Eaf3 Regulates the Global Pattern of Histone Acetylation in Saccharomyces cerevisiae

Molecular and Cellular Biology

Volumn 24, Issue 2, 2004, Pages 757-764

  Reid, Juliet L ^a   Moqtaderi, Zarmik ^a   Struhl, Kevin ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; HISTONE; HISTONE ACETYLASE NUA4; HISTONE ACETYLTRANSFERASE; HISTONE DEACETYLASE; HISTONE H3; HISTONE H4; PROTEIN EAF3; PROTEIN RPD3; UNCLASSIFIED DRUG;

ACETYLATION; AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME SUBUNIT; GENE LOSS; GENE TARGETING; GENETIC TRANSCRIPTION; GENOME; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE;

ACETYLATION; ACETYLTRANSFERASES; GENE DELETION; GENOME, FUNGAL; HISTONE ACETYLTRANSFERASES; HISTONES; PROMOTER REGIONS (GENETICS); RIBOSOMAL PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0347986672     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.2.757-764.2004     Document Type: Article

References (60)

1. Agalioti, T., G. Chen, and D. Thanos. 2002. Deciphering the transcriptional histone acetylation code for a human gene. Cell 111:381-392.
2. Allard, S., R. T. Utley, J. Savard, A. Clarke, P. Grant, C. J. Brandl, L. Pillus, J. L. Workman, and J. Cote. 1999. NuA4, an essential transcription adaptor/ histone H4 acetyltransferase complex containing Esalp and the ATF-related cofactor Tralp. EMBO J. 18:5108-5119.
3. Bannister, A. J., P. Zegerman, J. F. Partridge, E. A. Miska, J. O. Thomas, R. C. Allshire, and T. Kouzarides. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120-124.
4. Bertram, M. J., N. G. Bérub́, X. Hang-Swanson, Q. Ran, J. K. Leung, S. Bryce, K. Spurgers, R. J. Bick, A. Baldini, Y. Ning, L. J. Clark, E. K. Parkinson, J. C. Barrett, J. R. Smith, and O. M. Pereira-Smith. 1999. Identification of a gene that reverses the immortal phenotype of a subset of cells and is a member of a novel family of transcription factor-like genes. Mol. Cell. Biol. 19:1479-1485.
5. Bird, A. W., D. Y. Yu, M. G. Pray-Grant, Q. Qui, K. E. Harmon, P. C. Megee, P. A. Grant, M. M. Smith, and M. F. Christman. 2002. Acetylation of histone H4 by Esal is required for double-strand break repair. Nature 419:411-415.
6. Boudreault, A. A., D. Cronier, W. Selleck, N. Lacoste, R. T. Utley, S. Allard, J. Savard, W. S. Lane, S. Tan, and J. Cote. 2003. Yeast enhancer of polycomb defines global Esal-dependent acetylation of chromatin. Genes Dev. 17:1415-1428.
7. a. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
8. Clarke, A. S., J. E. Lowell, S. J. Jacobson, and L. Pillus. 1999. Esalp is an essential histone acetyltransferase required for cell cycle progression. Mol. Cell. Biol. 19:2515-2526.
9. Cosma, M. P., T. Tanaka, and K. Nasmyth. 1999. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell 97:299-311.
10. Deckert, J., and K. Struhl. 2002. Targeted recruitment of Rpd3 histone deacetylase represses transcription by inhibiting recruitment of Swi/Snf, SAGA, and TATA binding protein., Mol. Cell. Biol. 22:6458-6470.
11. Dhalluin, C., J. E. Carlson, L. Zeng, C. He, A. K. Aggarwal, and M. M. Zhou. 1999. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399:491-496.
12. Eisen, A., R. T. Utley, A. Nourani, S. Allard, P. Schmidt, W. S. Lane, J. C. Lucchesi, and J. Cote. 2001. The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J. Biol. Chem. 276:3484-3491.
13. Fujita, M., T. Takasaki, N. Nakajima, T. Kawano, Y. Shimura, and H. Sakamoto. 2002. MRG-1, a mortality factor-related chromodomain protein, is required maternally for primordial germ cells to initiate mitotic proliferation in C elegans. Mech. Dev. 114:61-69.
14. Galarneau, L., A. Nourani, A. A. Boudreault, Y. Zhang, L. Heliot, S. Allard, J. Savard, W. S. Lane, D. J. Stillman, and J. Cote. 2000. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol. Cell 5:927-937.
15. Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M. A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
16. Gorman, M., M. I. Kuroda, and B. S. Baker. 1993. Regulation of the sex-specific binding of the maleless dosage compensation protein to the male X-chromosome in Drosophila. Cell 72:39-49.
17. Grunstein, M. 1997. Histone acetylation in chromatin structure and transcription. Nature 389:349-352.
18. Hassan, A. H., K. E. Neely, and J. L. Workman. 2001. Histone acetyltransferase complexes stabilize Swi/Snf binding to promoter nucleosomes. Cell 104:817-827.
19. Hassan, A. H., P. Prochasson, K. E. Neely, S. C. Galasinski, M. Chandy, M. J. Carozza, and J. L. Workman. 2002. Function and selectivitv of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369-379.
20. Ho, Y., A. Gruhler, A. Heilbut, G. D. Bader, L. Moore, S. L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, L. Yang, C. Wolting, I. Donaldson, S. Schandorff, J. Shewnarane, M. Vo, J. Taggart, M. Goudreault, B. Muskat, C. Alfarano, D. Dewar, Z. Lin, K. Michalickova, A. R. Willems, H. Sassi, P. A. Nielsen, K. J. Rasmussen, J. R. Andersen, L. E. Johansen, L. H. Hansen, H. Jespersen, A. Podtelejnikov, E. Nielsen, J. Crawford, V. Poulsen, B. D. Sorensen, J. Matthiesen, R. C. Hendrickson, F. Gleeson, T. Pawson, M. F. Moran, D. Durocher, M. Mann, C. W. Hogue, D. Figeys, and M. Tyers. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183.
21. Hong, L., G. P. Schroth, H. R. Matthews, P. Yau, and E. M. Bradbury. 1993. Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 "tail" to DNA. J. Biol. Chem. 268:305-314.
22. 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.
23. Hudson, B. P., M. A. Martinez-Yamout, H. J. Dyson, and P. E. Wright. 2000. Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J. Mol. Biol. 304:355-370.
24. Iyer, V., and K. Struhl. 1996. Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 93: 5208-5212.
25. lyer, V. R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, and P. O. Brown. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538.
26. Jacobs, S. A., S. D. Taverna, Y. Zhang, S. D. Briggs, J. Li, J. C. Eissenberg, C. D. Allis, and S. Khorasanizadeh. 2001. Specificity of the HPI chromo domain for the methylated N-terminus of histone H3. EMBO J. 20:5232-5241.
27. Kadosh, D., and K. Struhl. 1997. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89:365-371.
28. Kadosh, D., and K. Struhl. 1998. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18:5121-5127.
29. Katan-Khaykovich, Y., and K. Struhl. 2002. Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors. Genes Dev. 16:743-752.
30. Krebs, J. E., M.-H. Kuo, C. D. Allis, and C. L. Peterson. 1999. Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev. 13:1412-1421.
31. Kristjuhan, A., J. Walker, N. Suka, M. Grunstein, D. Roberts, B. R. Cairns, and J. Q. Svejstrup. 2002. Transcriptional inhibition of genes with severe histone H3 hypoacetylation in the coding region. Mol. Cell 10:925-933.
32. Krogan, N. J., M. Kim, A. Tong, A. Golshani, G. Cagney, V. Canadien, D. P. Richards, B. K. Beattie, A. Emili, C. Boone, A. Shilatifard, S. Buratowski, and J. Greenblatt. 2003. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 23:4207-4218.
33. Kuo, M.-H., E. vom Baur, K. Struhl, and C. D. Allis. 2000. Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. Mol. Cell 6:1309-1320.
34. Kuo, M.-H., J. Zhou, P. Jambeck, M. E. A. Churchill, and C. D. Allis. 1998. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev. 12:627-639.
35. Kuras, L., and K. Struhl. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399:609-612.
36. Kurdistani, S. K., D. Robyr, S. Tavazoie, and M. Grunstein. 2002. Genomewide binding map of the histone deacetylase Rpd3 in yeast. Nat. Genet. 31:248-254.
37. Kwon, J., K. B. Morshead, J. R. Guyon, R. E. Kingston, and M. A. Oettinger. 2000. Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell 6:1037-1048.
38. Lachner, M., D. O'Carroll, S. Rea, K. Mechtler, and T. Jenuwein. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116-120.
39. Lee, D. Y., J. J. Hayes, D. Pruss, and A. P. Wolffe. 1993. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72:73-84.
40. Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 angstrom resolution. Nature 389:251-260.
41. Mai, X., S. Chou, and K. Struhl. 2000. Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements. Mol. Cell. Biol. 20:6668-6676.
42. Marin, I., and B. S. Baker. 2000. Origin and evolution of the regulatory gene male-specific lethal-3. Mol. Biol. Evol. 17:1240-1450.
43. Nakayama, J., G. Xiao, K. Noma, A. Malikzay, P. Bjerling, K. Ekwall, R. Kobayashi, and S. I. Grewal. 2003. Alpl3, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity. EMBO J. 22:2776-2787.
44. Ng, H. H., F. Robert, R. A. Young, and K. Struhl. 2003. Targeted recruitment of Setl histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11:709-719.
45. Nightingale, K. P., R. E. Wellinger, J. M. Sogo, and P. B. Becker. 1998. Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin. EMBO J. 17:2865-2876.
46. Owen, D. J., P. Ornaghi, J. C. Yang, N. Lowe, P. R. Evans, P. Ballario, D. Neuhaus, P. Filetici, and A. A. Travers. 2000. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5. EMBO J. 19:6141-6149.
47. Radcliffe, P., D. Hirata, D. Childs, L. Vardy, and T. Toda. 1998. Identification of novel temperature-sensitive lethal alleles in essential beta-tubulin and nonessential alpha 2-tubulin genes as fission yeast polarity mutants. Mol. Biol. Cell 9:1757-1771.
48. Reid, J. L., V. R. Iyer, P. O. Brown, and K. Struhl. 2000. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esal histone acetylase. Mol. Cell 6:1297-1307.
49. Robyr, D., Y. Suka, I. Xenarios, S. K. Kurdistani, A. Wang, N. Suka, and M. Grunstein. 2002. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109:437-446.
50. Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81-120.
51. Rundlett, S. E., A. A. Carmen, N. Suka, B. M. Turner, and M. Grunstein. 1998. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831-835.
52. Santos-Rosa, H., R. Schneider, A. J. Bannister, J. Sherriff, B. E. Bernstein, N. C. Emre, S. L. Schreiber, J. Mellor, and T. Kouzarides. 2002. Active genes are tri-methylated at K4 of histone H3. Nature 419:407-411.
53. Smith, E. R., A. Eisen, W. Gu, M. Sattah, A. Pannuti, J. Zhou, R. G. Cook, J. C. Lucchesi, and C. D. Allis. 1998. ESA1 is a histone acetyltransferase that is essential for growth in yeast. Proc. Natl. Acad. Sci. USA 95:3561-3565.
54. Steger, D. J., A. Eberharter, S. John, P. A. Grant, and J. L. Workman. 1998. Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc. Natl. Acad. Sci. USA 95: 12924-12929.
55. Struhl, K. 1998. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12:599-606.
56. Suka, N., Y. Suka, A. A. Carmen, J. Wu, and M. Grunstein. 2001. Highly specific antibodies determine histone acetylation in yeast heterochromatin and euchromatin. Mol. Cell 8:473-479.
57. Utley, R. T., K. Ikeda, P. A. Grant, J. Cote, D. J. Steger, A. Eberharter, S. John, and J. L. Workman. 1998. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 394:498-502.
58. Vettese-Dadey, M., P. A. Grant, T. R. Hebbes, C. Crane-Robinson, C. D. Allis, and J. L. Workman. 1996. Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J. 15:2508-2518.
59. Vignali, M., D. J. Steger, K. E. Neely, and J. L. Workman. 2000. Distribution of acetylated histones resulting from Ga14-VP16 recruitment of SAGA and NuA4 complexes. EMBO J. 19:2629-2640.
60. Vogelauer, M., J. Wu, N. Suka, and M. Grunstein. 2000. Global histone acetylation and deacetylation in yeast. Nature 408:495-498.