Purification of multiprotein histone acetyltransferase complexes

Methods in Molecular Biology

Volumn 809, Issue , 2012, Pages 427-443

  Wang, Yuan Liang ^a   Faiola, Francesco ^a   Martinez, Ernest ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Affinity purification; Cell line; FLAG tag; GCN5; Histone acetyltransferase; Protein complexes; S Sepharose; Transcription

Indexed keywords

EUKARYOTA; HEXAPODA; MAMMALIA;

EID: 84555187916     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-376-9_28     Document Type: Article

References (42)

1. Roeder, R. G. (2005) Transcriptional regulation and the role of diverse coactivators in animal cells. FEBS Lett 579, 909-915. (Pubitemid 40361864)
2. Kornberg, R. D., and Lorch, Y. (1999) Twentyfi ve years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294. (Pubitemid 29380564)
3. Berger, S. L. (2007) The complex language of chromatin regulation during transcription. Nature 447, 407-412. (Pubitemid 46816746)
4. Kingston, R. E., Bunker, C. A., and Imbalzano, A. N. (1996) Repression and activation by multiprotein complexes that alter chromatin structure. Genes & Dev 10, 905-920. (Pubitemid 26138703)
5. Eberharter, A., and Becker, P. B. (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics, EMBO Rep 3, 224-229. (Pubitemid 34269514)
6. Allfrey, V. G., Faulkner, R., and Mirsky, A. E. (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA. 51, 786-794.
7. Lee, D. Y., Hayes, J. J., Pruss, D., and Wolffe, A. P. (1993) A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72, 73-84. (Pubitemid 23029694)
8. Hebbes, T. R., Clayton, A. L., Thorne, A. W., and Crane-Robinson, C. (1994) Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain. EMBO J 13, 1823-1830. (Pubitemid 24124515)
9. Braunstein, M., Rose, A. B., Holmes, S. G., Allis, C. D., and Broach, J. R. (1993) Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes & Dev 7, 592-604. (Pubitemid 23125260)
10. Jeppesen, P., and Turner, B. M. (1993) The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74, 281-289. (Pubitemid 23221704)
11. Brownell, J. E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D. G., Roth, S. Y., and Allis, C. D. (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843-851. (Pubitemid 26106854)
12. Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408-411. (Pubitemid 26138177)
13. Cheung, W. L., Briggs, S. D., and Allis, C. D. (2000) Acetylation and chromosomal functions. Curr Opin Cell Biol 12, 326-333. (Pubitemid 30265062)
14. Narlikar, G. J., Fan, H. Y., and Kingston, R. E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475-487. (Pubitemid 34260873)
15. Lee, K. K., and Workman, J. L. (2007) Histone acetyltransferase complexes: one size doesn't fi t all. Nat Rev 8, 284-295. (Pubitemid 46474661)
16. Weake, V. M., Swanson, S. K., Mushegian, A., Florens, L., Washburn, M. P., Abmayr, S. M., and Workman, J. L. (2009) A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGAdependent gene expression. Genes & Dev 23, 2818-2823.
17. Tse, C., Sera, T., Wolffe, A. P., and Hansen, J. C. (1998) Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol 18, 4629-4638. (Pubitemid 28343048)
18. Carruthers, L. M., and Hansen, J. C. (2000) The core histone N termini function independently of linker histones during chromatin condensation. J Biol Chem 275, 37285-37290. (Pubitemid 32002152)
19. Wolffe, A. P., and Hansen, J. C. (2001) Nuclear visions: functional fl exibility from structural instability. Cell 104, 631-634. (Pubitemid 32241011)
20. Shogren-Knaak, M., Ishii, H., Sun, J. M., Pazin, M. J., Davie, J. R., and Peterson, C. L. (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844-847. (Pubitemid 43228847)
21. Yang, X. J. (2004) The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res 32, 959-976.
22. Berndsen, C. E., and Denu, J. M. (2008) Catalysis and substrate selection by histone/ protein lysine acetyltransferases. Curr Opin Struct Biol 18, 682-689.
23. An, W., Palhan, V. B., Karymov, M. A., Leuba, S. H., and Roeder, R. G. (2002) Selective requirements for histone H3 and H4 N termini in p300-dependent transcriptional activation from chromatin. Mol Cell 9, 811-821. (Pubitemid 34454891)
24. An, W., Kim, J., and Roeder, R. G. (2004) Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell 117, 735-748. (Pubitemid 38748890)
25. Dekker, F. J., and Haisma, H. J. (2009) Histone acetyl transferases as emerging drug targets. Drug Discov Today 14, 942-948.
26. Grant, P. A., Eberharter, A., John, S., Cook, R. G., Turner, B. M., and Workman, J. L. (1999) Expanded lysine acetylation specifi city of Gcn5 in native complexes. J Biol Chem 274, 5895-5900. (Pubitemid 29109247)
27. Grant, P. A., Duggan, L., Cote, J., Roberts, S. M., Brownell, J. E., Candau, R., Ohba, R., Owen-Hughes, T., Allis, C. D., Winston, F., Berger, S. L., and Workman, J. L. (1997) Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/ Ada) complex. Genes & Dev 11, 1640-1650. (Pubitemid 27300590)
28. Candau, R., Zhou, J. X., Allis, C. D., and Berger, S. L. (1997) Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivo. EMBO J 16, 555-565. (Pubitemid 27067785)
29. Grant, P. A., Schieltz, D., Pray-Grant, M. G., Steger, D. J., Reese, J. C., Yates, J. R., 3 rd, and Workman, J. L. (1998) A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94, 45-53. (Pubitemid 28347468)
30. Martinez, E., Kundu, T. K., Fu, J., and Roeder, R. G. (1998) A human SPT3-TAFII31- GCN5-L acetylase complex distinct from transcription factor IID. J Biol Chem 273, 23781-23785. (Pubitemid 28435711)
31. Martinez, E., Palhan, V. B., Tjernberg, A., Lymar, E. S., Gamper, A. M., Kundu, T. K., Chait, B. T., and Roeder, R. G. (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. (Pubitemid 32911240)
32. Ogryzko, V. V., Kotani, T., Zhang, X., Schiltz, R. L., Howard, T., Yang, X. J., Howard, B. H., Qin, J., and Nakatani, Y. (1998) Histone-like TAFs within the PCAF histone acetylase complex. Cell 94, 35-44. (Pubitemid 28347467)
33. Wang, Y. L., Faiola, F., Xu, M., Pan, S., and Martinez, E. (2008) Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein. J Biol Chem 283, 33808-33815.
34. Liu, X., Vorontchikhina, M., Wang, Y. L., Faiola, F., and Martinez, E. (2008) STAGA recruits Mediator to the MYC oncoprotein to stimulate transcription and cell proliferation. Mol Cell Biol 28, 108-121.
35. Atanassov, B. S., Evrard, Y. A., Multani, A. S., Zhang, Z., Tora, L., Devys, D., Chang, S., and Dent, S. Y. (2009) Gcn5 and SAGA regulate shelterin protein turnover and telomere maintenance. Mol Cell 35, 352-364.
36. Nagy, Z., Riss, A., Romier, C., le Guezennec, X., Dongre, A. R., Orpinell, M., Han, J., Stunnenberg, H., and Tora, L. (2009) The human SPT20- containing SAGA complex plays a direct role in the regulation of endoplasmic reticulum stressinduced genes,. Mol Cell Biol 29, 1649-1660.
37. Li, S., and Shogren-Knaak, M. A. (2009) The Gcn5 bromodomain of the SAGA complex facilitates cooperative and cross-tail acetylation of nucleosomes. J Biol Chen 284, 9411-9417.
38. Wysocka, J., Swigut, T., Milne, T. A., Dou, Y., Zhang, X., Burlingame, A. L., Roeder, R. G., Brivanlou, A. H., and Allis, C. D. (2005) WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121, 859-872. (Pubitemid 40806418)
39. Zhou, Q., Lieberman, P. M., Boyer, T. G., and Berk, A. J. (1992) Holo-TFIID supports transcriptional stimulation by diverse activators and from a TATA-less promoter. Genes & Dev 6, 1964-1974.
40. Chiang, C. M., Ge, H., Wang, Z., Hoffmann, A., and Roeder, R. G. (1993) Unique TATAbinding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and III. EMBO J 12, 2749-2762. (Pubitemid 23218324)
41. Guelman, S., Suganuma, T., Florens, L., Swanson, S. K., Kiesecker, C. L., Kusch, T., Anderson, S., Yates, J. R., 3 rd, Washburn, M. P., Abmayr, S. M., and Workman, J. L. (2006) Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila. Mol Cell Biol 26, 871-882. (Pubitemid 43146483)
42. Faiola, F., Liu, X., Lo, S., Pan, S., Zhang, K., Lymar, E., Farina, A., and Martinez, E. (2005) Dual regulation of c-Myc by p300 via acetylationdependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol Cell Biol 25, 10220-10234. (Pubitemid 41681950)