РЕГУЛЯЦИЯ ТРАНСКРИПЦИИ ГЕНОВ ТЕПЛОВОГО ШОКА У ДРОЖЖЕЙ Saccharomyces cerevisiae

Список литературы

1. Aasland, R., A. F. Stewart and T. Gibson. The SANT domain: a putative DNA-bindingdomain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFII1B. Trends Biochem Sci. 1996. 21(3): 87−88.
2. Agalioti, T., S. Lomvardas, B. Parekh, J. Yie, T. Maniatis and D. Thanos. Orderedrecruitment of chromatin modifying and general transcription’factors to the IFN-beta promoter. Cell. 2000. 103(4): 667−678:
3. Ahmad, K. and S. Henikoff. Histone H3 variants specify modes of chromatin assembly.
4. Proc Natl Acad Sci USA. 2002. 99 Suppl 4: 16 477−16 484.
5. Ahn, S. H., W. L. Cheung, J. Y. Hsu, R. L. Diaz, M. M. Smith and C. D. Allis. Sterile 20kinase phosphorylates histone H2B at serine 10 during hydrogen peroxide-induced apoptosis in S. cerevisiae. Cell. 2005.120(1): 25−36.
6. Aki, T., H. E. Choy and S. Adhya. Histone-like protein HU as a specific transcriptionalregulator: co- factor role in repression of gal transcription by GAL repressor. Genes Cells. 1996. 1(2): 179−188.
7. Alevizopoulos, A., Y. Dusserre, M. Tsai-Pflugfelder, T. von der Weid, W. Wahli and N.
8. Mermod. A proline-rich TGF-beta-responsive transcriptional activator interacts with histone H3. Genes Dev. 1995. 9(24): 3051−3066.
9. Aimer, A., H. Rudolph, A. Hinnen and W. Horz. Removal of positioned nucleosomesfrom the yeast PH05 promoter upon PH05 induction releases additional upstream activating DNA elements. Embo J. 1986. 5(10): 2689−2696.
10. Altmann, H., W. Wendler and E. L. Winnacker. Transcriptional activation by CTFproteins is mediated by a bipartite low-proline domain. Proc Natl Acad Sci USA. 1994. 91(9): 3901−3905.
11. Amin, J., J. Ananthan and R. Voellmy. Key features of heat shock regulatory elements.
12. Mol Cell Biol. 1988. 8(9): 3761−3769.
13. Amoros, M. and F. Estruch. Hsflp and Msn2/4p cooperate in the expression of
14. Saccharomyces cerevisiae genes HSP26 and HSP104 in a gene- and stress type-dependent manner. Mol Microbiol. 2001.39(6): 1523−1532.
15. Apone, L. M., C. A. Virbasius, F. C. Holstege, J. Wang, R. A. Young and M. R. Green.
16. Broad, but not universal, transcriptional requirement for yTAFI117, a histone H3-like TAFII present in TFIID and SAGA. Mol Cell. 1998. 2(5): 653−661.
17. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith and
18. K. Struhl. Current Protocols in Molecular Biology. 1995.
19. Azuara, V., P. Perry, S. Sauer, M. Spivakov, H. F. Jorgensen, R. M. John, M. Gouti, M.
20. Casanova, G. Warnes, M. Merkenschlager and A. G. Fisher. Chromatin signatures of pluripotent cell lines. Nat Cell Biol. 2006. 8(5): 532−538.
21. Badis, G., E. T. Chan, H. van Bakel, L. Pena-Castillo, D. Tillo, K. Tsui, C. D. Carlson,
22. Bakshi, R., T. Prakash, D. Dash and V. Brahmachari. In silico characterization of the1080 subfamily of SWI2/SNF2 chromatin remodeling proteins. Biochem Biophys Res Commun. 2004. 320(1): 197−204.
23. Bali, P., M. Pranpat, J. Bradner, M. Balasis, W. Fiskus, F. Guo, K. Rocha, S.
24. Bannister, A. J., P. Zegerman, J. F. Partridge, E. A. Miska, J. O. Thomas, R'. C. Allshireand T. Kouzarides. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Natuie. 2001.410(6824): 120−124.
25. Baiak, O., M. A. Lazzaro, W. S. Lane, D. W. Speicher, D. J. Picketts and R. Shiekhattar.1.olation of human NURF: a legulator of Engrailed gene expression. EMBO J. 2003. 22(22): 6089−6100.
26. Barbaric, S., J. Walker, A. Schmid, J. Q. Svejstrup and W. Horz. Increasing the rate ofchromatin remodeling and gene activation—a novel role for the histone acetyltransferase Gcn5. Embo J. 2001. 20(17): 4944−4951.
27. Barlev, N. A., R. Candau, L. Wang, P. Darpino, N. Silverman and S. L. Berger.
28. Characterization of physical interactions of the putative transcriptional adaptor, ADA2, with acidic activation domains and TATA- binding protein. J Biol Chem. 1995. 270(33): 19 337−19 344.
29. Baxter, B. K. and E. A. Craig. Suppression of an Hsp70 mutant phenotype in
30. Saccharomyces cerevisiae through loss of function of the chromatin component Sinlp/Spt2p. J Bacteriol. 1998. 180(24): 6484−6492.
31. Bazett-Jones, D. P., J. Cote, C. C. Landel, C. L. Peterson and J. L. Workman. The
32. SWI/SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains. Mol Cell Biol. 1999. 19(2): 14 701 478.
33. Becker, P. B. and W. Horz. ATP-dependent nucleosome remodeling. Annu Rev1. Biochem. 2002.71:247−273.
34. Bernstein, B. E., M. Kamal, K. Lindblad-Toh, S. Bekiranov, D. K. Bailey, D. J. Huebert,
35. S. McMahon, E. K. Karlsson, E. J. Kulbokas, 3rd, T. R. Gingeras, S. L. Schreiber and E. S. Lander. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005.120(2): 169−181.
36. Bhaumik, S. R. and M. R. Green. SAGA is an essential in vivo target of the yeast acidicactivator Gal4p. Genes Dev. 2001. 15(15): 1935−1945.
37. Birck, C., O. Poch, C. Romier, M. Ruff, G. Mengus, A. C. Lavigne, I. Davidson and D.
38. Moras. Human TAF (II)28 and TAF (II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. Cell. 1998. 94(2): 239−249.
39. Blank, T. A. and P. B. Becker. The effect of nucleosome phasing sequences and DNAtopology on nucleosome spacing. J Mol Biol. 1996. 260(1): 1−8.
40. Boeger, PI., J. Griesenbeck, J. S. Strattan and R. D. Kornberg. Removal of promoternucleosomes by disassembly rather than sliding in vivo. Mol Cell. 2004. 14(5): 667 673.
41. Borkovich, K. A., F. W. Farrelly, D. B. Finkelstein, J. Taulien and S. Lindquist. hsp82 isan essential protein that is required in higher concentrations for growth of cells at higher temperatures. Mol Cell Biol. 1989. 9(9): 3919−3930.
42. Boy-Marcotte, E., G. Lagniel, M. Perrot, F. Bussereau, A. Boudsocq, M. Jacquet and J.1.barre. The heat shock response in yeast: differential regulations and contributions of the Msn2p/Msn4p and Hsfl p regulons. Mol Microbiol. 1999. 33(2): 274−283.
43. Boyer, L. A., X. Shao, R. H. Ebright and C. L. Peterson. Roles of the histone H2A-H2Bdimers and the (H3-H4)(2) tetramer in nucleosome remodeling by the SWI-SNF complex. J Biol Chem. 2000. 275(16): 11 545−11 552.
44. Brown, C. E., L. Howe, K. Sousa, S. C. Alley, M. J. Carrozza, S. Tan and J. L.
45. J Workman. Recruitment of HAT complexes by direct activator interactions with the
46. ATM-related Tral subunit. Science. 2001. 292(5525): 2333−2337.
47. Brown, C. E., T. Lechner, L. Howe and J. L. Workman. The many HATs of transcriptioncoactivators. Trends Biochetn Sci. 2000. 25(1): 15−19.) 38. Brown, D. T. Histone HI and the dynamic regulation of chromatin function. Biochem
48. Cell Biol. 2003. 81(3): 221−227.
49. Brzeski, J. and A. Jerzmanowski. Deficient in DNA methylation 1 (DDM1) defines anovel family of chromatin-remodeling factors. J Biol Chem. 2003. 278(2): 823−828.
50. Buschmann, T" S. Y. Fuchs, C. G. Lee, Z. Q. Pan and Z. Ronai. SUMO-1 modificationof Mdm2 prevents its self-ubiquitination and increases Mdm2 ability to ubiquitinate p53. Cell. 2000. 101(7): 753−762.
51. Tempst, J. Du, B. Laurent and R. D. Kornberg. RSC, an essential, abundant chromatinremodeling complex. Cell. 1996. 87(7): 1249−1260.
52. Calderwood, S. K., M. A. Khaleque, D. B. Sawyer and D. R. Ciocca. Heat shock proteinsin cancer: chaperones of tumorigenesis. Trends Biochem Sci. 2006. 31(3): 164−172.
53. Carrozza, M. J., B. Li, L. Florens, T. Suganuma, S. K. Swanson, K. K. Lee, W. J. Shia, S.
54. Anderson, J. Yates, M. P. Washburn and J. L. Workman. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell. 2005. 123(4): 581−592.
55. Chen, J. and D. S. Pederson. A distal heat shock element promotes the rapid response toheat shock of the HSP26 gene in the yeast Saccharomyces cerevisiae. J Biol Chem. 1993. 268(10): 7442−7448.
56. Chen, Z., J. Zang, J. Whetstine, X. Hong, F. Davrazou, T. G. Kutateladze, M. Simpson,
57. Q. Mao, C. H. Pan, S. Dai, J. Hagman, K. Hansen, Y. Shi and G. Zhang. Structural insights into histone demethylation by JMJD2 family members. Cell. 2006.125(4): 691−702.
58. Cho, H., G. Orphanides, X. Sun, X. J. Yang, V. Ogryzko, E. Lees, Y. Nakatani and D.
59. Reinberg. A human RNA polymerase II complex containing factors that modify chromatin structure. Mol Cell Biol. 1998.18(9): 5355−5363.
60. Cho, H. S., C. W. Liu, F. F. Damberger, J. G. Pelton, H. C. Nelson and D. E. Wemmer. i Yeast heat shock transcription factor N-terminal activation domains are unstructured asf probed by heteronuclear NMR spectroscopy. Protein Sci. 1996. 5(2): 262−269.
61. Chou, S., S. Chatterjee, M. Lee and K. Struhl. Transcriptional activation in yeast cellslacking transcription factor 11 A. Genetics. 1999.153(4): 1573−1581.
62. Cirillo, L. A., F. R. Lin, I. Cuesta, D. Friedman, M. Jarnik and K. S. Zaret. Opening ofcompacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol Cell. 2002. 9(2): 279−289.i. t X
63. Clapier, C. R., G. Langst, D. F. Corona, P. B. Becker and K. P. Nightingale. Critical rolefor the histone H4 N terminus in nucleosome leinodeling by ISWI. Mol Cell Biol. 2001.21(3): 875−883.
64. Clark-Adams, C. D., D. Norris, M. A. Osley, J. S. Fassler and F. Winston. Changes inhistone gene dosage alter transcription in yeast. Genes Dev. 1988. 2(2): 150−159.
65. Corona, D. F., A. Eberharter, A. Budde, R. Deuring, S. Ferrari, P. Varga-Weisz, M.
66. Wilm, J. Tamkun and P. B. Becker. Two histone fold proteins, CHRAC-14 and CHRAC-16, are developmentally regulated subunits of chromatin accessibility complex (CHRAC). Embo J. 2000. 19(12): 3049−3059.
67. Cosma, M. P., T. Tanaka and K. Nasmyth. Ordered recruitment of transcription andchromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell. 1999. 97(3): 299−311.
68. Cote, J., J. Quinn, J. L. Workman and C. L. Peterson. Stimulation of GAL4 derivativebinding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994. 265(5168): 53−60.
69. Cuthbert, G. L., S. Daujat, A. W. Snowden, H. Erdjument-Bromage, T. Hagiwara, M.
70. Yamada, R. Schneider, P. D. Gregory, P. Tempst, A. J. Bannister and T. Kouzarides. Histone deimination antagonizes arginine methylation. Cell. 2004.118(5): 545−553.
71. Dai, C., L. Whitesell, A. B. Rogers and S. Lindquist. Heat shock factor 1 is a powerfulmultifaceted modifier of carcinogenesis. Cell. 2007. 130(6): 1005−1018.
72. Damelin, M., I. Simon, T. I. Moy, B. Wilson, S. Komili, P. Tempst, F. P. Roth, R. A.
73. Young, B. R. Cairns and P. A. Silver. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell. 2002. 9(3): 563−573.
74. Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder and T. J. Richmond. Solventmediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J Mol Biol. 2002. 319(5): 1097−1113.
75. Deckert, J. and K. Struhl. Histone acetylation at promoters is differentially affected byspecific activators and repressors. Mol Cell Biol. 2001. 21(8): 2726−2735.
76. Delmas, V., D. G. Stokes and R. P. Perry. A mammalian DNA-binding protein thatcontains a chromodomain and an SNF2/SWI2-like helicase domain. Proc Natl Acad Sci USA. 1993. 90(6): 2414−2418.
77. Dennis, K., T. Fan, T. Geiman, Q. Yan and K. Muegge. Lsh, a member of the SNF2family, is required for genome-wide methylation. Genes Dev. 2001. 15(22): 29 402 944.
78. Dhalluin, C., J. E. Carlson, L. Zeng, C. He, A. K. Aggarwal and M. M. Zhou. Structureand ligand of a histone acetyltransferase bromodomain. Nature. 1999. 399(6735): 491 496.
79. Di Mauro, E., S. G. Kendrew and M. Caserta. Two distinct nucleosome alterationscharacterize chromatin iemodeling at the Saccharomyces cerevisiae ADH2 promoter. J Biol Chem. 2000. 275(11): 7612−7618.
80. Drysdale, C. M., E. Duenas, B. M. Jackson, U. Reusser, G. H. Braus and A. G.
81. Hinnebusch. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol Cell Biol. 1995.15(3): 1220−1233.
82. Edmondson, D. G., M. M. Smith and S. Y. Roth. Repression domain of the yeast globalrepressor Tupl interacts directly with histones H3 and H4. Genes Dev. 1996. 10(10): 1247−1259.
83. Emre, N. C" K. Ingvarsdottir, A. Wyce, A. Wood, N. J. Krogan, K. W. Henry, K. Li, R.
84. Marmorstein, J. F. Greenblatt, A. Shilatifard and S. L. Berger. Maintenance of low histone ubiquitylation by Ubp 10 correlates with telomere-proximal Sir2 association and gene silencing. Mol Cell. 2005. 17(4): 585−594.
85. Erkina, T. Y. and A. M. Erkine. Displacement of histones at promoters of Saccharomycescerevisiae heat shock genes is differentially associated with histone H3 acetylation. Mol Cell Biol. 2006.26(20): 7587−7600.
86. Erkina, T. Y., P. A. Tschetter and A. M. Erkine. Different requirements of the SWI/SNFcomplex for robust nucleosome displacement at promoters of heat shock factor and Msn2- and Msn4-regulated heat shock genes. Mol Cell Biol. 2008.28(4): 1207−1217.
87. Erkina, T. Y., Y. Zou, S. Freeling, V. I. Vorobyev and A. M. Erkine. Functional interplaybetween chromatin remodeling complexes RSC, SWI/SNF and ISWI in regulation of yeast heat shock genes. Nucleic Acids Res. 2010.38(5): 1441−1449.
88. Erkine, A. M., C. C. Adams, M. Gao and D. S. Gross. Multiple protein-DNA interactionsover the yeast HSC82 heat shock gene promoter. Nucleic Acids Res. 1995. 23(10): 1822−1829.
89. Erkine, A. M. and D. S. Gross. Dynamic chromatin alterations triggered by natural andsynthetic activation domains. J Biol Chem. 2003. 278(10): 7755−7764.
90. Erkine, A. M., S. F. Magrogan, E. A. Sekinger and D. S. Gross. Cooperative binding ofheat shock factor to the yeast HSP82 promoter in vivo and in vitio. Mol Cell Biol.1999. 19(3): 1627−1639.
91. Erkine, A. M., C. Szent-Gyorgyi, S. F. Simmons and D. S. Gross. The upstreamsequences of the HSP82 and HSC82 genes of Saccharomyces cerevisiae: regulatory elements and nucleosome positioning motifs. Yeast. 1995. 11(6): 573−580.
92. Escher, D., M. Bodmer-Glavas, A. Barberis and W. Schaffner. Conservation ofglutamine-rich transactivation function between yeast and humans. Mol Cell Biol.2000. 20(8): 2774−2782.
93. Estruch, F. Stress-controlled transcription factors, stress-induced genes and stresstolerance in budding yeast. FEMS Microbiol Rev. 2000. 24(4): 469−486.
94. Fan, H. Y., K. W. Trotter, T. K. Archer and R. E. Kingston. Swapping function of twochromatin remodeling complexes. Mol Cell. 2005. 17(6): 805−815.
95. Feng, Q. and Y. Zhang. The NuRD complex: linking histone modification to nucleosomeremodeling. Curr Top Microbiol Immunol. 2003. 274: 269−290.
96. Ferguson, S. B., E. S. Anderson, R. B. Harshaw, T. Thate, N. L. Craig and H. C. Nelson.
97. Protein kinase A regulates constitutive expression of small heat-shock genes in an Msn2/4p-independent and Hsflp-dependent manner in Saccharomyces cerevisiae. Genetics. 2005. 169(3): 1203−1214.
98. Fischle, W., B. S. Tseng, H. L. Dormann, B. M. Ueberheide, B. A. Garcia, J.
99. Shabanowitz, D. F. Hunt, H. Funabiki and C. D. Allis. Regulation of HP 1-chromatin binding by histone H3 methylation and phosphorylation. Nature. 2005. 438(7071): 1116−1122.
100. Gangaraju, V. K. and B. Bartholomew. Dependency of ISWI a chromatin remodeling onextranucleosomal DNA. Mol Cell Biol. 2007. 27(8): 3217−3225.
101. Gardner, R. G., Z. W. Nelson and D. E. Gottschling. Ubpl0/Dot4p regulates thepersistence of ubiquitinated histone H2B: distinct roles in telomeric silencing and general chromatin. Mol Cell Biol. 2005. 25(14): 6123−6139.
102. Garreau, H., R. N. Hasan, G. Renault, F. Estruch, E. Boy-Marcotte and M. Jacquet.
103. Hyperphosphorylation of Msn2p and Msn4p in response to heat shock and the diauxic shift is inhibited by cAMP in Saccharomyces cerevisiae. Microbiology. 2000.146 (Pt 9): 2113−2120.
104. Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D.
105. Botstein and P. O. Brown. Genomic expression-programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000. 11(12): 4241−4257.
106. Gasser, S. M. and M. M. Cockell. The molecular biology of the SIR proteins. Gene.2001.279(1): 1−16-
107. Gaudreau, L., A. Schmid, D. Blaschke, M. Ptashne and W. Horz. RNA polymerase IIholoenzyme recruitment is sufficient to remodel chromatin at the yeast PH05 promoter. Cell. 1997. 89(1): 55−62.
108. Gerber, H. P., K. Seipel, O. Georgiev, M. Hofferer, M. Hug, S. Rusconi and W.
109. Schaffner. Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science. 1994. 263(5148): 808−811.
110. Giardina, C. and J. T. Lis. Dynamic protein-DNA architecture of a yeast heat shockpromoter. Mol Cell Biol. 1995.15(5): 2737−2744.
111. Gorner, W., E. Durchschlag, M. T. Martinez-Pastor, F. Estruch, G. Ammerer, B.
112. Hamilton, H. Ruis and C. Schuller. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein, kinase A activity. Genes Dev. 1998: 12(4): 586−597.
113. Green, G. R., P. Collas, A. Burrell and D. L. Poccia. Histone phosphorylation during seaurchin development. Semin Cell Biol. 1995. 6(4): 219−227.
114. Gross, D. S., C. C. Adams, S. Lee and B. Stentz. A critical role for heat shocktranscription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene. EMBO J. 1993. 12(10): 3931−3945.
115. Gross, D. S., K. E. English, K. W. Collins and S. W. Lee. Genomic footprinting of theyeast HSP82 promoter reveals marked distortion of the DNA helix and constitutive occupancy of heat shock and TATA elements. J Mol Biol. 1990.216(3): 611−631.
116. Grune, T., J. Brzeski, A. Eberharter, C. R. Clapier, D. F. Corona, P. B. Becker and C. W.
117. Muller. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol Cell. 2003.12(2): 449−460.
118. Grunstein, M. Histone acetylation in chromatin structure and transcription. Nature. 1997.389(6649): 349−352.
119. Gutierrez, J. L., M. Chandy, M. J. Carrozza and J. L. Workman- Activation domainsdrive nucleosome eviction by SWI/SNF. Embo J. 2007.26(3): 730−740.
120. Ha, N., K. Hellauer and B. Turcotte. Fusions with histone H3 result in highly specificalteration of gene expression. Nucleic Acids Res. 2000. 28(4): 1026−1035.
121. Hahn, J. S., Z. Hu, D. J. Thiele and V. R. Iyer. Genome-wide analysis of the biology ofstress responses through heat shock transcription factor. Mol Cell Biol. 2004. 24(12): 5249−5256.
122. Hannum, G., R. Srivas, A. Guenole, H. van Attikum, N. J. Krogan, R. M. Karp and T. Ideker. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009. 5(12): el000782.
123. Hashikawa, N. and H. Sakurai. Phosphorylation of the yeast heat shock transcriptionfactor is implicated in gene-specific activation dependent on the architecture of the heat shock element. Mol Cell Biol. 2004. 24(9): 3648−3659.
124. Hassa, P. O., S. S. Haenni, M. Elscr and M. O. Hottiger. Nuclear ADP-ribosylationleactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev. 2006. 70(3): 789−829.
125. Hassan, A. H., K. E. Neely, M. Vignali, J. C. Reese and J. L. Workman. Promotertargeting of chromatin-modifying complexes. Front Biosci. 2001. 6: D1054−1064.
126. Hassan, A. H., K. E. Neely and J. L. Workman. Histone Acetyltransferase Complexes
127. Stabilize SWI/SNF Binding to Promoter Nucleosomes. Cell. 2001.104(6): 817−827.
128. Hassan, A. H., P. Prochasson, K. E. Neely, S. C. Galasinski, M. Chandy, M. J. Carrozzaand J. L. Workman. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell. 2002.111(3): 369−379.
129. Havas, K., A. Flaus, M. Phelan, R. Kingston, P. A. Wade, D. M. Lilley and T. Owen
130. Hughes. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell. 2000.103(7): 1133−1142.
131. Haynes, S. R., C. Dollard, F. Winston, S. Beck, J. Trowsdale and I. B. Dawid. Thebromodomain: a conserved sequence found in human, Drosophila and yeast proteins. Nucleic Acids Res. 1992. 20(10): 2603.
132. He, X., H. Y. Fan, G. J. Narlikar and R. E. Kingston. Human ACF1 alters the remodelingstrategy of SNF2h. J Biol Chem. 2006. 281(39): 28 636−28 647.
133. Hecht, A., S. Strahl-Bolsinger and M. Grunstein. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature. 1996. 383(6595): 92−96.
134. Henriksson, A., T. Almlof, J. Ford, I. J. McEwan, J. A. Gustafsson and A. P. Wiight.
135. Role of the Ada adaptor complex in gene activation by the glucocorticoid receptor. Mol Cell Biol. 1997.17(6): 3065−3073.
136. Hoeck, W. and B. Groner. Hormone-dependent phosphorylation of the glucocorticoidreceptor occurs mainly in the amino-terminal transactivation domain. J Biol Chem. 1990. 265(10): 5403−5408.
137. Hoj, A. and B. K. Jakobsen. A short element required for turning off heat shock transcription factor: evidence that phosphorylation enhances deactivation. Ernbo J. 1994.13(11): 2617−2624.
138. Jacquet, M., G. Renault, S. Lallet, J. De Mey and A. Goldbeter. Oscillatory nucleocytoplasmic shuttling of the general stress lesponse transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae. J Cell Biol. 2003.161(3): 497−505.
139. Jakobsen, B. K. and H. R. Pelham. Constitutive binding of yeast heat shock factor to
140. DNA in vivo. Mol Cell Biol. 1988. 8(11): 5040−5042.
141. James, P., J. Halladay and E. A. Craig. Genomic libraries and a host strain designed forhighly efficient two- hybrid selection in yeast. Genetics. 1996. 144(4): 1425−1436.
142. Jenuwein, T. The epigenetic magic of histone lysine methylation. FEBS J. 2006. 273(14): 3121−3135.
143. Jenuwein, T. and C. D. Allis. Translating the histone code. Science. 2001. 293(5532):1074−1080.
144. Jin, J., Y. Cai, T. Yao, A. J. Gottschalk, L. Florens, S. K. Swanson, J. L. Gutierrez, M. K.
145. Coleman, J. L. Workman, A. Mushegian, M. P. Washburn, R. C. Conaway and J. W. Conaway. A mammalian chromatin remodeling complex with similarities to the yeast IN080 complex. J Biol Chem. 2005. 280(50): 41 207−41 212.
146. Joshi, A. A. and K. Struhl. Eaf3 chromodomain interaction with methylated H3-K36links histone deacetylation to Pol II elongation. Mol Cell. 2005. 20(6): 971−978.
147. Ju, B. G., V. V. Lunyak, V. Perissi, I. Garcia-Bassets, D. W. Rose, C. K. Glass and M. G.
148. Rosenfeld. A topoisomerase Ilbeta-mediated dsDNA break required for regulated transcription. Science. 2006.312(5781): 1798−1802.
149. Kadonaga, J. T. Eukaryotic transcription: an interlaced network of transcription factorsand chromatin-modifying machines. Cell. 1998. 92(3): 307−313.
150. Kadosh, D. and K. Struhl. Repression by Ume6 involves recruitment of a complexcontaining Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell. 1997. 89(3): 365−371.
151. Kamakaka, R. T. and S. Biggins. Histone variants: deviants? Genes Dev. 2005.19(3): 295−310.
152. Kassabov, S. R., B. Zhang, J. Persinger and B. Bartholomew. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol Cell. 2003.11(2): 391−403.
153. Katan-Khaykovich, Y. and K. Struhl. Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal’histone acetylation status upon removal of activators and repressors. Genes Dev. 2002. 16(6): 743−752.
154. Kaufmann, J., C. P. Verrijzer, J. Shao and S. T. Smale. CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 1996.10(7): 873−886.
155. Keener, J., J. A. Dodd, D. Lalo and M. Nomura. Histones H3 and H4 are components ofupstream activation factor required for the high-level transcription of yeast rDNA by RNA polymerase I. ProcNatl Acad Sci USA. 1997. 94(25): 13 458−13 462.
156. Kelbauskas, L., J. Yodh, N. Woodbury and D. Lohr. Intrinsic promoter nucleosomestability/dynamics variations support a novel targeting mechanism. Biochemistry. 2009. 48(20): 4217−4219.
157. Keogh, M. C., S. K. Kurdistani, S. A. Morris, S. H. Ahn, V. Podolny, S. R. Collins, M.
158. Kim, Y., N. McLaughlin, K. Lindstrom, T. Tsukiyama and D. J. Clark. Activation of
159. Saccharomyces cerevisiae HIS3 results in Gcn4p-dependent, SWI/SNF-dependent mobilization of nucleosomes over the entire gene. Mol Cell Biol. 2006. 26(22): 86 078 622.
160. Kingston, R. E. and G. J. Narlikar. ATP-dependent remodeling and acetylation asregulators of chromatin fluidity. Genes Dev. 1999.13(18): 2339−2352.
161. Klemm, R. D., J. A. Goodrich, S. Zhou and R. Tjian. Molecular cloning and expression of the 32-kDa subunit of human TFIID reveals interactions with VP16 and TFIIB that mediate transcriptional activation. Proc Natl Acad Sci USA. 1995. 92(13): 57 885 792.
162. Koh, S. S., A. Z. Ansari, M. Ptashne and R. A. Young. An activator target in the RNA polymerase II holoenzyme. Mol Cell. 1998. 1(6): 895−904.
163. Korber, P., T. Luckenbach, D. Blaschke and W. Horz. Evidence for histone eviction in trans upon induction of the yeast PH05 promoter. Mol Cell Biol. 2004. 24(24): 1 096 510 974.
164. Kornberg, R. D. and J. O. Thomas. Chromatin structure- oligomers of the histones. Science. 1974.184(139): 865−868.
165. Korolev, S., J. Hsieh, G. H. Gauss, T. M. Lohman and G. Waksman. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell. 1997. 90(4): 635−647.
166. Kouzarides, T. Chromatin modifications and their function. Cell. 2007.128(4): 693−705.
167. Krebs, J. E., C. J. Fry, M. L. Samuels and C. L. Peterson. Global role for chromatinremodeling enzymes in mitotic gene expression. Cell. 2000.102(5): 587−598.
168. Krishnamoorthy, T" X. Chen, J. Govin, W. L. Cheung, J. Dorsey, K. Schindler, E.
169. Winter, C. D. Allis, V. Guacci, S. Khochbin, M. T. Fuller and S. L. Berger. Phosphorylation of histone H4 Serl regulates sporulation in yeast and is conserved in fly and mouse spermatogenesis. Genes Dev. 2006. 20(18): 2580−2592.
170. Kristjuhan, A. and J. Q. Svejstrup. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. Embo J. 2004.23(21): 4243−4252.
171. Kundu, S., P. J. I lorn and C. L. Peterson. SWI/SNF is required for transcriptionalmemoiy at the yeast GAL gene cluster. Genes Dev. 2007. 21(8): 997−1004.
172. Kwon, H., A. N. Imbalzano, P. A. Khavari, R. E. Kingston and M. R. Green. Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex see comments. Nature. 1994. 370(6489): 477−481.
173. Lallet, S., H. Garreau, C. Poisier, E. Boy-Marcotte and M. Jacquet. Heat shock-induced degradation of Msn2p, a Saccharomyces cerevisiae transcription factor, occurs in the nucleus. Mol Genet Genomics. 2004. 272(3): 353−362.
174. Larschan, E. and F. Winston. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev. 2001.15(15): 19 461 956.
175. Lee, C. K., Y. Shibata, B. Rao, B. D. Strahl and J. D. Lieb. Evidence for nucleosomedepletion at active regulatory regions genome-wide. Nat Genet. 2004. 36(8): 900−905.
176. Lee, D. and J. T. Lis. Transcriptional activation independent ofTFIIH kinase and the
177. RNA polymerase II mediator in vivo. Nature. 1998. 393(6683): 389−392.
178. Lee, D. K., S. Kim and J. T. Lis. Different upstream transcriptional activators havedistinct coactivator requirements. Genes Dev. 1999.13(22): 2934−2939.
179. Lee, D. Y., C. Teyssier, B. D. Strahl and M. R. Stallcup. Role of protein methylation inregulation of transcription. Endocr Rev. 2005.26(2): 147−170.
180. Lee, K. K., P. Prochasson, L. Florens, S. K. Swanson, M. P. Washburn and J. L.
181. Workman. Proteomic analysis of chromatin-modifying complexes in Saccharomyces cerevisiae identifies novel subunits. Biochem Soc Trans. 2004.32(Pt 6): 899−903.
182. Lee, S. and D. S. Gross. Conditional silencing: the HMRE mating-type silencer exerts arapidly reversible position effect on the yeast HSP82 heat shock gene. Mol Cell Biol. 1993.13(2): 727−738.
183. Lenfant, F., R. K. Mann, B. Thomsen, X. Ling and M. Grunstein. All four core histone N-termini contain sequences required for the repression of basal transcription in yeast. EmboJ. 1996. 15(15): 3974−3985.
184. Li, G., M. Levitus, C. Bustamante and J. Widom. Rapid spontaneous accessibility ofnucleosomal DNA. Nat Struct Mol Biol. 2005. 12(1): 46−53.
185. Lia, G., E. Praly, H. Ferreira, C. Stockdale, Y. C. Tse-Dinh, D. Dunlap, V. Croquette, D. Bensimon and T. Owen-Hughes. Direct observation of DNA distortion by the RSC complex. Mol Cell. 2006. 21(3): 417−425.
186. Liaw, P. C. and C. J. Brandl. Defining the sequence specificity of the Saccharomyces cerevisiae DNA binding protein REBlp by selecting binding sites from random-sequence oligonucleotides. Yeast. 1994. 10(6): 771−787.
187. Lindquist, S. and E. A. Craig. The heat-shock proteins. Annu Rev Genet. 1988. 22: 631 677.
188. Lindstrom, K. C., J. C. Vary, Jr., M. R. Parthun, J. Deliovv and T. Tsukiyama. Iswlfunctions. in parallel with the NuA4 and Swrl complexes in stress-induced gene repression. Mol Cell Biol. 2006:26(16): 6117−6129.
189. Liu, C. L., T. Kaplan, M. Kim, S. Buratowski, S. L. Schreiber, N. Friedman and O. J.
190. Rando: Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 2005. 3(10): e328.
191. Liu, X. D. and D. J. Thiele. Oxidative stress induced heat shock factor phosphorylationand HSF- dependent activation of yeast metallothionein gene transcription. Genes Dev. 1996. 10(5): 592−603.
192. Logie, C. and C. L. Peterson. Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays. Embo J. 1997. 16(22): 6772−6782.
193. Lorch, Y., B. Maier-Davis and R. D. Kornberg. Chromatin remodeling by nucleosomedisassembly in vitro. Proc Natl Acad Sci USA. 2006. 103(9): 3090−3093.
194. Lorch, Y., M. Zhang and R. D. Kornberg. Histone octamer transfer by a chromatinremodeling complex. Cell. 1999. 96(3): 389−392.
195. Lu, X., A. Z. Ansari and M. Ptashne. An artificial transcriptional activating region withunusual properties. Proc Natl Acad Sci USA. 2000. 97(5): 1988−1992.
196. Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent and T. J. Richmond. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997. 389(6648): 251−260.
197. Lusser, A., D. L. Unvin and J. T. Kadonaga. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat Struct Mol Biol. 2005.12(2): 160−166.
198. Ma, J. and M. Ptashne. A new class of yeast transcriptional activators. Cell. 1987. 51(1):113.119.
199. Macdonald, N., J. P. Welburn, M. E. Noble, A. Nguyen, M. B. Yaffe, D. Clynes, J. G.
200. Moggs, G. Orphanides, S. Thomson, J. W. Edmunds, A. L. Clayton, J. A. Endicott and L. C. Mahadevan. Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14−3-3. Mol Cell. 2005. 20(2): 199−211.
201. Margueron, R., P. Trojer and D. Reinberg. The key to development: interpreting thehistone code? Curr Opin Genet Dev. 2005. 15(2): 163−176.
202. Martens, J. A. and F. Winston. Recent advances in understanding chromatin remodelingby Swi/Snf complexes. Curr Opin Genet Dev. 2003.13(2): 136−142.
203. Martens, J. A., P. Y. Wu and F. Winston. Regulation of an intergenic transcript controlsadjacent gene transcription in Saccharomyces cerevisiae. Genes Dev. 2005.19(22): 2695−2704.
204. Martinez-Pastor, M. T., G. Marchler, C. Schuller, A. Marchler-Bauer, H. Ruis and F.
205. Estruch. The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). Embo J. 1996.15(9): 2227−2235.
206. McNeil, J. B., H. Agah and D. Bentley. Activated transcription independent of the RNApolymerase II holoenzyme in budding yeast. Genes Dev. 1998.12(16): 2510−2521.
207. MeIlor, J. and A. Morillon. ISWI complexes in Saccharomyces cerevisiae. Biochim BiophysActa. 2004.1677(1−3): 100−112.
208. Metivier, R., G. Penot, M. R. Hubner, G. Reid, H. Brand, M. Kos and F. Gannon. Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell. 2003. 115(6): 751−763.
209. Metzger, E., M. Wissmann, N. Yin, J. M. Muller, R. Schneider, A. H. Peters, T. Gunther, R. Buettner and R. Schule. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature. 2005. 437(7057): 436−439.
210. Mizuguchi, G., X. Shen, J. Landry, W. H. Wu, S. Sen and C. Wu. ATP-driven exchangeof histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 2004. 303(5656): 343−348.
211. Mohrmann, L. and C. P. Verrijzer. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim Biophys Acta. 2005. 1681(2−3): 59−73.
212. Moqtaderi, Z., M. Keaveney and K. Struhl. The histone H3-like TAF is broadly requiredfor transcription in yeast. Mol Cell. 1998. 2(5): 675−682.
213. Morano, K. A., N. Santoro, K. A. Koch and D. J. Thiele. A trans-activation domain in yeast heat-shock transcription factor is essential for cell cycle progression during stress. Mol Cell Biol. 1999.19(1): 402−411.
214. Morillon, A., N. Karabetsou, J. O’Sullivan, N. Kent, N. Proudfoot and J. Mellor. Iswl chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell. 2003. 115(4): 425−435.
215. Morillon, A., J. O’Sullivan, A. Azad, N. Proudfoot and J. Mellor. Regulation of elongating RNA polymerase II by forkhead transcription factors in yeast. Science. 2003. 300(5618): 492−495.
216. Morimoto, R. I. Regulation of the heat shock transcriptional response: cross talk betweena family of heat shock factors, molecular chaperones, and negative regulators. Genes Dev. 1998. 12(24): 3788−3796.
217. Moskvina, E., C. Schuller, C. T. Maurer, W. H. Mager and H. Ruis. A search in the genome of Saccharomyces cerevisiae for genes regulated via stress response elements. Yeast. 1998. 14(11): 1041−1050.
218. Muller, J. M., B. Krauss, C. Kaltschmidt, P. A. Baeuerle and R. A. Rupee. Hypoxiainduces c-fos transcription via a mitogen-activated protein kinase-dependent pathway. J Biol Chem. 1997. 272(37): 23 435−23 439.
219. Naar, A. M., B. D. Lemon and R. Tjian. Transcriptional coactivator complexes. Annu RevBiochem. 2001.70:475−501.
220. Nakamura, T. and S. A. Lipton. Cell death: protein misfolding and neurodegenerative diseases. Apoptosis. 2009. 14(4): 455−468.
221. Natarajan, K., B. M. Jackson, H. Zhou, F. Winston and A. G. Hinnebusch. Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator. Mol Cell. 1999.4(4): 657−664.
222. Neef, D. W., M. L. Turski and D. J. Thiele. Modulation of heat shock transcription factor 1 as a therapeutic target for small molecule intervention in neurodegenerative disease. PLoS Biol. 2010. 8(1): el000291.
223. Neely, K. E., A. H. Hassan, C. E. Brown, L. Howe and J. L. Workman. Transcription activator interactions with multiple SWI/SNF subunits. Mol Cell Biol. 2002. 22(6): 1615−1625.
224. Nelson, C. J., H. Santos-Rosa and T. Kouzarides. Pioline isomerization of histone H3 regulates lysine methylation and gene expression. Cell. 2006.126(5): 905−916.
225. Nieto-SoteIo, J., G. Wiederrecht, A. Okuda and C. S. Parker. The yeast heat shock transcription factor contains a transcriptional activation’domain whose activity is repiessed under nonshock conditions. Cell. 1990. 62(4): 807−817.
226. Nowak, S. J. and V. G. Corces. Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation. Trends Genet. 2004. 20(4): 214−220.
227. Nyanguile, O., M. Uesugi, D. J. Austin and G. L. Verdine. A nonnatural transcriptional coactivator. Proc Natl Acad Sci USA. 1997. 94(25): 13 402−13 406.
228. Ogryzko, V. V., T. Kotani, X. Zhang, R. L. Schlitz, T. Howard, X. J. Yang, B. H.
229. Howard, J. Qin and Y. Nakatani. Histone-like TAFs within the PCAF histone acetylase complex. Cell. 1998. 94(1): 35−44.
230. Owen-Hughes, T. and J. L. Workman. Remodeling the chromatin structure of anucleosome array by transcription factor-targeted trans-displacement of histones. Embo J. 1996.15(17): 4702−4712.
231. Papamichos-Chronakis, M., J. E. Krebs and C. L. Peterson. Interplay between lno80 and Swrl chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. Genes Dev. 2006. 20(17): 2437−2449.
232. Parnell, T. J., J. T. Huff and B. R. Cairns. RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes. EMBO J. 2008. 27(1): 100−110.
233. Parthun, M. R. and J. A. Jaehning. A tianscriptionally active form of GAL4 isphosphorylated and associated with GAL80. Mol Cell Biol. 1992. 12(11): 4981−4987.
234. Pavri, R., B. Zhu, G. Li, P. Trojer, S. Mandal, A. Shilatifard and D. Reinberg. Histone
235. H2B monoubiquitination functions cooperatively with FACT to iegulate elongation by RNA polymerase II. Cell. 2006. 125(4): 703−717. 206 Peterson, C. L. and M. A. Laniel. Histones and histone modifications. Curr Biol. 2004. 14(14): R546−551.
236. Poot, R. A., G. Dellaire, B. B. Hulsmann, M. A. Grimaldi, D. F. Corona, P. B. Becker,
237. W. A. Bickmore and P. D. Varga-Weisz. HuCHRAC, a human ISWI chromatin remodelling complex contains hACFl and two novel histone-fold proteins. Embo J. 2000.19(13): 3377−3387.
238. Piochasson, P., K. E. Neely, A. H. Hassan, B. Li and J. L. Workman. Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains. Mol Cell. 2003.12(4): 983−990.
239. Regier, J. L., F. Shen and S. J. Triezenberg. Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP І б transcriptional activator. Proc Natl Acad Sci USA. 1993. 90(3): 883−887.
240. Reid, J. L., V. R. Iyer, P. O. Brown and K. Struhl. Coordinate Regulation of Yeast
241. Ribosomal Protein Genes Is Associated with Targeted Recruitment of Esal Histone Acetylase. Мої Cell. 2000. 6(6): 1297−1307.
242. Reinke, PI., P. D. Gregory and W. Horz. A transient histone hyperacetilation-signal marks nucleosonies for remodeling at the PH08 promoter in vivo. Мої. Cell. 2001. 7: 529 538.
243. Reinke, H. and W. Horz. Histones are first hyperacetylated and then lose contact with the activated PH05 promoter. Мої Cell. 2003.11(6): 1599−1607.
244. Ruden, D. M., J. Ma, Y. Li, K. Wood and M. Ptashne. Generating yeast transcriptional activators containing no yeast protein sequences. Nature. 1991. 350(6315): 250−252.
245. Rutherford, S. L. and S. Lindquist. Hsp90 as a capacitor for morphological evolution.
246. Saha, A., J. Wittmeyer and B. R. Cairns. Chromatin remodelling: the industrialrevolution of DNA around histones. Nat Rev Мої Cell Biol. 2006. 7(6): 437−447.
247. Saha, S., A. Z. Ansari, K. A. Jarrell, M. Ptashne and K. A. Jarell. RNA sequences thatwork as transcriptional activating regions. Nucleic Acids Res. 2003. 31(5): 1565−1570.
248. Sauer, F., J. D. Fondell, Y. Ohkuma, R. G. Roeder and H*. Jackie. Control of transcriptionby Kruppel through interactions with TFIIB and TFIIE beta see comments. Nature. 1995.375(6527): 162−164.
249. Schwanbeck, R., H. Xiao and C. Wu. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J Biol Chem. 2004. 279(38): 39 933−39 941.
250. Segal, E., Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I. K. Moore, J. P.
251. Wang and J. Widom. A genomic code for nucleosome positioning. Nature. 2006. 442(7104): 772−778.
252. Sekinger, E. A. and D. S. Gross. Silenced chromatin is permissive to activator bindingand PIC recruitment. Cell. 2001.105: 403−414.
253. Sengupta, S. M., M. VanKanegan, J. Persinger, C. Logie, B. R. Cairns, C. L. Petersonand B. Bartholomew. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J Biol Chem. 2001. 276(16): 12 636−12 644.
254. Shahbazian, M. D. and M. Grunstein. Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem. 2007. 76: 75−100.
255. Shen, X., G. Mizuguchi, A. Hamiche and C. Wu. A chromatin remodelling complexinvolved in transcription and DNA processing. Nature. 2000. 406(6795): 541−544.
256. Shi, Y., F. Lan, C. Matson, P. Mulligan, J. R. Whetstine, P. A. Cole and R. A. Casero.
257. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. 2004. 119(7): 941−953.
258. Shilatifard, A. Chromatin modifications by methylation and ubiquitination: implicationsin the regulation of gene expression. Annu Rev Biochem. 2006. 75: 243−269.
259. Shivaswamy, S. and V. R. Iyer. Stress-dependent dynamics of global chromatinremodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Mol Cell Biol. 2008. 28(7): 2221−2234.
260. Shogren-Knaak, M., H. Ishii, J. M. Sun, M. J. Pazin, J. R. Davie and C. L. Peterson.
261. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science. 2006. 311(5762): 844−847.
262. Singh, H., A. M. Erkine, S. B. Kremer, H. M. Duttweiler, D. A. Davis, J. Iqbal, R. R.
263. Gross and D. S. Gross. A functional module of yeast mediator that governs the dynamic range of heat-shock gene expression. Genetics. 2006.172(4): 2169−2184.
264. Singleton, M. R. and D. B. Wigley. Modularity and specialization in superfamily 1 and 2helicases. J Bacterid. 2002.184(7): 1819−1826.
265. Smith, C. L., R. Horowitz-Scherer, J. F. Flanagan, C. L. Woodcock and C. L. Peterson.
266. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat Struct Biol. 2003. 10(2): 141−145.
267. Smith, C. L. and C. L. Peterson. ATP-dependent chiomatin remodeling. Curr Top Dev1. Biol. 2005.65: 115−148.
268. Sorger, P. K. Yeast heat shock factor contains separable transient and sustained responsetranscriptional activators. Cell. 1990. 62(4): 793−805.
269. Sorger, P. K., M. J. Lewis and H. R. Pelham. Heat shock factor is regulated differently inyeast and HeLa cells. Nature. 1987. 329(6134): 81 -84.
270. Sorger, P. K. and H. R. Pelham. Yeast heat shock factor is an essential DNA-bindingprotein that exhibits temperature-dependent phosphorylation. Cell. 1988. 54(6): 855 864.
271. Stafford, G. A. and R. H. Morse. Chromatin remodeling by transcriptional activationdomains in a yeast episome. J Biol Chem. 1997. 272(17): 11 526−11 534.
272. Sterner, D. E. and S. L. Berger. Acetylation of histones and transcription-related factors.
273. Microbiol Mol Biol Rev. 2000. 64(2): 435−459.
274. Steward, M. M., J. S. Lee, A. O’Donovan, M. Wyatt, B. E. Bernstein and A. Shilatifard.
275. Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes. Nat Struct Mol Biol. 2006.13(9): 852−854.
276. Stockdale, C., M. Bruno, H. Ferreira, E. Gaicia-Wilson, N. Wiechens, M. Engeholm, A.
277. Flaus and T. Owen-Hughes. Nucleosome dynamics. Biochem Soc Symp. 2006. (73): 109−119.
278. Strahl, B. D. and C. D. Allis. The language of covalent histone modifications. Nature.2000. 403(6765): 41−45.
279. Strohner, R" A. Nemeth, P. Jansa, U Hofmann-Rohrer, R. Santoro, G. Langst and I.
280. Grummt. NoRC~a novel member of mammalian ISWI-containing chiomatin remodeling machines. EMBO J. 2001. 20(17): 4892−4900.
281. Szent-Gyorgyi, C., D. B. Finkelstein and W. T. Garrard. Sharp boundaries demarcate thechromatin structure of a yeast heat- shock gene. J Mol Biol. 1987. 193(1): 71−80.
282. Taylor, I. C., J. L. Workman, T. J. Schuetz and R. E. Kingston. Facilitated binding of
283. GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev. 1991. 5(7): 1285−1298.
284. Thoma, N. H., B. K. Czyzewski, A. A. Alexeev, A. V. Mazin, S. C. Kowalczykowski and N. P. Pavletich. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat Struct Mol Biol. 2005. 12(4): 350−356.
285. Thut, C. J., J. L. Chen, R. Klemm and R. Tjian. p53 transcriptional activation mediated by coactivators TAFII40 and TAFII60. Science. 1995. 267(5194): 100−104.
286. Tran, H. G., D. J. Steger, V. R. Iyer and A. D. Johnson. The chromo domain protein chdlp from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 2000.19(10): 2323−2331.
287. Triezenberg, S. J. Structure and function of transcriptional activation domains. Curr Opin Genet Dev. 1995. 5(2): 190−196.
288. Tsukiyama, T. and C. Wu. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell. 1995. 83(6): 1011−1020.
289. Uesugi, M., O. Nyanguile, H. Lu, A. J. Levine and G. L. Verdine. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. Science. 1997. 277(5330): 1310−1313.
290. Utley, R. T., J. Cote, T. Owen-Hughes and J. L. Workman. SWI/SNF stimulates theformation of disparate activator-nucleosome complexes but is partially redundant with cooperative binding. J Biol Chem. 1997.272(19): 12 642−12 649.
291. Utley, R. T., K. Ikeda, P. A. Grant, J. Cote, D. J. Steger, A. Eberharter, S. John and J. L.
292. Vaquero, A., M. B. Scher, D. H. Lee, A. Sutton, H. L. Cheng, F. W. Alt, L. Serrano, R.
293. Sternglanz and D. Reinberg. SirT2 is a histone deacetylase with preference for histone H4 Lys 16 during mitosis. Genes Dev. 2006. 20(10): 1256−1261.
294. Varga-Weisz, P. D., T. A. Blank and P. B. Becker. Energy-dependent chromatinaccessibility and nucleosome mobility in a cell-free system. EMBO J. 1995.14(10): 2209−2216.
295. Vary, J. C., Jr., V. K. Gangaraju, J. Qin, C. C. Landel, C. Kooperberg, B. Bartholomewand T. Tsukiyama. Yeast Iswlp forms two separable complexes in vivo. Mol Cell Biol. 2003.23(1): 80−91.
296. Vignali, M., A. H. Hassan, K. E. Neely and J. L. Workman. ATP-dependent chromatinremodeling complexes. Mol Cell Biol. 2000.20(6): 1899−1910.
297. Voelliny, R. On mechanisms that control heat shock transcription factor activity inmetazoan cells. Cell Stress Chaperones. 2004. 9(2): 122−133.
298. Wade, P. A., P. L. Jones, D. Vermaak, G. J<. Veenstra, A. Imhofj T. Sera, C. Tse, H. Ge,
299. Y: B. Shi, J. C. Hansen and A. P. Wolffe. Histone deacetylase directs the dominant. • silencing of transcription in chromatin: association with MeCP2 and the Mi-2 chromodomain. SWI/SNF ATPase. Cold Spring Harb Symp Quant Biol: 1998. 63: 435 445.
300. Wang, W. The SWI/SNF family of ATP-dependent chromatin remodelers: similarmechanisms for diverse functions. Curr Top Microbiol Immunol. 2003. 274: 143−169.
301. Wang, Y., J. Wysocka, J. R. Perlin, L. Leonelli, C. D. Allis and S. A. Coonrod. Linkingcovalent histone modifications to epigenetics: the rigidity and plasticity of the marks. Cold Spring Harb Symp Quant Biol. 2004. 69: 161−169.
302. Wenzelides, S., H. Altmann, W. Wendler and E. L. Winnacker. CTF5-a newtranscriptional activator of the NFI/CTF family. Nucleic Acids Res. 1996. 24(12): 2416−2421.
303. White, C. L., R. K. Suto and K. Luger. Structure of the yeast nucleosome core particlereveals fundamental changes in internucleosome interactions. EMBO J. 2001. 20(18): 5207−5218.
304. Whitehouse, I., C. Stockdale, A. Flaus, M. D. Szczelkun and T. Owen-Hughes. Evidencefor DNA translocation by the ISWI chromatin-remodeling enzyme. Mol Cell Biol. 2003.23(6): 1935−1945.
305. Whitehouse, I. and T. Tsukiyama. Antagonistic forces that position nucleosomes in vivo.
306. Nat Struct Mol Biol. 2006. 13(7): 633−640.
307. Wilson, C. J., D. M. Chao, A. N. Imbalzano, G. R. Schnitzler, R. E. Kingston and R. A.
308. Young. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell. 1996. 84(2): 235−244. 281. Winston, F. and C. D. Allis. The bromodomain: a chromatin-targeting module? Nat Struct Biol. 1999. 6(7): 601−604.
309. Woodcock, C. L. Chromatin architecture. Curr Opin Struct Biol. 2006. 16(2): 213−220.
310. Workman, J. L. Nucleosome displacement in transcription. Genes Dev. 2006. 20(15):2009−2017.
311. Wu, C. Heat shock transcription factors: structure and regulation. Ann Rev Cell Dev1. Biol. 1995.11:441−469:
312. Xella, B., C. Goding, E. Agricola, E. Di Mauro and M. Caseria. The ISWI and CHD1 chromatin remodelling activities influence ADH2 expression and chromatin organization. Mol Microbiol. 2006.59(5): 1531−1541.
313. Xiao, L., X. Lu and D. M. Ruden. Effectiveness of hsp90 inhibitors as anti-cancer drugs.
314. Mini Rev Med Chem. 2006. 6(10): 1137−1143.
315. Xu, F., K. Zhang and M. Grunstein. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell. 2005. 121(3): 375−385.
316. Yamamoto, A., Y. Mizukami and H. Sakurai. Identification of a novel class of targetgenes and a novel type of binding sequence of heat shock transcription factor in Saccharomyces cerevisiae. J Biol Chem. 2005. 280(12): 11 911−11 919.
317. Yanagisawa, S. The transcriptional activation domain of the plant-specific Dofl factorfunctions in plant, animal, and yeast cells. Plant Cell Physiol. 2001. 42(8): 813−822.
318. Young, M. R. and E. A. Craig. Saccharomyces cerevisiae HSP70 heat shock elements arefunctionally distinct. Mol Cell Biol. 1993. 13(9): 5637−5646.
319. Yudkovsky, N., C. Logie, S. Hahn and C. L. Peterson. Recruitment of the SWI/SNFchromatin remodeling complex by transcriptional activators. Genes Dev. 1999. 13(18): 2369−2374.
320. Zhang, L., S. Schroeder, N. Fong and D. L. Bentley. Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'. EMBO J. 2005. 24(13): 2379−2390.
321. Zhang, Y. and D. Reinberg. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 2001. 15(18): 2343−2360.
322. Zhang, Y., C. L. Smith, A. Saha, S. W. Grill, S. Mihardja, S. B. Smith, B. R. Cairns, C. L. Peterson and C. Bustamante. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell. 2006. 24(4): 559−568.
323. Zhao, J., J. Herrera-Diaz and D. S. Gross. Domain-Wide Displacement of Histones by Activated Heat Shock Factor Occurs Independently of Swi/Snf and Is Not Correlated with RNA Polymerase II Density. Mol Cell Biol. 2005. 25(20): 8985−8999.
324. Zhao, R. and W. A. Houry. Hsp90: a chaperone for protein folding and gene regulation.
325. Biochem Cell Biol. 2005. 83(6): 703−710.
326. ZofalI, M., J. Persinger, S. R. Kassabov and B. Bartholomew. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat Struct Mol Biol. 2006. 13(4): 339−346.