Механизмы активации транскрипции, осуществляемой РНК-полимеразой II

Список литературы

1. Structure and functional organization of the nuclear matrix. Academic Press. International review of cytology & survey of cell biology.
2. Nonradioactive in situ hybridization application manual. .(1996). Bochringer Manheim GmbH, Biochemica. p211
3. Aasland, R., Gibson, T.J., Stewart, A.F. (1995) The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci 20,56−9
4. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990) Basic local alignment search tool. JMol Biol 215,403−10
5. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389−402
6. Alvarez, M., Rhodes, S.J., Bidwell, J.P. (2003) Context-dependent transcription: all politics is local. Gene 313,43−57
7. Anderson, M.G., Scoggin, K.E., Simbulan-Rosenthal, C.M., Steadman, J.A. (2000) Identification of poly (ADP-ribose) polymerase as a transcriptional coactivator of the human T-cell leukemia virus type 1 Tax protein. J Virol 74, 2169−77
8. Aoyagi, N., Wassarman, D.A. (2000) Genes encoding Drosophila melanogaster RNA polymerase II general transcription factors: diversity in TFIIA and TFIID components contributes to gene-specific transcriptional regulation. J Cell Biol 150, F45−50
9. Aravind, L., Iyer, L.M., Koonin, E.V. (2003) Scores of RINGS but no PHDs in ubiquitin signaling. Cell Cycle 2,123−6
10. Aravind, L., Landsman, D. (1998) AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res 26,4413−21
11. Armache, K.J., Mitterweger, S., Meinhart, A., Cramer, P. (2005) Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem 280,71 314
12. Ashburner M. (1989) Drosophila. A laboratory manual. CSH laboratory press, Cambridge
13. Asturias, F.J. (2004) RNA polymerase II structure, and organization of the preinitiation complex. Curr Opin Struct Biol 14,121−9
14. Asturias, F.J., Jiang, Y.W., Myers, L.C., Gustafsson, C.M., Kornberg, R.D. (1999) Conserved structures of mediator and RNA polymerase II holoenzyme. Science 283, 985−7
15. Ayoubi, T.A., Van De Ven, W.J. (1996) Regulation of gene expression by alternative promoters. FASEB /10,453−60
16. Babb, R., Cleary, M.A., Herr, W. (1997) OCA-B is a functional analog of VP16 but targets a separate surface of the Oct-1 POU domain. Mol Cell Biol 17,7 295 305
17. Baek, H.J., Malik, S., Qin, J" Roeder, R.G. (2002) Requirement of TRAP/mediator for both activator-independent and activator-dependent transcription in conjunction with TFIID-associated TAF (II)s. Mol Cell Biol 22, 2842−52
18. Balasubramanian, R., Pray-Grant, M.G., Selleck, W., Grant, P.A., Tan, S. (2002) Role of the Ada2 and Ada3 transcriptional coactivators in histone acetylation. J Biol Chem 277, 7989−95
19. Barlev, N.A., et al (2003) A novel human Ada2 homologue functions with Gcn5 or Brgl to coactivate transcription. Mol Cell Biol 23, 6944−57
20. Baskar J.F., Smith, P.P., Ciment G.S., Hoffman S., et.al. (1996) Developmental analysis of the cytomegalovirus enhancer in transgenic animals. J Virol 70,3215−26
21. Bateman, A., et al (2004) The Pfam protein families database. Nucleic Acids Res 32 Database issue, D138−41
22. Becker, P.B., Horz, W. (2002) ATP-dependent nucleosome remodeling. Annu Rev Biochem 71, 247−73
23. Belenkaya, Т., Barseguyan, K., Hovhannisyan, H., Biryukova, I., Kochieva, E.Z., Georgiev, P. (1998) P element sequences can compensate for a deletion of the yellow regulatory region in Drosophila melanogaster. Mol Gen Genet 259, 79−87
24. Belmont, A. (2003) Dynamics of chromatin, proteins, and bodies within the cell nucleus. Curr Opin Cell Biol 15,304−10
25. Berezney, R. (2002) Regulating the mammalian genome: the role of nuclear architecture. Adv Enzyme Regul 42, 39−52
26. Berger, S.L. (2002) Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12, 142−8
27. Bhaumik, S.R., Green, M.R. (2002) Differential requirement of SAGA components for recruitment of TATA-box-binding protein to promoters in vivo. Mol Cell Biol 22, 7365−71
28. Bhaumik, S.R., Raha, Т., Aiello, D.P., Green, M.R. (2004) In vivo target of a transcriptional activator revealed by fluorescence resonance energy transfer. Genes Dev 18,333−43
29. Bjorklund, S., Almouzni, G., Davidson, I., Nightingale, K.P., Weiss, K. (1999) Global transcription regulators of eukaryotes. Cell 96, 759−67
30. Boehm, A.K., Saunders, A., Werner, J., Lis, J.T. (2003) Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol Cell Biol 23, 7628−37
31. Bordoli, L., Netsch, M., Luthi, U., Lutz, W., Eckner, R. (2001) Plant orthologs of рЗОО/CBP: conservation of a core domain in metazoan рЗОО/CBP acetyltransferase-related proteins. Nucleic Acids Res 29, 589−97
32. Borggrefe, Т., Davis, R., Erdjument-Bromage, H., Tempst, P., Kornberg, R.D. (2002) A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J Biol Chem 277,44 202−7
33. Boube, M., Faucher, C., Joulia, L., Cribbs, D.L., Bourbon, H.M. (2000) Drosophila homologs of transcriptional mediator complex subunits are required for adult cell and segment identity specification. Genes Dev 14, 2906−17
34. Boube, M., Joulia, L., Cribbs, D.L., Bourbon, H.M. (2002) Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110,143−51
35. Boudreault, A.A., et al (2003) Yeast enhancer of polycomb defines global Esal-dependent acetylation of chromatin. Genes Dev 17,1415−28
36. Brady, M.E., Ozanne, D.M., Gaughan, L., Waite, I., Cook, S., Neal, D.E., Robson, C.N. (1999) Tip60 is a nuclear hormone receptor coactivator. J Biol Chem 274,17 599−604
37. Brand, M., Yamamoto, K., Staub, A., Tora, L. (1999) Identification of TATA-binding protein-free TAFII-containing complex subunits suggests a role in nucleosome acetylation and signal transduction. J Biol Chem 274, 18 285−9
38. Brandeis, M., Frank, D., Keshet, I., Siegfried, Z., Mendelsohn, M., Nemes, A., Temper, V., Razin, A., Cedar, H. (1994) Spl elements protect a CpG island from de novo methylation. Nature 371,435−8
39. Brehm, A., Langst, G., Kehle, J., Clapier, C.R., Imhof, A., Eberharter, A., Muller, J., Becker, P.B. (2000) dMi-2 and ISWI chromatin remodelling factors have distinct nucleosome binding and mobilization properties. EMBO J19,4332−41
40. Brou, C., Chaudhary S., Davidson I., Lutz Y., Wu J., Egly J., Tora L., Chambon P. (1993) Distinct TFIID complexes mediate the effect of different transcriptional activators. EMBO J12,489−99
41. Brown, C.E., Lechner, Т., Howe, L., Workman, J.L. (2000) The many HATs of transcription coactivators. Trends Biochem Sci 25,15−9
42. Brownell, J.E., Zhou, J., Ranalli, Т., Kobayashi, R., Edmondson, D.G., Roth, S.Y., Allis, C.D. (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843−51
43. Burke, T.W., Cook, J.G., Asano, M., Nevins, J.R. (2001) Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBOl. J Biol Chem 276,15 397−408
44. Burke, T.W., Kadonaga, J.T. (1996) Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev 10,711−24
45. Burke, T.W., Kadonaga, J.T. (1997) The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 11, 3020−31
46. Burley, S.K., Roeder, R.G. (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem 65, 769−99
47. Bushmeyer, S., Park, K., Atchison, M.L. (1995) Characterization of functional domains within the multifunctional transcription factor, YY1. J Biol Chem 270, 30 213−20
48. Candau, R., Moore, P.A., Wang, L., Barlev, N., Ying, C.Y., Rosen, C.A., Berger, S.L. (1996) Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5. Mol Cell Biol 16, 593−602
49. Cang, Y., Prelich, G. (2002) Direct stimulation of transcription by negative cofactor 2 (NC2) through TATA-binding protein (TBP). Proc Natl Acad Sci USA 99, 12 727−32
50. Capili, A.D., Schultz, D.C., Rauscherlll, F.J., Borden, K.L. (2001) Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J 20, 165−77
51. Carey, M. (1998) The enhanceosome and transcriptional synergy. Cell 92, 5−8
52. Carey, M. and Smale, S.T. (2000) Transcriptional regulation in eucariotes CSHL Press, New York
53. Carrozza, M.J., Utley, R.T., Workman, J.L., Cote, J. (2003) The diverse functions of histone acetyltransferase complexes. Trends Genet 19,321−9
54. Champagne, N., Bertos, N.R., Pelletier, N., Wang, A.H., Vezmar, M., Yang, Y., Heng, H.H., Yang, X.J. (1999) Identification of a human histone acetyltransferase related to monocytic leukemia zinc finger protein. J Biol Chem 274,28 528−36
55. Chan, H.M., La Thangue, N.B. (2001) p300/CBP proteins: HATs for transcriptional bridges and scaffolds. J Cell Sci 114,2363−73
56. Chen, B.S., Hampsey, M. (2002) Transcription activation: unveiling the essential nature of TFIID. Curr Biol 12, R620−2
57. Chen, J.L., Attardy L.D., Verrijzer, C.P., Yokomori, K., Tjin, R. (1994) Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 19, 93−105
58. Chestkov, A.V., Baka I.D., Kost, M.V., Georgiev, G.P., Buchman, V.L. (1996) The d4 gene family in the human genome Genomics 36,174−177.
59. Chen, B.S., Mandal, S.S., Hampsey, M. (2004) High-resolution protein-DNA contacts for the yeast RNA polymerase II general transcription machinery. Biochemistry 43,12 741−9
60. Chen, D., Dundr, M., Wang, C., Leung, A., Lamond, A., Misteli, Т., Huang, S. (2005) Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins. J Cell Biol 168,41−54
61. Chen, H.T., Hahn, S. (2004) Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell 119, 169−80
62. Chinenov, Y. (2002) A second catalytic domain in the Elp3 histoneacetyl transferases: a candidate for histone demethylase activity? Trends Biochem Sci 27,115−7
63. Corona, D.F., Tamkun, J.W. (2004) Multiple roles for ISWI in transcription, chromosome organization and DNA replication. Biochim Biophys Acta 1677,1139
64. Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16,10 881−90
65. Cosma, M.P. (2002) Ordered recruitment: gene-specific mechanism of transcription activation. Mol Cell 10,227−36
66. Cryderman, D.E., Cuaycong, M.H., Elgin, S.C., Wallrath, L.L. (1998) Characterization of sequences associated with position-effect variegation at pericentric sites in Drosophila heterochromatin. Chromosoma 107,277−85
67. Cryderman, D.E., Morris, E.J., Biessmann, H., Elgin, S.C., Wallrath, L.L. (1999) Silencing at Drosophila telomeres: nuclear organization and chromatin structure play critical roles. EMBO J18, 3724−35
68. Currie, R.A. (1998) NF-Y is associated with the histone acetyltransferases GCN5 and P/CAF. J Biol Chem 273,1430−4
69. Dasgupta, A., Darst, R.P., Martin, K.J., Afshari, C.A., Auble, D.T. (2002) Motl activates and represses transcription by direct, ATPase-dependent mechanisms. Proc Natl Acad Sci USA 99,2666−71
70. DeCamillis, M" Cheng, N.S., Pierre, D., Brock, H.W. (1992) The polyhomeotic gene of Drosophila encodes a chromatin protein that shares polytene chromosome-binding sites with Polycomb. Genes Dev 6,223−32
71. Dellino, G.I., Schwartz, Y.B., Farkas, G., McCabe, D., Elgin, S.C., Pirrotta, V. (2004) Polycomb silencing blocks transcription initiation. Mol Cell 13, 887−93
72. Deng, W.G., Wu, K.K. (2003) Regulation of inducible nitric oxide synthase expression by p300 and p50 acetylation. J Immunol 171, 6581−8
73. Dilworth, F.J., Seaver, K.J., Fishburn, A.L., Htet, S.L., Tapscott, S.J. (2004) In vitro transcription system delineates the distinct roles of the coactivators pCAF and p300 during MyoD/E47-dependent transactivation. Proc Natl Acad Sci USA 101, 11 593−8
74. Dimova, D., Nackerdien, Z., Furgeson, S., Eguchi, S., Osley, M.A. (1999) A role for transcriptional repressors in targeting the yeast Swi/Snf complex. Mol Cell 4, 75−83
75. DiRenzo, J., Shang, Y., Phelan, M., Sif, S., Myers, M., Kingston, R., Brown, M. (2000) BRG-1 is recruited to estrogen-responsive promoters and cooperates with factors involved in histone acetylation. Mol Cell Biol 20, 7541−9
76. Doyon, Y., Selleck, W., Lane, W.S., Tan, S., Cote, J. (2004) Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeastto humans. Mol Cell Biol 24,1884−96
77. Dubrovskaya V., Lavigne A.-C., Davidson I., Acker J., Staub, A., Tora L (1996) Distinct domains of hTAFIIlOO are reqired for functional interaction with transcription factor TFIIFb (RAP30) and incorporation into the TFIID complex. EMBOJ15, 3702−12
78. Eberharter, A., Becker, P.B. (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep 3,224−9
79. Eberharter, A., Becker, P.B. (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep 3,224−9
80. Eberharter, A., Sterner, D.E., Schieltz, D., Hassan, A., Yates, J.R. 3rd, Berger, S.L., Workman, J.L. (1999) The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae. Mol Cell Biol 19,6621−31
81. Ehling, U.H., Cumming, R.B., Mailing, H.V. (1968) Induction of dominant lethal mutations by alkylating agents in male mice. Mutat Res 5,417−428
82. Ehrenhofer-Murray, A.E., Rivier, D.H., Rine, J. (1997) The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics 145, 923−34
83. Eisen, A., Utley, R.T., Nourani, A., Allard, S., Schmidt, P., Lane, W.S., Lucchesi, J.C., Cote, J. (2001) The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J Biol Chem 276, 3484−91
84. Eissenberg, J.C., Elgin, S.C. (2000) The HP1 protein family: getting a grip on chromatin. Curr Opin Genet Dev 10,204−10
85. Eissenberg, J.C., Elgin, S.C. (2000) The HP1 protein family: getting a grip on chromatin. Curr Opin Genet Dev 10,204−10
86. Emami, K.H., Jain, A., Smale, S.T. (1997) Mechanism of synergy between TATA and initiator: synergistic binding of TFIID following a putative TFILA-induced isomerization. Genes Dev 11, 3007−19
87. Emerson, B.M. (2002) Specificity of gene regulation. Cell 109,267−70
88. Erkine, A.M. (2004) Activation domains of gene-specific transcription factors: are histones among their targets? Biochem Cell Biol 82, 453−9
89. Ezzat, S., Yu, S., Asa, S.L. (2003) Ikaros isoforms in human pituitary tumors: distinct localization, histone acetylation, and activation of the 5' fibroblast growth factor receptor-4 promoter. Am J Pathol 163,1177−84
90. Fazzio, T.G., Kooperberg, C., Goldmark, J.P., Neal, C., Basom, R., Delrow, J., Tsukiyama, T. (2001) Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol Cell Biol 21, 6450−60
91. Featherstone, M. (2002) Coactivators in transcription initiation: here are your orders. Curr Opin Genet Dev 12, 149−55
92. Fourel, G., Magdinier, F., Gilson, E. (2004) Insulator dynamics and the setting of chromatin domains. Bioessays 26, 523−32
93. Fox, C.A., McConnell, K.H. (2004) Toward biochemical understanding of a transcriptionally silenced chromosomal domain in Saccharomyces cerevisiae. J Biol Chem
94. Galarneau, L., et/ al (2000) Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell 5,92 737
95. Ge, H., Roeder, R.G. (1994) Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class II genes. Cell 78, 513−23
96. Geer, L.Y., Domrachev, M., Lipman, D.J., Bryant, S.H. (2002) CDART: protein homology by domain architecture. Genome Res 12,1619−23
97. Georgiev, P., Kozycina, M. (1996) Interaction between mutations in the suppressor of Hairy wing and modifier of mdg4 genes of Drosophila melanogaster affecting the phenotype of gypsy-induced mutations. Genetics 142,425−36
98. Georgiev, P.G. (1994) Identification of mutations in three genes that interact with zeste in the control of white gene expression in Drosophila melanogaster. Genetics 138,733−9
99. Georgiev, P.G., Gerasimova, T.I. (1989) Novel genes influencing the expression of the yellow locus and mdg4 (gypsy) in Drosophila melanogaster. Mol Gen Genet 220, 121−6
100. Georgiev, P.G., Kiselev, S.L., Simonova, O.B., Gerasimova, T.I. (1990) A novel transposition system in Drosophila melanogaster depending on the Stalker mobile genetic element. EMBO J9,2037−44
101. Georgieva, S., et al (2000) Two novel Drosophila TAF (II)s have homology with human TAF (II)30 and are differentially regulated during development. Mol Cell Biol 20, 1639−48
102. Georgieva, S.G., Nabirochkina, E.N., Georgiev, P.G., Soldatov, A.V. (2000) Gene enhancer of yellow 1 of Drosophila melanogaster codes for protein TAFII40. Dokl Biochem 375, 228−30
103. Geyer, P.K. (1997) The role of insulator elements in defining domains of gene expression. Curr Opin Genet Dev 7, 242−8
104. Geyer, P.K., Corces, V.G. (1987) Separate regulatory elements are responsible for the complex pattern of tissue-specific and developmental transcription of the yellow locus in Drosophila melanogaster. Genes Dev 1, 996−1004
105. Geyer, P.K., Green, M.M., Corces, V.G. (1988) Reversion of a gypsy-induced mutation at the yellow (y) locus of Drosophila melanogaster is associated with the insertion of a newly defined transposable element. Proc Natl Acad Sci USA 85, 3938−42
106. Geyer, P.K., Green, M.M., Corces, V.G. (1988) Mutant gene phenotypes mediated by a Drosophila melanogaster retrotransposon require sequences homologous to mammalian enhancers. Proc Natl Acad Sci US ASS, 8593−7
107. Geyer, P.K., Richardson, K.L., Corces, V.G., Green, M.M. (1988) Genetic instability in Drosophila melanogaster: P-element mutagenesis by gene conversion. Proc Natl Acad Sci US ASS, 6455−9
108. Geyer, P.K., Spana, C., Corces, V.G. (1986) On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster. EMBO J 5,2657−62
109. Giaccia, A.J., Kastan, M.B. (1998) The complexity of p53 modulation: emerging patterns from divergent signals. Genes Dev 12, 2973−83
110. Gill, G. (2003) Post-translational modification by the small ubiquitin-related modifier SUMO has big effects on transcription factor activity. Curr Opin Genet Devil, 108−13
111. Goodrich, J.A., Hoey, Т., Thut, C.J., Admon, A., Tjian, R. (1993) Drosophila TAFII40 interacts with both a VP 16 activation domain and the basal transcription factor TFIIB. Cell 75, 519−30
112. Gotzmann, J., Foisner, R. (1999) Lamins and lamin-binding proteins in functional chromatin organization. Crit Rev Eukaryot Gene Expr 9, 257−65
113. Grant, P.A., Eberharter, A., John, S., Cook, R.G., Turner, B.M., Workman, J.L. (1999) Expanded lysine acetylation specificity of Gcn5 in native complexes. J Biol Chem 274,5895−900
114. Grant, P.A., Schieltz, D., Pray-Grant, M.G., Yates, J.R. 3rd, Workman, J.L. (1998) The ATM-related cofactor Tral is a component of the purified SAGA complex. Mol Cell 2, 863−7
115. Green, M.R. (2000) TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem Sci 25, 59−63
116. Grunstein, M. (1992) Histones as regulators of genes. SciAm 267, 68−74B
117. Gu, W., Szauter, P., Lucchesi, J.C. (1998) Targeting of MOF, a putative histone acetyl transferase, to the X chromosome of Drosophila melanogaster. Dev Genet 22,56−64
118. Gustafsson, C.M., Myers, L.C., Beve, J., Spahr, H., Lui, M., Erdjument-Bromage, H., Tempst, P., Kornberg, R.D. (1998) Identification of new mediator subunits in the RNA polymerase II holoenzyme from Saccharomyces cerevisiae. J Biol Chem 273,30 851−4
119. Gustafsson, C.M., Samuelsson, T. (2001) Mediator-a universal complex in transcriptional regulation. Mol Microbiol 41,1−8
120. Hall, I.M., Shankaranarayana, G.D., Noma, K., Ayoub, N., Cohen, A., Grewal, S.I. (2002) Establishment and maintenance of a heterochromatin domain. Science 297,2232−7
121. Halle, J.P., Stelzer, G., Goppelt, A., Meisterernst, M. (1995) Activation of transcription by recombinant upstream stimulatory factor 1 is mediated by a novel positive cofactor. J Biol Chem 270,21 307−11
122. Hansen, J.C., Tse, C., Wolffe, A.P. (1998) Structure and function of the core histone N-termini: more than meets the eye. Biochemistry 37, 17 637−41
123. Hapgood, J.P., Riedemann, J., Scherer, S.D. (2001) Regulation of gene expression by GC-rich DNA cis-elements. Cell Biol Int 25,17−31
124. Harvey, D.M., Levine, A.J. (1991) p53 alteration is a common event in the spontaneous immortalization of primary BALB/c murine embryo fibroblasts. Genes Dev 5, 2375−85
125. Hassan, A.H., Neely, K.E., Vignali, M., Reese, J.C., Workman, J.L. (2001) Promoter targeting of chromatin-modifying complexes. Front Biosci 6, D1054−64
126. Hayes, J.J., Hansen, J.C. (2001) Nucleosomes and the chromatin fiber. Curr Opin Genet Dev 11, 124−9
127. Hengartner, C.J., Thompson, C.M., Zhang, J., Chao, D.M., Liao, S.M., Koleske, A.J., Okamura, S., Young, R.A. (1995) Association of an activator with an RNA polymerase II holoenzyme. Genes Dev 9, 897−910
128. Henke, W., Herdel, K., Jung, K., Schnorr, D., Loening, S.A. Betaine improves the PCR amplification of GC-rich DNA sequences. (1997) Nucleic Acids Res 25, 395 758.
129. Henry, K.W., et al (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Devil, 2648−63
130. Henry, K.W., et al (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev 17, 2648−63
131. Hilfiker, A., Hilfiker-Kleiner, D., Pannuti, A., Lucchesi, J.C. (1997) mof, a putative acetyl transferase gene related to the Tip60 and MOZ human genes and to the SAS genes of yeast, is required for dosage compensation in Drosophila. EMBO J16, 2054−60
132. Hochheimer, A., Tjian, R. (2003) Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. Genes Dev 17, 1309−20
133. Hofmann, W.A., et al (2004) Actin is part of pre-initiation complexes and is necessary for transcription by RNA polymerase II. Nat Cell Biol 6,1094−101
134. Holstege, F.C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., Young, R.A. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95,717−28
135. Horn, P.J., Peterson, C.L. (2002) Molecular biology. Chromatin higher order folding—wrapping up transcription. Science 291, 1824−7
136. Howe, L., Kusch, Т., Muster, N., Chateiji, R., Yates, J.R. 3rd, Workman, J.L. (2002) Ynglp modulates the activity of Sas3p as a component of the yeast NuA3 Hhistone acetyltransferase complex. Mol Cell Biol 22,5047−53
137. Huisinga, K.L., Pugh, B.F. (2004) A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell 13, 573−85
138. Iizuka, M., Stillman, B. (1999) Histone acetyltransferase HBOl interacts with the ORC1 subunit of the human initiator protein. J Biol Chem 214,23 027−34
139. Ikura, Т., Ogryzko, V.V., Grigoriev, M., Groisman, R., Wang, J., Horikoshi, M., Scully, R., Qin, J., Nakatani, Y. (2000) Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102,463−73
140. Jacobs, S.A., Taverna, S.D., Zhang, Y., Briggs, S.D., Li, J., Eissenberg, J.C., Allis, C.D., Khorasanizadeh, S. (2001) Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J 20, 5232−41
141. Jacq, X., Brou, C., Lutz, Y., Davidson, I., Chambon P., Tora L. (1994) Human TAFII30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor. Cell 19,107−117
142. Jenuwein, Т., Allis, C.D. (2001) Translating the histone code. Science 293,107 480
143. Johnson, S.A., Dubeau, L., White, R.J., Johnson, D.L. (2003) The TATA-binding protein as a regulator of cellular transformation. Cell Cycle 2,442−4
144. Jones, D.O., Cowell, I.G., Singh, P.B. (2000) Mammalian chromodomainproteins: their role in genome organisation and expression. Bioessays 22, 124−37
145. Kadonaga, J.T. (2004) Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116,247−57
146. Kaiser, K., Meisterernst, M. (1996) The human general co-factors. Trends Biochem Sci 21, 342−5
147. Kalkhoven, E. (2004) СВР and p300: HATs for different occasions. Biochem Pharmacol 68, 1145−55
148. Kalkhoven, E., Teunissen, H., Houweling, A., Verrijzer, C.P., Zantema, A. (2002) The PHD type zinc finger is an integral part of the СВР acetyltransferase domain. Mol Cell Biol 22, 1961−70
149. Kamine, J., Elangovan, В., Subramanian, Т., Coleman, D., Chinnadurai, G. (1996) Identification of a cellular protein that specifically interacts with the essential cysteine region of the HIV-1 Tat transactivator. Virology 216,357−66
150. Karpova, T.S., Chen, T.Y., Sprague, B.L., McNally, J.G. (2004) Dynamic interactions of a transcription factor with DNA are accelerated by a chromatin remodeller. EMBO Rep 5, 1064−70
151. Kelly, W.G., Fire, A. (1998) Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. Development 125,2451−6
152. Kim, Т.К., Maniatis, T. (1997) The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome. Mol Cell 1,119−29
153. Kim, Т.К., Zhao, Y., Ge, H., Bernstein, R., Roeder, R.G. (1995) TATA-binding protein residues implicated in a functional interplay between negative cofactor NC2 (Drl) and general factors TFIIA and TFIIB. J Biol Chem 270,10 976−81
154. Kingston, R.E., Bunker, C.A., Imbalzano, A.N. (1996) Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev 10, 905−20
155. Kleff, S" Andrulis, E.D., Anderson, C.W., Sternglanz, R. (1995) Identification of a gene encoding a yeast histone H4 acetyltransferase. J Biol Chem 270,24 674−7
156. Klemm, R.D., Goodrich, J.A., Zhou, S., Tjian, R. (1995) 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 92, 5788−92
157. Kouskouti, A., Scheer, E., Staub, A., Tora, L., Talianidis, I. (2004) Gene-specific modulation of TAF10 function by SET9-mediated methylation. Mol Cell 14,17 582
158. Kouzarides, T. (2003) Wellcome Trust Award Lecture. Chromatin-modifyingenzymes in transcription and cancer. Biochem Soc Trans 31, 741−3
159. Kouzarides, T. (2003) Wellcome Trust Award Lecture. Chromatin-modifying enzymes in transcription and cancer. Biochem Soc Trans 31, 741−3
160. Kretzschmar, M., Meisterernst, M., Roeder, R.G. (1993) Identification of human DNA topoisomerase I as a cofactor for activator-dependent transcription by RNA polymerase II. Proc Natl Acad Sci USA 90, 11 508−12
161. Kuo, M.H., Allis, C.D. (1998) Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays 20, 615−26
162. Kurdistani, S.K., Grunstein, M. (2003) Histone acetylation and deacetylation in yeast. Nat Rev Mol Cell Biol 4,276−84
163. Kusch, Т., Guelman, S., Abmayr, S.M., Workman, J.L. (2003) Two Drosophila Ada2 homologues function in different multiprotein complexes. Mol Cell Biol 23, 3305−19
164. Kusch, Т., Guelman, S., Abmayr, S.M., Workman, J.L. (2003) Two Drosophila Ada2 homologues function in different multiprotein complexes. Mol Cell Biol 23, 3305−19
165. Kwan, A.H., Gell, D.A., Verger, A., Crossley, M., Matthews, J.M., Mackay, J.P. (2003) Engineering a protein scaffold from a PHD finger. Structure (Camb) 11, 803−13
166. Lai, E., Darnell, J.E. (1991) Transcriptional control in hepatocytes: a window on development. Trends Biochem Sci 16, 427−30
167. Lam, G., Hall, B.L., Bender, M., Thummel, C.S. (1999) DHR3 is required for the prepupal-pupal transition and differentiation of adult structures during Drosophila metamorphosis. Dev Biol 212, 204−16
168. Lam, G.T., Jiang, C., Thummel, C.S. (1997) Coordination of larval and prepupal gene expression by the DHR3 orphan receptor during Drosophila metamorphosis. Development 124,1757−69
169. Lee, D.Y., Hayes, J.J., Pruss, D., Wolffe, A.P. (1993) A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72, 73−84
170. Lee, D.Y., Teyssier, C., Strahl, B.D., Stallcup, M.R. (2004) Role of Protein Methylation in Regulation of Transcription. Endocr Rev
171. Lee, T.I., et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799−804
172. Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H., Kim, V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J23,4051−60
173. Legube, G., Linares, L.K., Tyteca, S., Caron, C., Scheffiier, M., Chevillard-Briet, M., Trouche, D. (2004) Role of the histone acetyl transferase Tip60 in the p53 pathway. J Biol Chem 279,44 825−33
174. Lemon, В., Tjian, R. (2000) Orchestrated response: a symphony of transcription factors for gene control. Genes Dev 14,2551−69
175. Leresche, A., Wolf, V.J., Gottesfeld, J.M. (1996) Repression of RNA polymerase II and III transcription during M phase of the cell cycle. Exp Cell Res 229, 282−8
176. Levine, M., Tjian, R. (2003) Transcription regulation and animal diversity. Nature 424, 147−51
177. Levis, R., Hazelrigg, Т., Rubin, G.M. (1985) Separable cis-acting control elements for expression of the white gene of Drosophila. EMBO J4,3489−99
178. Lewis, B.A., Reinberg, D. (2003) The mediator coactivator complex: functional and physical roles in transcriptional regulation. J Cell Sci 116,3667−75
179. Lewis, B.A., Reinberg, D. (2003) The mediator coactivator complex: functional and physical roles in transcriptional regulation. J Cell Sci 116,3667−75
180. Li, X., Zhao, X., Jiang, X. et.al. (1998) Generation of destabilized green fluorescent protein as a transcription reporter. J Biol Chem 273, 34 970−75
181. Li, Y., Danzer, J.R., Alvarez, P., Belmont, A.S., Wallrath, L.L. (2003) Effects of tethering HP1 to euchromatic regions of the Drosophila genome. Development 130, 1817−24
182. Lim, C.Y., Santoso, В., Boulay, Т., Dong, E., Ohler, U., Kadonaga, J.T. (2004) The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev 18,1606−17
183. Lin, H., Spradling, A.C. (1993) Germline stem cell division and egg chamber development in transplanted Drosophila germaria. Dev Biol 159, 140−52
184. Linder, В., Newman, R., Jones, L.K., Debernardi, S., Young, B.D., Freemont, P., Verrijzer, C.P., Saha, V. (2000) Biochemical analyses of the AF10 protein: the extended LAP/PHD-finger mediates oligomerisation. J Mol Biol 299, 369−78
185. Lindsley D., Zimm G. The genome of Drosophila melanogaster. (1992) Academic Press, New-York. (GENERIC)
186. Lodish, H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.P., Zipursky, L., and Darnell, J. (2003) Molecular Cell Biology W.H.Freeman & Co.,
187. Loewith, R., Meijer, M., Lees-Miller, S.P., Riabowol, K., Young, D. (2000) Three yeast proteins related to the human candidate tumor suppressor p33(INGl) are associated with histone acetyltransferase activities. Mol Cell Biol 20,3807−16
188. Lorch, Y., Beve, J., Gustafsson, C.M., Myers, L.C., Kornberg, R.D. (2000) Mediator-nucleosome interaction. Mol Cell 6, 197−201
189. Lu, B.Y., Emtage, P.C., Duyf, B.J., Hilliker, A.J., Eissenberg, J.C. (2000)
190. Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila. Genetics 155, 699−708
191. Lu, H., Levine, A.J. (1995) Human TAFII31 protein is a transcriptional coactivator of the p53 protein. Proc Natl Acad Sci USA 92, 5154−8
192. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., Richmond, T.J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251−60
193. Lusser, A., Kadonaga, J.T. (2003) Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25,1192−200
194. Maile, Т., Kwoczynski, S., Katzenberger, R.J., Wassarman, D.A., Sauer, F. (2004) TAF1 activates transcription by phosphorylation of serine 33 in histone H2B. Science 304, 1010−4
195. Majello, В., De Luca, P., Lania, L. (1997) Sp3 is a bifimctional transcription regulator with modular independent activation and repression domains. J Biol Chem 272, 4021−6
196. Maldonado, E., Hampsey, M., Reinberg, D. (1999) Repression: targeting the heart of the matter. Cell 99,455−8
197. Malik, S., Gu, W., Wu, W., Qin, J., Roeder, R.G. (2000) The USA-derived transcriptional coactivator PC2 is a submodule of TRAP/SMCC and acts synergistically with other PCs. Mol Cell 5,753−60
198. Malik, S., Roeder, R.G. (2000) Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem Sci 25, 277−83
199. Marinescu, V.D., Kohane, I.S., Riva, A. (2005) The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 33 Database Issue, D91−7
200. Martin, M., Meng, Y.B., Chia, W. (1989) Regulatory elements involved in the tissue-specific expression of the yellow gene of Drosophila. Mol Gen Genet 218, 118−26
201. Martinez, E., Ge, H., Tao, Y., Yuan, C.X., Palhan, V., Roeder, R.G. (1998) Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex. Mol Cell Biol 18, 6571−83
202. Mason, P.B., Struhl, K. (2003) The FACT complex travels with elongating RNApolymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol 23, 8323−33
203. Mazo, A.M., Huang, D.H., Mozer, B.A., Dawid, I.B. (1990) The trithorax gene, a trans-acting regulator of the bithorax complex in Drosophila, encodes a protein with zinc-binding domains. Proc Natl Acad Sci US A 87, 2112−6
204. Melnikova, L., Kulikov, A., Georgiev, P. (1996) Interactions between cut wing mutations and mutations in zeste, and the enhancer of yellow and Polycomb group genes of Drosophila melanogaster. Mol Gen Genet 252, 230−6
205. Melnikova, L., Kulikov, A., Georgiev, P. (1996) Interactions between cut wing mutations and mutations in zeste, and the enhancer of yellow and Polycomb group genes of Drosophila melanogaster. Mol Gen Genet 252,230−6
206. Mertsalov I.V., Kulikova D.A., Alimova-Kost, M.V., Ninkina N.N., Korochkin, L.I., Buchman V.L. (2000) Structure and expression of two members of the d4 gene family in mouse. Mamm. Genome 11, 72−4.
207. Mitsiou, D.J., Stunnenberg, H.G. (2003) p300 is involved in formation of the TBP-TFIIA-containing basal transcription complex, TAC. EMBO J22,4501−11
208. Mizzen, C.A., et al (1996) The TAF (II)250 subunit of TFIID has histone acetyltransferase activity. Cell 87,1261−70
209. Moazed, D. (2001) Common themes in mechanisms of gene silencing. Mol Cell 8,489−98
210. Moqtadery Z., Keaveney M., Struhl K. (1998) The histone H3-like TAF is broadly required for the transcription in yest. Mol Cell 2,675−682
211. Morales, V., Giamarchi, C., Chailleux, C., Moro, F., Marsaud, V., Le Ricousse, S., Richard-Foy, H. (2001) Chromatin structure and dynamics: functional implications. Biochimie 83,1029−39
212. Morris, J.R., Geyer, P.K., Wu, C.T. (1999) Core promoter elements can regulate transcription on a separate chromosome in trans. Genes Dev 13,253−8
213. Morris, J.R., Petrov, D.A., Lee, A.M., Wu, C.T. (2004) Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics 167,173 947
214. Muller, F., Tora, L. (2004) The multicoloured world of promoter recognition complexes. EMBO J 23,2−8
215. Muratani, M., Tansey, W.P. (2003) How the ubiquitin-proteasome system controls transcription. Nat Rev Mol Cell Biol 4, 192−201
216. Muth, V., Nadaud, S., Grummt, I., Voit, R. (2001) Acetylation of TAF (I)68, a subunit of TIF-IB/SL1, activates RNA polymerase I transcription. EMBO J 20, 1353−62
217. Naar, A.M., Lemon, B.D., Tjian, R. (2001) Transcriptional coactivator complexes. Annu Rev Biochem 70,475−501
218. Naar, A.M., Lemon, B.D., Tjian, R. (2001) Transcriptional coactivator complexes. Annu Rev Biochem 70,475−501
219. Naar, A.M., Lemon, B.D., Tjian, R. (2001) Transcriptional coactivator complexes. Annu Rev Biochem 70,475−501
220. Nagaich, A.K., Hager, G.L. (2004) UV laser cross-linking: a real-time assay to study dynamic protein/DNA interactions during chromatin remodeling. Sci STKE 2004, pU3
221. Nakamura, Т., et al (2002) ALL-1 is a histone methyltransferase that assembles a supercomplex of proteins involved in transcriptional regulation. Mol Cell 10,111 928
222. Nakatani, Y., Bagby, S., Ikura, M. (1996) The histone folds in transcription factor TFIID. J Biol Chem 271, 6575−8
223. Narlikar, G.J., Fan, H.Y., Kingston, R.E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108,475−87
224. Narlikar, G.J., Fan, H.Y., Kingston, R.E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108,475−87
225. Narlikar, G.J., Fan, H.Y., Kingston, R.E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108,475−87
226. Nash, W.G., Yarkin, R.J. (1974) Genetic regulation and pattern formation: a study of the yellow locus in Drosophila melanogaster. Genet Res 24, 19−26
227. Nedialkov, Y.A., Triezenberg, S.J. (2004) Quantitative assessment of in vitro interactions implicates TATA-binding protein as a target of the VP16C transcriptional activation region. Arch Biochem Biophys 425, 77−86
228. Nelson, D.E., See, V., Nelson, G., White, M.R. (2004) Oscillations in transcription factor dynamics: a new way to control gene expression. Biochem Soc Trans 32,1090−2
229. Nibu, Y., Senger, K., Levine, M. (2003) CtBP-independent repression in the Drosophila embryo. Mol Cell Biol 23,3990−9
230. Nikolov, D.B., Burley, S.K. (1997) RNA polymerase II transcription initiation: a structural view. Proc Natl Acad Sci USA94, 15−22
231. Noma, K., Allis, C.D., Grewal, S.I. (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293,11 505
232. Nourani, A., Howe, L., Pray-Grant, M.G., Workman, J.L., Grant, P.A., Cote, J. (2003) Opposite role of yeast ING family members in p53-dependent transcriptional activation. J Biol Chem 278,19 171−5
233. Nourani, A., Utley, R.T., Allard, S., Cote, J. (2004) Recruitment of the NuA4 complex poises the PH05 promoter for chromatin remodeling and activation. EMBO J 23,2597−607
234. O’Connell, S., Wang, L., Robert, S., Jones, C.A., Saint, R., Jones, R.S. (2001) Polycomblike PHD fingers mediate conserved interaction with enhancer of zeste protein. J Biol Chem 276,43 065−73
235. Ogryzko, V.V., Kotani, Т., Zhang, X., Schiltz, R.L., Howard, Т., Yang, X.J., Howard, B.H., Qin, J., Nakatani, Y. (1998) Histone-like TAFs within the PCAF histone acetylase complex. Cell 94, 35−44
236. Ogryzko, V.V., Schiltz, R.L., Russanova, V., Howard, B.H., Nakatani, Y. (1996) The transcriptional coactivators p300 and СВР are histone acetyltransferases. Cell 87,953−9
237. Ohler, U., Liao, G.C., Niemann, H., Rubin, G.M. (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol 3, RESEARCH0087
238. Oki, M., Valenzuela, L., Chiba, Т., Ito, Т., Kamakaka, R.T. (2004) Barrier proteins remodel and modify chromatin to restrict silenced domains. Mol Cell Biol 24,1956−67
239. Orphanides, G., Lagrange, Т., Reinberg, D. (1996) The general transcription factors of RNA polymerase II. Genes Dev 10,2657−83
240. Orphanides, G., Reinberg, D. (2002) A unified theory of gene expression. Cell 108, 439−51
241. Orphanides, G., Reinberg, D. (2002) A unified theory of gene expression. Cell 108,439−51
242. Pal-Bhadra, M., Leibovitch, B.A., Gandhi, S.G., Rao, M., Bhadra, U., Birchler, J.A., Elgin, S.C. (2004) Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303, 669−72
243. Panagopoulos, I., Fioretos, Т., Isaksson, M., Samuelsson, U., Billstrom, R., Strombeck, В., Mitelman, F., Johansson, B. (2001) Fusion of the MORF and СВР genes in acute myeloid leukemia with the t (10−16)(q22-pl3). Hum Mol Genet 10, 395−404
244. Parthun, M.R., Widom, J., Gottschling, D.E. (1996) The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism. Cell 87, 85−94
245. Parvin, J.D., Young, R.A. (1998) Regulatory targets in the RNA polymerase II holoenzyme. Curr Opin Genet Dev 8, 565−70
246. Pascual, J., Martinez-Yamout, M., Dyson, H.J., Wright, P.E. (2000) Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor. J Mol Biol 304, 723−9
247. Pelletier, N., Champagne, N., Lim, H., Yang, X.J. (2003) Expression, purification, and analysis of MOZ and MORF histone acetyltransferases. Methods 31,24−32
248. Pelletier, N. Champagne, N., Stifani, S., Yang, X.J. (2002) MOZ and MORF histone acetyltransferases interact with the Runt-domain transcription factor Runx2. Oncogene 21, 2729−40
249. Persengiev, S.P., Zhu, X., Dixit, B.L., Maston, G.A., Kittler, E.L., Green, M.R. (2003) TRF3, a TATA-box-binding protein-related factor, is vertebrate-specific and widely expressed. Proc Natl Acad Sci USA 100, 14 887−91
250. Piacentini, L., Fanti, L., Berloco, M., Perrini, В., Pimpinelli, S. (2003) Heterochromatin protein 1 (HP1) is associated with induced gene expression in Drosophila euchromatin. J Cell Biol 161, 707−14
251. Piacentini, L., Fanti, L., Berloco, M., Perrini, В., Pimpinelli, S. (2003) Heterochromatin protein 1 (HP1) is associated with induced gene expression in Drosophila euchromatin. J Cell Biol 161, 707−14
252. Pirrotta, V. (1988) Vectors for P-mediated transformation in Drosophila. Biotechnology 10,437−56
253. Pirrotta, V. (1999) Transvection and chromosomal trans-interaction effects. Biochim Biophys Acta 1424, Ml-8
254. Pirrotta, V., Steller, H., Bozzetti, M.P. (1985) Multiple upstream regulatory elements control the expression of the Drosophila white gene. EMBO J 4, 3501−8
255. Pollard, W., Walker, J (1990) Methods in molecular Biology. Animal cell culture. Humana press. 718 p.
256. Pugh, B.F. (2000) Control of gene expression through regulation of the TATA-binding protein. Gene 255,1−14
257. Qian, S., Vaijavand, В., Pirrotta, V. (1992) Molecular analysis of the zeste-white interaction reveals a promoter-proximal element essential for distant enhancer-promoter communication. Genetics 131, 79−90
258. Ragvin, A., et al (2004) Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. J Mol Biol 337, 773−88
259. Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D. (1997) GeneCards: encyclopedia for genes, proteins and diseases. Weizmann Institute of Science, Bioinformatics Unit and Genome Center (Rehovot, Israel). GeneCard for PHF10 (2003).
260. Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D. (1997) GeneCards: encyclopedia for genes, proteins and diseases. Weizmann Institute of Science, Bioinformatics Unit and Genome Center (Rehovot, Israel). GeneCard for PHF10 (2003).
261. Redi, C.A., Garagna, S., Zacharias, H., Zuccotti, M., Capanna, E. (2001) The other chromatin. Chromosoma 110, 136−47
262. Reese, J.C., Apone, L., Walker, S.S., Griffin, L.A., Green, M.R. (1994) Yeast TAFIIS in a multisubunit complex required for activated transcription. Nature 371, 523−7
263. Reid, J.L., Moqtaderi, Z., Struhl, K. (2004) Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol Cell Biol 24, 757−64
264. Reifsnyder, C., Lowell, J., Clarke, A., Pillus, L. (1996) Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat Genet 14,42−9
265. Rekdal, C., Sjottem, E., Johansen, T. (2000) The nuclear factor SPBP contains different functional domains and stimulates the activity of various transcriptional activators. J Biol Chem 275,40 288−300
266. Rendic, S. (2002) Summary of information on human CYP enzymes: human P450 metabolism data. Drug Metab Rev 34, 83−448
267. Richards, E.J., Elgin, S.C. (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108,489−500
268. Richards, E.J., Elgin, S.C. (2002) Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 108,489−500
269. Rochette-Egly, C., Adam, S., Rossignol, M" Egly, J.M., Chambon, P. (1997) Stimulation of RAR alpha activation function AF-1 through binding to the general transcription factor TFIIH and phosphorylation by CDK7. Cell 90, 97−107
270. Roeder, R.G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 21, 327−35
271. Roeder, R.G. (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 21, 327−35
272. Roseman, R.R., Johnson, E.A., Rodesch, C.K., Bjerke, M., Nagoshi, R.N., Geyer, P.K. (1995) A P element containing suppressor of hairy-wing binding regions has novel properties for mutagenesis in Drosophila melanogaster. Genetics 141,106 174
273. Roseman, R.R., Pirrotta, V., Geyer, P.K. (1993) The su (Hw) protein insulates expression of the Drosophila melanogaster white gene from chromosomal position-effects. EMBOJ12,435−42
274. Rosen, C., Dorsett, D., Jack, J. (1998) A proline-rich region in the Zeste protein essential for transvection and white repression by Zeste. Genetics 148, 1865−74
275. Rothwell, W.F. and Sullivan, W. (2000) Fluorescent Analysis of Drosophila Embryos. Drosophila Protocols (Sullivan, W., Ashburner, M., and Harwley R.S., eds) pp. 141−159, Cold Spring Harbor Laboratory Press, New York1. Rec #:
276. Rouleau, M., Aubin, R.A., Poirier, G.G. (2004) Poly (ADP-ribosyl)ated chromatin domains: access granted. J Cell Sci 117, 815−25
277. Rubin, G.M., Spradling, A.C. (1982) Genetic transformation of Drosophila with transposable element vectors. Science 218,348−53
278. Ruiz-Garcia, A.B., Sendra, R., Galiana, M., Pamblanco, M., Perez-Ortin, J.E., Tordera, V. (1998) HAT1 and HAT2 proteins are components of a yeast nuclear histone acetyltransferase enzyme specific for free histone H4. J Biol Chem 273, 12 599−605
279. Saleh, A., Schieltz, D., Ting, N. McMahon, S.B., Litchfield, D.W., Yates, J.R. 3rd, Lees-Miller, S.P., Cole, M.D., Brandl, C.J. (1998) Tralp is a component of the yeast Ada. Spt transcriptional regulatory complexes. J Biol Chem 273,26 559−65
280. Sambrook, J., Fritsch, E.F., and Maniatis, T. (2001) Molecular Cloning. A laboratory manual. CSHL Press,
281. Samuelsen, C.O., Baraznenok, V., Khorosjutina, O., Spahr, H., Kieselbach, Т., Holmberg, S., Gustafsson, C.M. (2003) TRAP230/ARC240 and TRAP240/ARC250 Mediator subunits are functionally conserved through evolution. Proc Natl Acad Sci USA 100,6422−7
282. Sandaltzopoulos, R., Quivy, J.P., Becker P.B. (1995) Analysis of protein/DNA interactions by solid-phase footprinting. Methods Mol. Cell. Biol. 5,176−181
283. Sauer, F., Fondell, J.D., Ohkuma, Y., Roeder, R.G., Jackie, H. (1995) Control of transcription by Kruppel through interactions with TFIIB and TFIIE beta. Nature 375,162−4
284. Sauer, F., Wassarman, D.A., Rubin, G.M., Tjian, R. (1996) TAF (II)s mediate activation of transcription in the Drosophila embryo. Cell 87,1271−84
285. Saurin, A.J., Shao Z., et. al. (2001) A Drosophila Polycomb group complex includes Zeste and dTAFII protein. Nature 412, 655−660
286. Seeler, J.S., Dejean, A. (2003) Nuclear and unclear functions of SUMO. Nat Rev Mol Cell Biol A, 690−9
287. Sendra, R., Tse, C., Hansen, J.C. (2000) The yeast histone acetyltransferase A2 complex, but not free Gcn5p, binds stably to nucleosomal arrays. J Biol Chem 275, 24 928−34
288. Shamay, M., Barak, O., Shaul, Y. (2002) HBXAP, a novel PHD-finger protein, possesses transcription repression activity. Genomics 79, 523−9
289. Shen, W.C., Bhaumik, S.R., Causton, H.C., Simon, I., Zhu, X., Jennings, E.G.,
290. Wang, Т.Н., Young, R.A., Green, M.R. (2003) Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly. EMBO J22, 3395−402
291. Shikama, N., Chan, H.M., Krstic-Demonacos, M., Smith, L., Lee, C.W., Cairns, W., La Thangue, N.B. (2000) Functional interaction between nucleosome assembly proteins and p300/CREB-binding protein family coactivators. Mol Cell Biol 20, 8933−43
292. Shimono, Y., Murakami, H., Kawai, K., Wade, P.A., Shimokata, K., Takahashi, M. (2003) Mi-2 beta associates with BRG1 and RET finger protein at the distinct regions with transcriptional activating and repressing abilities. J Biol Chem 278, 51 638−45
293. Shimono, Y., Murakami, H., Kawai, K., Wade, P.A., Shimokata, K., Takahashi, M. (2003) Mi-2 beta associates with BRG1 and RET finger protein at the distinct regions with transcriptional activating and repressing abilities. J Biol Chem 278, 51 638−45
294. Shuen, M., Awakumov, N., Torchia, J., Mymryk, J.S. (2003) The El A proteins of all six human adenovirus subgroups target the рЗОО/CBP acetyltransferases and the SAGA transcriptional regulatory complex. Virology 316,75−83
295. Sims, R.J. 3rd, Belotserkovskaya, R., Reinberg, D. (2004) Elongation by RNA polymerase II: the short and long of it. Genes Dev 18, 2437−68
296. Sims, R.J. 3rd, Mandal, S.S., Reinberg, D. (2004) Recent highlights of RNA-polymerase-II-mediated transcription. Curr Opin Cell Biol 16,263−71
297. Smale, S.T., Kadonaga, J.T. (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72,449−79
298. Smith, E.R., Belote, J.M., Schiltz, R.L., Yang, X.J., Moore, P.A., Berger, S.L., Nakatani, Y., Allis, C.D. (1998) Cloning of Drosophila GCN5: conserved features among metazoan GCN5 family members. Nucleic Acids Res 26,2948−54
299. Smith, E.R., Eisen, A., Gu, W., Sattah, M., Pannuti, A" Zhou, J., Cook, R.G., Lucchesi, J.C., Allis, C.D. (1998) ESA1 is a histone acetyltransferase that is essential for growth in yeast. Proc Natl Acad Sci US A 95,3561−5
300. Smith, E.R., Pannuti, A., Gu, W., Steurnagel, A., Cook, R.G., Allis, C.D., Lucchesi, J.C. (2000) The drosophila MSL complex acetylates histone H4 at lysine 16, a chromatin modification linked to dosage compensation. Mol Cell Biol 20, 312−8
301. Spector, D.L. (2001) Nuclear domains. J Cell Sci 114,2891−3
302. Spradling, A.C., Rubin, G.M. (1982) Transposition of cloned P elements into Drosophila germ line chromosomes. Science 218, 341−7
303. Sterner, D.E., Berger, S.L. (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64, 435−59
304. Studitsky, V.M., Walter, W., Kireeva, M., Kashlev, M., Felsenfeld, G. (2004)
305. Chromatin remodeling by RNA polymerases. Trends Biochem Sci 29, 127−35
306. Sudarsanam, P., Iyer, V.R., Brown, P.O., Winston, F. (2000) Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci USA91, 3364−9
307. Sun, F.L., Cuaycong, M.H., Craig, C.A., Wallrath, L.L., Locke, J., Elgin, S.C. (2000) The fourth chromosome of Drosophila melanogaster: interspersed euchromatic and heterochromatic domains. Proc Natl Acad Sci U S A 91, 5340−5
308. Svejstrup, J.Q. (2004) The RNA polymerase II transcription cycle: cycling through chromatin. Biochim Biophys Acta 1677, 64−73
309. Svejstrup, J.Q., Vichi, P., Egly, J.M. (1996) The multiple roles of transcription/repair factor TFIIH. Trends Biochem Sci 21, 346−50
310. Syntichaki, P., Topalidou, I., Thireos, G. (2000) The Gcn5 bromodomain coordinates nucleosome remodelling. Nature 404, 414−7
311. Taatjes, D.J., Naar, A.M., Andel, F. 3rd, Nogales, E., Tjian, R. (2002) Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295, 1058−62
312. Taatjes, D.J., Marr, M.T., Tjian, R. (2004) Regulatory diversity among metazoan co-activator complexes. Nat Rev Mol Cell Biol 5,403−10
313. Takechi, S., Nakayama, T. (1999) Sas3 is a histone acetyltransferase and requires a zinc finger motif. Biochem Biophys Res Commun 266, 405−10
314. Tansey, W.P., Herr, W. (1997) TAFs: guilt by association? Cell 88, 729−32
315. Thiagalingam, S., Cheng, K.H., Lee, H.J., Mineva, N., Thiagalingam, A., Ponte, J.F. (2003) Histone deacetylases: unique players in shaping the epigenetic histone code. Ann NY Acad Sci 983, 84−100
316. Thiel, G., Lietz, M., Bach, K., Guethlein, L., Cibelli, G. (2001) Biological activity of mammalian transcriptional repressors. Biol Chem 382, 891−902
317. Thut, C.J., Chen, J.L., Klemm, R., Tjian, R. (1995) p53 transcriptional activation mediated by coactivators TAFII40 and TAFII60. Science 267,100−4
318. Tjian, R., Maniatis, T. (1994) Transcriptional activation: a complex puzzle with few easy pieces. Cell 11, 5−8
319. Tora, L. (2002) A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev 16, 673−5
320. Tsukiyama, T. (2002) The in vivo functions of ATP-dependent chromatin-remodelling factors. Nat Rev Mol Cell Biol 3, 422−9
321. Tupler, R., Perini, G., Green, M.R. (2001) Expressing the human genome. Nature 409, 832−3
322. Tyler, J.K. (2002) Chromatin assembly. Cooperation between histone chaperones223and ATP-dependent nucleosome remodeling machines. Eur J Biochem 269, 226 874
323. Veenstra, G.J., Wolffe, A.P. (2001) Gene-selective developmental roles of general transcription factors. Trends Biochem Sci 26, 665−71
324. Veenstra, G.J., Wolffe, A.P. (2001) Gene-selective developmental roles of general transcription factors. Trends Biochem Sci 26, 665−71
325. Verrijzer, C.P., Chen, J.L., Yokomori, K., Tjian, R. (1995) Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 81,1115−25
326. Verrijzer, C.P., Tjian, R. (1996) TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem Sci 21, 338−42
327. Vettese-Dadey, M" Grant, P.A., Hebbes, T.R., Crane- Robinson, C., Allis, C.D., Workman, J.L. (1996) Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J15, 2508−18
328. Vignali, M., Hassan, A.H., Neely, K.E., Workman, J.L. (2000) ATP-dependent chromatin-remodeling complexes. Mol Cell Biol 20,1899−910
329. Vogel, J.L., Kristie, T.M. (2000) Autocatalytic proteolysis of the transcription factor-coactivator CI (HCF): a potential role for proteolytic regulation of coactivator function. Proc Natl Acad Sci USA91, 9425−30
330. Waga, S., Mizuno, S., Yoshida, M. (1990) Chromosomal protein HMG1 removes the transcriptional block caused by the cruciform in supercoiled DNA. J Biol Chem 265,19 424−8
331. Wallrath, L.L. (1998) Unfolding the mysteries of heterochromatin. Curr Opin Genet Dev 8, 147−53
332. Wallrath, L.L., Elgin, S.C. (1995) Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev 9,1263−77
333. Wanker, E.E., Rovira, C., Scherzinger, E., Hasenbank, R., Walter, S., Tait, D., Colicelli, J., Lehrach, H. (1997) HIP-I: a huntingtin interacting protein isolated by the yeast two-hybrid system. Hum Mol Genet 6,487−95
334. Wassarman, D.A., Aoyagi, N., Pile, L.A., Schlag, E.M. (2000) TAF250 is required for multiple developmental events in Drosophila. Proc Natl Acad Sci JJ S A 91, 1154−9
335. Weiler, K.S., Wakimoto, B.T. (1995) Heterochromatin and gene expression in Drosophila. Annu Rev Genet 29, 577−605
336. Wery, M., Shematorova, E., Van Driessche, В., Vandenhaute, J., Thuriaux, P., Van Mullem, V. (2004) Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J 23, 4232−42
337. Whitmarsh, A.J., Davis, R.J. (2000) Regulation of transcription factor function by phosphorylation. Cell Mol Life Sci 57, 1172−83
338. Wieczorek, E., Brand, M., Jacq, X., Tora, L. (1998) Function of TAF (II)-containing complex without TBP in transcription by RNA polymerase II. Nature 393,187−91
339. Winkler, G.S., Kristjuhan, A., Erdjument-Bromage, H., Tempst, P., Svejstrup, J.Q. (2002) Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo. Proc Natl Acad Sci USA 99, 3517−22
340. Winkler, G.S., Petrakis, T.G., Ethelberg, S., Tokunaga, M., Erdjument-Bromage, H., Tempst, P., Svejstrup, J.Q. (2001) RNA polymerase II elongator holoenzyme is composed of two discrete subcomplexes. J Biol Chem 276, 32 743−9
341. Winston, F., Sudarsanam, P. (1998) The SAGA of Spt proteins and transcriptional analysis in yeast: past, present, and future. Cold Spring Harb Symp Quant Biol 63, 553−61
342. Wittschieben, B.O., Fellows, J., Du, W., Stillman, D.J., Svejstrup, J.Q. (2000) Overlapping roles for the histone acetyltransferase activities of SAGA and elongator in vivo. EMBO J19,3060−8
343. Woychik, N.A., Hampsey, M. (2002) The RNA polymerase II machinery: structure illuminates function. Cell 108,453−63
344. Wyrick, J.J., Young, R.A. (2002) Deciphering gene expression regulatory networks. Curr Opin Genet Dev 12, 130−6
345. Xu, W., Edmondson, D.G., Roth, S.Y. (1998) Mammalian GCN5 and P/CAF acetyltransferases have homologous amino-terminal domains important for recognition of nucleosomal substrates. Mol Cell Biol 18, 5659−69
346. Yamagoe, S., et al (2003) Interaction of histone acetylases and deacetylases in vivo. Mol Cell Biol 23, 1025−33
347. Yamamoto, Т., Horikoshi, M. (1997) Novel substrate specificity of the histone acetyltransferase activity of HIV-1-Tat interactive protein Tip60. J Biol Chem 272, 30 595−8
348. Yanagisawa, J., et al (2002) Nuclear receptor function requires a TFTC-type histone acetyl transferase complex. Mol Cell 9, 553−62
349. Yang, X.J. (2004) The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res 32, 959−76
350. Yang, X.J., Ogryzko, V.V., Nishikawa, J., Howard, B.H., Nakatani, Y. (1996) A рЗОО/CBP-associated factor that competes with the adenoviral oncoprotein El A. Nature 382, 319−24
351. Yudkovsky, N., Ranish, J.A., Hahn, S. (2000) A transcription reinitiation intermediate that is stabilized by activator. Nature 408,225−9
352. Zhang, Y. (2003) Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev 17, 2733−40
353. Zhao, C., Meng, A. (2005) Spl-like transcription factors are regulators of embryonic development in vertebrates. Dev Growth Differ 47, 201−11
354. Zhen, L., Swank, R.T. (1993) A simple and high yeld method for recovering DNA from agarose gels. BioTech 14, 894−8
355. Zurita, M., Merino, C. (2003) The transcriptional complexity of the TFIIH complex. Trends Genet 19, 578−84
356. Георгиева, С.Г., Набирочкина, E.H., Ладыгина, Н.Г., Георгиев, П.Г., Солдатов, А.В. (2001) Ядерный белок е (у)2 Drosophila melanogaster участвует в контроле транскрипции. Генетика 37, 24−8
357. Георгиева С.Г., Е.Н.Набирочкина, М. В. Пустовойтов, А. Н. Краснов,.А. В. Солдатов (2001) Молекулярная характеристика нового эволюционно консервативного ядерного белка е (у)2. Генетика 37(1), 18−23
358. Голл, Дж. (2003) Роль телец Кахала в сборке ядерного аппарата транскрипции. Цитология 45, 971−5
359. Набирочкина Е.Н., А.В.Солдатов, С. Г. Георгиева. Два гомолога человеческого TAFII30 у Drosophila melanogaster имеют различающиеся функции. Доклады Академии наук 376,423−425
360. Набирочкина Е.Н., А.В.Солдатов, С. Г. Георгиева (2000) Молекулярная характеристика двух новых гомологов TAFII30 у Drosophila melanogaster. Молекулярная биология 34(5), 783−787(Abstract)
361. Жимулев, И.Ф., Беляева, Е.С. (2003) Гетерохроматин, эффект положения гена и сайленсинг гена. Генетика 39,187−201
362. Козицына, М.В., Георгиев, П.Г. (1992) Получение и анализ новых мутаций гена mod (mdg4) у Drosophila melanogaster. Генетика 28, 75−82
363. Лебедева, Л.А., Тиллиб, С.В. (2003) Глобальный фактор поддержания тканеспецифичного активного состояния генов Drosophila melanogaster, белок Tritorax, ассоциирован с ядерным матиксом. Генетика 39,250−8
364. Патрушев, Л.И. (2000) Экспрессия генов Наука, Москва
365. Солдатов А.В., Набирочкина Е. Н., Дзитоева С. Г., Матюнина JI.B., Георгиев П.Г. (1996) Генетика 32,1714−1716
366. Сьяксте, Н.И., Сьяксте, Т.Г. (2001) Транскрипционные факторы и ядерный матрикс. Молекулярная биология 35, 739−49
367. Фрешни Р. (1989) Культура животных клеток. Методы, Москва, издательство «Мир», 331 стр. 1. БЛАГОДАРНОСТИ
368. Отдельно хочется поблагодарить дирекцию Института биологии гена РАН за обеспечение условий для научных исследований, а также коллектив института за создание атмосферы доброжелательности и взаимопомощи.