama. 2005. GCN5: a supervisor in all-inclusive control of vertebrate cell cycle progression through transcription regulation of various cell cycle-related genes. Gene 347:83–97.
   PubMedGoogle Scholar
• Kusch, T., L. Florens, W. H. Macdonald, S. K. Swanson, R. L. Glaser, J. R. Yates III, S. M. Abmayr, M. P. Washburn, and J. L. Workman. 2004. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306:2084–2087.
   PubMed Web of Science ®Google Scholar
• Kusch, T., S. Guelman, S. M. Abmayr, and J. L. Workman. 2003. Two Drosophila Ada2 homologues function in different multiprotein complexes. Mol. Cell. Biol. 23:3305–3319.
   PubMedGoogle Scholar
• Lee, K. K., L. Florens, S. K. Swanson, M. P. Washburn, and J. L. Workman. 2005. The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol. Cell. Biol. 25:1173–1182.
   PubMed Web of Science ®Google Scholar
• Lee, K. K., P. Prochasson, L. Florens, S. K. Swanson, M. P. Washburn, and J. L. Workman. 2004. Proteomic analysis of chromatin-modifying complexes in Saccharomyces cerevisiae identifies novel subunits. Biochem. Soc. Trans. 32:899–903.
   PubMedGoogle Scholar
• Luciano, R. L., and A. C. Wilson. 2003. HCF-1 functions as a coactivator for the zinc finger protein Krox20. J. Biol. Chem. 278:51116–51124.
   PubMedGoogle Scholar
• Luciano, R. L., and A. C. Wilson. 2000. N-terminal transcriptional activation domain of LZIP comprises two LxxLL motifs and the host cell factor-1 binding motif. Proc. Natl. Acad. Sci. USA 97:10757–10762.
   PubMedGoogle Scholar
• Lusser, A., and J. T. Kadonaga. 2003. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192–1200.
   PubMed Web of Science ®Google Scholar
• Mahajan, S. S., K. M. Johnson, and A. C. Wilson. 2003. Molecular cloning of Drosophila HCF reveals proteolytic processing and self-association of the encoded protein. J. Cell. Physiol. 194:117–126.
   PubMedGoogle Scholar
• Marmorstein, R. 2001. Structure and function of histone acetyltransferases. Cell. Mol. Life Sci. 58:693–703.
   PubMedGoogle Scholar
• Martinez, E., V. B. Palhan, A. Tjernberg, E. S. Lymar, A. M. Gamper, T. K. Kundu, B. T. Chait, and R. G. Roeder. 2001. Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol. Cell. Biol. 21:6782–6795.
   PubMed Web of Science ®Google Scholar
• Muratoglu, S., S. Georgieva, G. Papai, E. Scheer, I. Enunlu, O. Komonyi, I. Cserpan, L. Lebedeva, E. Nabirochkina, A. Udvardy, L. Tora, and I. Boros. 2003. Two different Drosophila ADA2 homologues are present in distinct GCN5 histone acetyltransferase-containing complexes. Mol. Cell. Biol. 23:306–321.
   PubMed Web of Science ®Google Scholar
• Ogryzko, V. V. 2001. Mammalian histone acetyltransferases and their complexes. Cell. Mol. Life Sci. 58:683–692.
   PubMed Web of Science ®Google Scholar
• Ogryzko, V. V., T. Kotani, X. Zhang, R. L. Schlitz, T. Howard, X.-J. Yang, B. H. Howard, J. Qin, and Y. Nakatani. 1998. Histone-like TAFs within the PCAF histone acetylase complex. Cell 94:35–44.
   PubMedGoogle Scholar
• Peterson, C. L., and M. A. Laniel. 2004. Histones and histone modifications. Curr. Biol. 14:R546–R551.
   PubMed Web of Science ®Google Scholar
• Puig, O., F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, and B. Seraphin. 2001. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218–229.
   PubMed Web of Science ®Google Scholar
• Qi, D., J. Larsson, and M. Mannervik. 2004. Drosophila Ada2b is required for viability and normal histone H3 acetylation. Mol. Cell. Biol. 24:8080–8089.
   PubMedGoogle Scholar
• Rigaut, G., A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17:1030–1032.
   PubMed Web of Science ®Google Scholar
• Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81–120.
   PubMed Web of Science ®Google Scholar
• Sanders, S. L., J. Jennings, A. Canutescu, A. J. Link, and P. A. Weil. 2002. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22:4723–4738.
   PubMed Web of Science ®Google Scholar
• Sato, S., C. Tomomori-Sato, T. J. Parmely, L. Florens, B. Zybailov, S. K. Swanson, C. A. Banks, J. Jin, Y. Cai, M. P. Washburn, J. W. Conaway, and R. C. Conaway. 2004. A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol. Cell 14:685–691.
   PubMed Web of Science ®Google Scholar
• Schneider, I. 1972. Cell lines derived from late embryonic stages of Drosophila melanogaster. J. Embryol. Exp. Morphol. 27:353–365.
   PubMedGoogle Scholar
• Smith, E. R., J. M. Belote, R. L. Schiltz, X. J. Yang, P. A. Moore, S. L. Berger, Y. Nakatani, and C. D. Allis. 1998. Cloning of Drosophila GCN5: conserved features among metazoan GCN5 family members. Nucleic Acids Res. 26:2948–2954.
   PubMedGoogle Scholar
• Sterner, D. E., X. Wang, M. H. Bloom, G. M. Simon, and S. L. Berger. 2002. The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complex. J. Biol. Chem. 277:8178–8186.
   PubMedGoogle Scholar
• Vlachonasios, K. E., M. F. Thomashow, and S. J. Triezenberg. 2003. Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15:626–638.
   PubMed Web of Science ®Google Scholar
• Washburn, M. P., D. Wolters, and J. R. Yates III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:242–247.
   PubMed Web of Science ®Google Scholar
• Wieczorek, E., M. Brand, X. Jacq, and L. Tora. 1998. Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II. Nature 393:187–191.
   PubMedGoogle Scholar
• Wilson, A. C., M. Boutros, K. M. Johnson, and W. Herr. 2000. HCF-1 amino- and carboxy-terminal subunit association through two separate sets of interaction modules: involvement of fibronectin type 3 repeats. Mol. Cell. Biol. 20:6721–6730.
   PubMedGoogle Scholar
• Wysocka, J., and W. Herr. 2003. The herpes simplex virus VP16-induced complex: the makings of a regulatory switch. Trends Biochem. Sci. 28:294–304.
   PubMed Web of Science ®Google Scholar
• Wysocka, J., M. P. Myers, C. D. Laherty, R. N. Eisenman, and W. Herr. 2003. Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev. 17:896–911.
   PubMed Web of Science ®Google Scholar
• Xu, W., D. G. Edmondson, Y. A. Evrard, M. Wakamiya, R. R. Behringer, and S. Y. Roth. 2000. Loss of Gcn5l2 leads to increased apoptosis and mesodermal defects during mouse development. Nat. Genet. 26:229–232.
   PubMedGoogle Scholar
• Yamauchi, T., J. Yamauchi, T. Kuwata, T. Tamura, T. Yamashita, N. Bae, H. Westphal, K. Ozato, and Y. Nakatani. 2000. Distinct but overlapping roles of histone acetylase PCAF and of the closely related PCAF-B/GCN5 in mouse embryogenesis. Proc. Natl. Acad. Sci. USA 97:11303–11306.
   PubMedGoogle Scholar
• Yokoyama, A., Z. Wang, J. Wysocka, M. Sanyal, D. J. Aufiero, I. Kitabayashi, W. Herr, and M. L. Cleary. 2004. Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol. Cell. Biol. 24:5639–5649.
   PubMed Web of Science ®Google Scholar
• Yu, J., Y. Li, T. Ishizuka, M. G. Guenther, and M. A. Lazar. 2003. A SANT motif in the SMRT corepressor interprets the histone code and promotes histone deacetylation. EMBO J. 22:3403–3410.
   PubMed Web of Science ®Google Scholar
• Zhang, W., J. R. Bone, D. G. Edmondson, B. M. Turner, and S. Y. Roth. 1998. Essential and redundant functions of histone acetylation revealed by mutation of target lysines and loss of the Gcn5p acetyltransferase. EMBO J. 17:3155–3167.
   PubMed Web of Science ®Google Scholar