Chromatin organization and transcriptional control of gene expression in Drosophila

Gene

Volumn 253, Issue 2, 2000, Pages 117-136

  Farkas, Gabriella ^a   Leibovitch, Boris A ^a   Elgin, Sarah C R ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Cellular memory; Chromatin remodeling complexes; Gene silencing; Heat shock genes; PcG and trxG proteins

Indexed keywords

DNA BINDING PROTEIN; HEAT SHOCK PROTEIN;

CELL NUCLEUS; CHROMATIN STRUCTURE; DNA PACKAGING; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; DROSOPHILA; GENE EXPRESSION REGULATION; GENE SILENCING; GENOME; HOMEOBOX; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; REGULATOR GENE; REVIEW; TRANSCRIPTION REGULATION;

ANIMALS; CHROMATIN; DROSOPHILA; GENE EXPRESSION REGULATION; NUCLEOSOMES; TRANSCRIPTION, GENETIC;

EID: 0034622637     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(00)00240-7     Document Type: Review

References (160)

1. Adams C.R., Kamakaka R.T. Chromatin assembly: biochemical identities and genetic redundancy. Curr. Opin. Genet. Dev. 9:1999;185-190.
2. Arkhipova I.R. Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics. 139:1995;1359-1369.
3. Bate M., Arias A.M. The Development of Drosophila melanogaster. 1993;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
4. Bell A.C., Felsenfeld G. Stopped at the border: boundaries and insulators. Curr. Opin. Genet. Dev. 9:1999;191-198.
5. Bender W., Akam M., Karch F., Beachy P.A., Peifer M., Spierer P., Lewis E.B., Hogness D.S. Molecular genetics of the bithorax complex in Drosophila melanogaster. Science. 221:1983;23-29.
6. Benyajati C., Mueller L., Xu N., Pappano M., Gao J., Mosammaparast M., Conklin D., Granok H., Craig C., Elgin S.C.R. Multiple isoforms of GAGA factor a critical component of chromatin structure. Nucleic Acids Res. 25:1997;3345-3353.
7. Bhat K.M., Farkas G., Karch F., Gyurkovics H., Gausz J., Schedl P. The GAGA factor is required in the early Drosophila embryo not only for transcriptional regulation but also for nuclear division. Development. 122:1996;1113-1124.
8. Biggin M.D., Tjian R. Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts. Cell. 53:1988;699-711.
9. Brand A.H., Manoukian A.S., Perrimon N. Ectopic expression in Drosophila. Meth. Cell. Biol. 44:1994;635-654.
10. Breiling A., Bonte E., Ferrari S., Becker P.B., Paro R. The Drosophila Polycomb protein interacts with nucleosomal core particles in vitro via its repression domain. Mol. Cell. Biol. 19:1999;8451-8460.
11. Brown K.E., Guest S.S., Smale S.T., Hahm K., Merkenschlager M., Fisher A.G. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell. 91:1997;845-854.
12. Brown J.L., Mucci D., Whiteley M., Dirksen M.L., Kassis J.A. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol. Cell. 1:1998;1057-1064.
13. Buchenau P., Hodgson J., Strutt H., Arndt-Jovin D.J. The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. J. Cell Biol. 141:1998;469-481.
14. Busturia A., Bienz M. Silencers in abdominal-B, a homeotic Drosophila gene. EMBO J. 12:1993;1415-1425.
15. Cairns B.R. Chromatin remodeling machines: similar motors ulterior motives. Trends Biochem. Sci. 23:1998;20-25.
16. Carrington E.A., Jones R.S. The Drosophila Enhancer of zeste gene encodes a chromosomal protein: examination of wild-type and mutant protein distribution. Development. 12:1996;4073-4083.
17. Cartwright I.L., Elgin S.C.R. Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster. Mol. Cell. Biol. 6:1986;779-791.
18. Cavalli G., Paro R. The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell. 93:1998;505-518.
19. Cavalli G., Paro R. Epigenetic inheritance of active chromatin after removal of the main transactivator. Science. 286:1999;955-958.
20. Chan C.S., Rastelli L., Pirrotta V. A Polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression. EMBO J. 13:1994;2553-2564.
21. Chiang A., O'Connor M.B., Paro R., Simon J., Bender W. Discrete Polycomb-binding sites in each parasegmental domain of the bithorax complex. Development. 121:1995;1681-1689.
22. Chinwalla V., Jane E.P., Harte P.J. The Drosophila trithorax protein binds to specific chromosomal sites and is co-localized with Polycomb at many sites. EMBO J. 14:1995;2056-2065.
23. Corona D.F.V., Langst G., Clapier C.R., Bonte E.J., Ferrari S., Tamkun J.W., Becker P.B. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell. 3:1999;239-245.
24. Crosby M.A., Miller C., Alon T., Watson K.L., Verrijzer C.P., Goldman-Levi R., Zak N.B. The trithorax group gene moira encodes a brahma-associated putative chromatin-remodeling factor in Drosophila melanogaster. Mol. Cell. Biol. 19:1999;1159-1170.
25. Croston G.E., Kerrigan L.A., Lira L.M., Marshak D.R., Kadonaga J.T. Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science. 251:1991;643-649.
26. Cryderman D.E., Morris E.J., Biessmann H., Elgin S.C.R., Wallrath L.L. Silencing at Drosophila telomeres: nuclear organization and chromatin structure play critical roles. EMBO J. 18:1999;3724-3735.
27. Cryderman D.E., Tang H., Bell C., Gilmour D.S., Wallrath L.L. Heterochromatic silencing of Drosophila heat shock genes acts at the level of promoter potentiation. Nucleic Acids Res. 27:1999;3364-3370.
28. Daubresse G., Deuring R., Moore L., Papoulas O., Zakrajsek I., Waldrip W.R., Scott M.P., Kennison J.A., Tamkun J.W. The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. Development. 126:1999;1175-1187.
29. Dietzel S., Niemann H., Bruckner B., Maurange C., Paro R. The nuclear distribution of Polycomb during Drosophila melanogaster development shown with a GFP fusion protein. Chromosoma. 108:1999;83-94.
30. Duncan I. The bithorax complex. Annu. Rev. Genet. 21:1987;285-319.
31. Elfring L.K., Deuring R., McCallum C.M., Peterson C.L., Tamkun J.W. Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2. Mol. Cell. Biol. 14:1994;2225-2234.
32. Elgin S.C.R. The formation and function of DNase I hypersensitive sites in the process of gene activation. J. Biol. Chem. 263:1988;19259-19262.
33. Espinas M.L., Jimenez-Garcia E., Vaquero A., Canudas S., Bernues J., Azorin F. The N-terminal POZ domain of GAGA mediates the formation of oligomers that bind DNA with high affinity and specificity. J. Biol. Chem. 274:1999;16461-16469.
34. Farkas G., Gausz J., Galloni M., Reuter G., Gyurkovics H., Karch F. The Trithorax-like gene encodes the Drosophila GAGA factor. Nature. 371:1994;806-808.
35. Foe V.E., Odell G.M., Edgar B.A. Mitosis and morphogenesis in the Drosophila embryo: point and counterpoint. Bate M., Arias A.M. The Development of Drosophila melanogaster. 1993;149-300 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
36. Franke A., DeCamillis M., Zink D., Cheng N., Brock H.W., Paro R. Polycomb and polyhomeotic are constituents of a multimeric protein complex in chromatin of Drosophila melanogaster. EMBO J. 11:1992;2941-2950.
37. Fritsch C., Brown J.L., Kassis J.A., Muller J. The DNA-binding Polycomb group protein Pleiohomeotic mediates silencing of a Drosophila homeotic gene. Development. 126:1999;3905-3913.
38. Gasser S.M., Paro R., Stewart F., Aasland R. The genetics of epigenetics. Cell. Mol. Life Sci. 54:1998;1-5.
39. Gdula D.A., Sandaltzopoulos R., Tsukiyama T., Ossipow V., Wu C. Inorganic pyrophosphatase is a component of the Drosophila nucleosome remodeling factor complex. Genes Dev. 12:1998;3206-3216.
40. Gellon G., McGinnis W. Shaping animal body plans in development and evolution by modulation of Hox expression patterns. Bioessays. 20:1998;116-125.
41. Georgel P.T., Tsukiyama T., Wu C. Role of histone tails in nucleosome remodeling by Drosophila NURF. EMBO J. 16:1997;4717-4726.
42. Gerasimova T.I., Corces V.G. Polycomb and trithorax group proteins mediate the function of a chromatin insulator. Cell. 92:1998;511-521.
43. Giancotti V., Russo E., de Cristini F., Graziosi G., Micali F., Crane-Robinson C. Histone modification in early and late Drosophila embryos. Biochem. J. 218:1984;321-329.
44. Gindhart J.G., Kaufman T.C. Identification of Polycomb and trithorax group responsive elements in the regulatory region of the Drosophila homeotic gene Sex combs reduced. Genetics. 139:1995;797-814.
45. Granok H., Leibovitch B.A., Shaffer C.D., Elgin S.C.R. Chromatin Ga-ga over GAGA factor. Curr. Biol. 5:1995;238-241.
46. Gross D.S., Garrard W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57:1988;159-197.
47. Grunstein M. Histone acetylation in chromatin structure and transcription. Nature. 389:1997;349-352.
48. Hagstrom K., Schedl P. Remembrance of things past: maintaining gene expression patterns with altered chromatin. Curr. Opin. Genet. Dev. 7:1997;814-821.
49. Hagstrom K., Muller M., Schedl P. A Polycomb and GAGA dependent silencer adjoins the Fab-7 boundary in the Drosophila bithorax complex. Genetics. 146:1997;1365-1380.
50. Hamiche A., Sandaltzopoulos R., Gdula D.A., Wu C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell. 97:1999;833-842.
51. Horard B., Tatout C., Poux S., Pirrotta V. Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor. Mol. Cell. Biol. 20:2000;3187-3197.
52. Ioshikhes I., Trifonov E.N., Zhang M.Q. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. USA. 96:1999;2891-2895.
53. Ito T., Bulger M., Pazin M.J., Kobayashi R., Kadonaga J.T. ACF an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell. 90:1997;145-155.
54. Ito T., Levenstein M.E., Fyodorov D.V., Kutach A.K., Kobayashi R., Kadonaga J.T. ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13:1999;1529-1539.
55. Jones R.S., Gelbart W.M. The Drosophila Polycomb-group gene Enhancer of zeste contains a region with sequence similarity to trithorax. Mol. Cell. Biol. 13:1993;6357-6366.
56. Jones C.A., Ng J., Peterson A.J., Morgan K., Simon J., Jones R.S. The Drosophila esc and E(z) proteins are direct partners in polycomb group-mediated repression. Mol. Cell. Biol. 18:1998;2825-2834.
57. Karch F., Galloni M., Sipos L., Gausz J., Gyurkovics H., Schedl P. Mcp and Fab-7: molecular analysis of putative boundaries of cis-regulatory domains in the bithorax complex of Drosophila melanogaster. Nucleic Acids Res. 22:1994;3138-3146.
58. Kassis J.A., VanSickle E.P., Sensabaugh S.M. A fragment of engrailed regulatory DNA can mediate transvection of the white gene in Drosophila. Genetics. 128:1991;751-761.
59. Kassis J.A. Unusual properties of regulatory DNA from the Drosophila engrailed gene: three 'pairing-sensitive' sites within a 1.6-kb region. Genetics. 136:1994;1025-1038.
60. Katsani K.R., Hajibagheri M.A.N., Verrijzer C.P. Co-operative DNA binding by GAGA transcription factor requires the conserved BTB/POZ domain and reorganizes promoter topology. EMBO J. 18:1999;698-708.
61. Kehle J., Beuchle D., Treuheit S., Christen B., Kennison J.A., Bienz M., Muller J. dMi-2, a hunchback-interacting protein that functions in polycomb repression. Science. 282:1998;1897-1900.
62. Kennison J.A., Tamkun J.W. Dosage-dependent modifiers of polycomb and antennapedia mutations in Drosophila. Proc. Natl. Acad. Sci. USA. 85:1988;8136-8140.
63. Kennison J.A. Transcriptional activation of Drosophila homeotic genes from distant regulatory elements. Trends Genet. 9:1993;75-79.
64. Kennison J.A. The Polycomb and trithorax group proteins of Drosophila: trans-regulators of homeotic gene function. Annu. Rev. Genet. 29:1995;289-303.
65. Kingston R.E., Narlikar G.J. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13:1999;2339-2352.
66. Kornberg A. On the metabolic significance of phosphorolytic and pyrophosphorolytic reactions. Kasha M., Pullman B. Horizons in Biochemistry. 1962;251-264 Academic Press, New York.
67. Kornberg R.D., Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell. 98:1999;285-294.
68. Krude T. Chromatin assembly during DNA replication in somatic cells. Eur. J. Biochem. 263:1999;1-5.
69. Kyba M., Brock H.W. The Drosophila polycomb group protein Psc contacts ph and Pc through specific conserved domains. Mol. Cell. Biol. 18:1998;2712-2720.
70. LaJeunesse D., Shearn A. E(z): a polycomb group gene or a trithorax group gene? Development. 122:1996;2189-2197.
71. Lamond A.I., Earnshaw W.C. Structure and function in the nucleus. Science. 280:1998;547-553.
72. Langst G., Bonte E.J., Corona D.F.V., Becker P.B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell. 97:1999;843-852.
73. Law A., Hirayoshi K., O'Brien T., Lis J.T. Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila. Nucleic Acids Res. 26:1998;919-924.
74. Leibovitch B.A., Benjamin L.R., Gilmour D.S., Elgin S.C.R. The TFIID binding region is required for formation of DH sites at the hsp26 gene promoter. Abstract of the Symposium on the Eukaryotic Nucleus, Coolfront, WV. 1999.
75. Lewis E.B. A gene complex controlling segmentation in Drosophila. Nature. 276:1978;565-570.
76. Lewis E.B., Knafels J.D., Mathog D.R., Celniker S.E. Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila. Proc. Natl. Acad. Sci. USA. 92:1995;8403-8407.
77. Lis J., Wu C. Promoter potentiation and activation: chromatin structure and transcriptional induction of heat shock genes. Elgin S.C.R. Chromatin Structure and Gene Expression. 1995;71-88 IRL Press, Oxford.
78. Lonie A., D'Andrea R., Paro R., Saint R. Molecular characterisation of the Polycomblike gene of Drosophila melanogaster, a trans-acting negative regulator of homeotic gene expression. Development. 120:1994;2629-2636.
79. Lowenhaupt K., Cartwright I.L., Keene M.A., Zimmerman J.L., Elgin S.C.R. Chromatin structure in pre- and postblastula embryos of Drosophila. Dev. Biol. 99:1983;194-201.
80. Lu Q., Wallrath L.L., Granok H., Elgin S.C.R. CT)n·(GA)n repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene. Mol. Cell. Biol. 13:1993;2802-2814.
81. Lu Q., Wallrath L.L., Emanuel P.E., Elgin S.C.R., Gilmour D.S. Insensitivity of the preset hsp26 chromatin structure to a TATA box mutation in Drosophila. J. Biol. Chem. 269:1994;15906-15911.
82. Lu Q., Wallrath L.L., Elgin S.C.R. The role of a positioned nucleosome at the Drosophila melanogaster hsp26 promoter. EMBO J. 14:1995;4738-4746.
83. Lyko F., Paro R. Chromosomal elements conferring epigenetic inheritance. Bioessays. 21:1999;824-832.
84. Martin C.H., Mayeda C.A., Davis C.A., Ericsson C.L., Knafels J.D., Mathog D.R., Celniker S.E., Lewis E.B., Palazzolo M.J. Complete sequence of the bithorax complex of Drosophila. Proc. Natl. Acad. Sci. USA. 92:1995;8398-8402.
85. Martinez-Balbas M.A., Dey A., Rabindran S.K., Ozato K., Wu C. Displacement of sequence-specific transcription factors from mitotic chromatin. Cell. 83:1995;29-38.
86. Martinez-Balbas M.A., Tsukiyama T., Gdula D., Wu C. Drosophila NURF-55, a WD repeat protein involved in histone metabolism. Proc. Natl. Acad. Sci. USA. 95:1998;132-137.
87. Mason P.B., Lis J.T. Cooperative and competitive protein interactions at the hsp70 promoter. J. Biol. Chem. 272:1997;33227-33233.
88. Michelotti E.F., Sanford S., Levens D. Marking of active genes on mitotic chromosomes. Nature. 388:1997;895-899.
89. Mihaly J., Hogga I., Gausz J., Gyurkovics H., Karch F. In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element. Development. 124:1997;1809-1820.
90. Mihaly J., Hogga I., Barges S., Galloni M., Mishra R.K., Hagstrom K., Muller M., Schedl P., Sipos L., Gausz J., Gyurkovics H., Karch F. Chromatin domain boundaries in the bithorax complex. Cell. Mol. Life Sci. 54:1998;60-70.
91. Mihaly J., Mishra R.K., Karch F. A conserved sequence motif in Polycomb-response elements. Mol. Cell. 1:1998;1065-1066.
92. Milne T.A., Sinclair D.A., Brock H.W. The Additional sex combs gene of Drosophila is required for activation and repression of homeotic loci, and interacts specifically with Polycomb and super sex combs. Mol. Gen. Genet. 261:1999;753-761.
93. Mizuguchi G., Tsukiyama T., Wisniewski J., Wu C. Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin. Mol. Cell. 1:1997;141-150.
94. Morimoto R.I., Tissieres A., Georgopoulos C. Progress and perspectives on the biology of heat shock proteins and molecular chaperones. Morimoto R.I., Tissieres A., Georgopoulos C. The Biology of Heat Shock Proteins and Molecular Chaperones. 1994;1-30 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
95. Muchardt C., Yaniv M. ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job. J. Mol. Biol. 293:1999;187-198.
96. Muller J., Bienz M. Long range repression conferring boundaries of Ultrabithorax expression in the Drosophila embryo. EMBO J. 10:1991;3147-3155.
97. Muller M., Hagstrom K., Gyurkovics H., Pirrotta V., Schedl P. The Mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions. Genetics. 153:1999;1333-1356.
98. Nightingale K.P., Wellinger R.E., Sogo J.M., Becker P.B. Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin. EMBO J. 17:1998;2865-2876.
99. O'Brien T., Lis J.T. Rapid changes in Drosophila transcription after an instantaneous heat shock. Mol. Cell. Biol. 13:1993;3456-3463.
100. O'Brien T., Wilkins R.C., Giardina C., Lis J.T. Distribution of GAGA protein on Drosophila genes in vivo. Genes Dev. 9:1995;1098-1110.
101. Orlando V., Paro R. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Cell. 75:1993;1187-1198.
102. Orlando V., Jane E.P., Chinwalla V., Harte P.J., Paro R. Binding of Trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J. 17:1998;5141-5150.
103. Papoulas O., Beek S.J., Moseley S.L., McCallum C.M., Sarte M., Shearn A., Tamkun J.W. The Drosophila trithorax group proteins BRM, ASH1 and ASH2 are subunits of distinct protein complexes. Development. 125:1998;3955-3966.
104. Pazin M.J., Bhargava P., Geiduschek E.P., Kadonaga J.T. Nucleosome mobility and the maintenance of nucleosome positioning. Science. 276:1997;809-812.
105. Pazin M.J., Kadonaga J.T. Transcriptional and structural analysis of chromatin assembled in vitro. Gould H. Chromatin. A Practical Approach. 1998;173-194 Oxford University Press, Oxford.
106. Pirrotta V. Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression. Trends Genet. 13:1997;314-318.
107. Pirrotta V. Polycomb silencing and the maintenance of stable chromatin states. Results Probl. Cell. Differ. 25:1999;205-228.
108. Platero J.S., Csink A.M., Quintanilla A., Henikoff S. Changes in chromosomal localization of heterochromatin-binding proteins during the cell cycle in Drosophila. J. Cell Biol. 140:1998;1297-1306.
109. Poux S., Kostic C., Pirrotta V. Hunchback-independent silencing of late Ubx enhancers by a Polycomb Group Response Element. EMBO J. 15:1996;4713-4722.
110. Raff J.W., Kellum R., Alberts B. The Drosophila GAGA transcription factor is associated with specific regions of heterochromatin throughout the cell cycle. EMBO J. 13:1994;5977-5983.
111. Schild C., Claret F.X., Wahli W., Wolffe A.P. A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J. 12:1993;423-433.
112. Shao Z., Raible F., Mollaaghababa R., Guyon J.R., Wu C.T., Bender W., Kingston R.E. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell. 98:1999;37-46.
113. Shopland L.S., Hirayoshi K., Fernandes M., Lis J.T. HSF access to heat shock elements in vivo depends critically on promoter architecture defined by GAGA factor, TFIID, and RNA polymerase II binding sites. Genes Dev. 9:1995;2756-2769.
114. Shrader T.E., Crothers D.M. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. USA. 86:1989;7418-7422.
115. Sigrist C.J., Pirrotta V. Chromatin insulator elements block the silencing of a target gene by the Drosophila polycomb response element (PRE) but allow trans interactions between PREs on different chromosomes. Genetics. 147:1997;209-221.
116. Simon J., Peifer M., Bender W., OConnor M. Regulatory elements of the bithorax complex that control expression along the anterior-posterior axis. EMBO J. 9:1990;3945-3956.
117. Simon J. Locking in stable states of gene expression: transcriptional control during Drosophila development. Curr. Opin. Cell Biol. 7:1995;376-385.
118. Sinclair D.A., Milne T.A., Hodgson J.W., Shellard J., Salinas C.A., Kyba M., Randazzo F., Brock H.W. The Additional sex combs gene of Drosophila encodes a chromatin protein that binds to shared and unique Polycomb group sites on polytene chromosomes. Development. 125:1998;1207-1216.
119. Soeller W.C., Poole S.J., Kornberg T. In vitro transcription of the Drosophila engrailed gene. Genes Dev. 2:1988;68-81.
120. Sogo J.M., Laskey R.A. Chromatin replication and assembly. Elgin S.C.R. Chromatin Structure and Gene Expression. 1995;49-70 Oxford University Press, Oxford.
121. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature. 403:2000;41-45.
122. Struhl K. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell. 98:1999;1-4.
123. Strutt H., Paro R. The polycomb group protein complex of Drosophila melanogaster has different compositions at different target genes. Mol. Cell. Biol. 17:1997;6773-6783.
124. Strutt H., Cavalli G., Paro R. Co-localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J. 16:1997;3621-3632.
125. Tamkun J.W., Deuring R., Scott M.P., Kissinger M., Pattatucci A.M., Kaufmann T.C., Kennison J.A. brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2. Cell. 68:1992;561-572.
126. Thomas G.H., Elgin S.C.R. Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO J. 7:1988;2191-2201.
127. Thomas M.J., Seto E. Unlocking the mechanisms of transcription factor YY1: are chromatin modifying enzymes the key? Gene. 236:1999;197-208.
128. Tie F., Furuyama T., Harte P.J. The Drosophila Polycomb Group proteins ESC and E(Z) bind directly to each other and co-localize at multiple chromosomal sites. Development. 125:1998;3483-3496.
129. Tillib S., Petruk S., Sedkov Y., Kuzin A., Fujioka M., Goto T., Mazo A. Trithorax- and Polycomb-group response elements within an Ultrabithorax transcription maintenance unit consist of closely situated but separable sequences. Mol. Cell. Biol. 19:1999;5189-5202.
130. Travers A., Drew H. DNA recognition and nucleosome organization. Biopolymers. 44:1997;423-433.
131. Tsukiyama T., Becker P.B., Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature. 367:1994;525-532.
132. Tsukiyama T., Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell. 83:1995;1011-1020.
133. Tsukiyama T., Daniel C., Tamkun J., Wu C. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kD subunit of the nucleosome remodeling factor. Cell. 83:1995;1021-1026.
134. Tsukiyama T., Palmer J., Landel C.C., Shiloach J., Wu C. Characterization of the Imitation Switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13:1999;686-697.
135. Turner B.M. Histone acetylation as an epigenetic determinant of long-term transcriptional competence. Cell. Mol. Life Sci. 54:1998;21-31.
136. Tyler J.K., Bulger M., Kamakaka R.T., Kobayashi R., Kadonaga J.T. The p55 subunit of Drosophila chromatin assembly factor 1 is homologous to a histone deacetylase-associated protein. Mol. Cell. Biol. 16:1996;6149-6159.
137. Tyler J.K., Kadonaga J. The 'dark side' of chromatin remodeling: repressive effects on transcription. Cell. 99:1999;443-446.
138. Tyler J.K., Adams C.R., Chen S.R., Kobayashi R., Kamakaka R.T., Kadonaga J.T. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature. 402:1999;555-560.
139. Varga-Weisz P.D., Wilm M., Bonte E., Dumas K., Mann M., Becker P.B. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature. 388:1997;598-602.
140. Vazquez M., Moore L., Kennison J.A. The trithorax group gene osa encodes an ARID-domain protein that genetically interacts with the brahma chromatin-remodeling factor to regulate transcription. Development. 126:1999;733-742.
141. Vignali M., Hassan A.H., Neely K.E., Workman J.L. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20:2000;1899-1910.
142. Wade P.A., Jones P.L., Vermaak D., Wolffe A.P. A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr. Biol. 8:1998;843-846.
143. Wall G., Varga-Weisz P.D., Sandaltzopoulos R., Becker P.B. Chromatin remodeling by GAGA factor and heat shock factor at the hypersensitive Drosophila hsp26 promoter in vitro. EMBO J. 14:1995;1727-1736.
144. Wallrath L.L., Lu Q., Granok H., Elgin S.C.R. Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays. 16:1994;165-170.
145. Wallrath L.L., Elgin S.C.R. Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev. 9:1995;1263-1277.
146. Wallrath L.L. Unfolding the mysteries of heterochromatin. Curr. Opin. Genet. Dev. 8:1998;147-153.
147. Weber J.A., Taxman D.J., Lu Q., Gilmour D.S. Molecular architecture of the hsp70 promoter after deletion of the TATA box or the upstream regulation region. Mol. Cell. Biol. 17:1997;3799-3808.
148. Weeks J.R., Hardin S.E., Shen J., Lee J.M., Greenleaf A.L. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 7:1993;2329-2344.
149. Weiler K.S., Wakimoto B.T. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 29:1995;577-605.
150. Whitehouse I., Flaus A., Cairns B.R., White M.F., Workman J.L., Owen-Hughes T. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature. 400:1999;784-787.
151. Widlund H.R., Kuduvalli P.N., Bengtsson M., Cao H., Tullius T.D., Kubista M. Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence. J. Biol. Chem. 274:1999;31847-31852.
152. Widom J. Equilibrium and dynamic nucleosome stability. Becker P.B. Chromatin Protocols. 1999;61-77 Humana Press, Totowa.
153. Wilkins R.C., Lis J.T. Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation. Nucleic Acids Res. 25:1997;3963-3968.
154. Wilkins R.C., Lis J.T. GAGA factor binding to DNA via a single trinucleotide sequence element. Nucleic Acids Res. 26:1998;2672-2678.
155. Wilkins R.C., Lis J.T. DNA distortion and multimerization: novel functions of the glutamine-rich domain of GAGA factor. J. Mol. Biol. 285:1999;515-525.
156. Wolffe A.P. Chromatin structure and DNA replication: implications for transcriptional activity. DePamphilis M.L. Concepts in Eukaryotic DNA Replication. 1999;271-293 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
157. Workman J.L., Kingston R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:1998;545-579.
158. Wu C., Clos J., Giorgi G., Haroun R.I., Kim S.J., Rabindran S.K., Westwood J.T., Wisniewski J., Yim G. Structure and regulation of heat shock transcription factor. Morimoto R.I., Tissieres A., Georgopoulos C. The Biology of Heat Shock Proteins and Molecular Chaperones. 1994;395-416 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
159. Wu C., Tsukiyama T., Gdula D., Georgel P., Martinez-Balbas M., Mizuguchi G., Ossipow V., Sandaltzopoulos R., Wang H.M. ATP-dependent remodeling of chromatin. Cold Spring Harb. Symp. Quant. Biol. 63:1998;525-534.
160. Zink D., Paro R. Drosophila Polycomb-group regulated chromatin inhibits the accessibility of a trans-activator to its target DNA. EMBO J. 14:1995;5660-5671.