Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes (original) (raw)

Abstract

Mechanisms controlling transcription and its regulation are fundamental to our understanding of molecular biology and, ultimately, cellular biology. Our knowledge of transcription initiation and integral factors such as RNA polymerase is considerable, and more recently our understanding of the involvement of enhancers and complexes such as holoenzyme and mediator has increased dramatically. However, an understanding of transcriptional repression is also essential for a complete understanding of promoter structure and the regulation of gene expression. Transcriptional repression in eukaryotes is achieved through 'silencers', of which there are two types, namely 'silencer elements' and 'negative regulatory elements' (NREs). Silencer elements are classical, position-independent elements that direct an active repression mechanism, and NREs are position-dependent elements that direct a passive repression mechanism. In addition, 'repressors' are DNA-binding trasncription factors that interact directly with silencers. A review of the recent literature reveals that it is the silencer itself and its context within a given promoter, rather than the interacting repressor, that determines the mechanism of repression. Silencers form an intrinsic part of many eukaryotic promoters and, consequently, knowledge of their interactive role with enchancers and other transcriptional elements is essential for our understanding of gene regulation in eukaryotes.

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Selected References

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  1. Afar R., Silverman R., Aguanno A., Albert V. R. Positive and negative elements contribute to the cell-specific expression of the rat dopamine beta-hydroxylase gene. Brain Res Mol Brain Res. 1996 Feb;36(1):79–92. doi: 10.1016/0169-328x(95)00247-p. [DOI] [PubMed] [Google Scholar]
  2. Alkema M. J., Bronk M., Verhoeven E., Otte A., van 't Veer L. J., Berns A., van Lohuizen M. Identification of Bmi1-interacting proteins as constituents of a multimeric mammalian polycomb complex. Genes Dev. 1997 Jan 15;11(2):226–240. doi: 10.1101/gad.11.2.226. [DOI] [PubMed] [Google Scholar]
  3. Amati B., Dalton S., Brooks M. W., Littlewood T. D., Evan G. I., Land H. Transcriptional activation by the human c-Myc oncoprotein in yeast requires interaction with Max. Nature. 1992 Oct 1;359(6394):423–426. doi: 10.1038/359423a0. [DOI] [PubMed] [Google Scholar]
  4. Antalis T. M., Costelloe E., Muddiman J., Ogbourne S., Donnan K. Regulation of the plasminogen activator inhibitor type-2 gene in monocytes: localization of an upstream transcriptional silencer. Blood. 1996 Nov 15;88(10):3686–3697. [PubMed] [Google Scholar]
  5. Arnold R., Burcin M., Kaiser B., Muller M., Renkawitz R. DNA bending by the silencer protein NeP1 is modulated by TR and RXR. Nucleic Acids Res. 1996 Jul 15;24(14):2640–2647. doi: 10.1093/nar/24.14.2640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Arnosti D. N., Gray S., Barolo S., Zhou J., Levine M. The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo. EMBO J. 1996 Jul 15;15(14):3659–3666. [PMC free article] [PubMed] [Google Scholar]
  7. Atouf F., Czernichow P., Scharfmann R. Expression of neuronal traits in pancreatic beta cells. Implication of neuron-restrictive silencing factor/repressor element silencing transcription factor, a neuron-restrictive silencer. J Biol Chem. 1997 Jan 17;272(3):1929–1934. doi: 10.1074/jbc.272.3.1929. [DOI] [PubMed] [Google Scholar]
  8. Ayer D. E., Lawrence Q. A., Eisenman R. N. Mad-Max transcriptional repression is mediated by ternary complex formation with mammalian homologs of yeast repressor Sin3. Cell. 1995 Mar 10;80(5):767–776. doi: 10.1016/0092-8674(95)90355-0. [DOI] [PubMed] [Google Scholar]
  9. Baker C. C., Ziff E. B. Promoters and heterogeneous 5' termini of the messenger RNAs of adenovirus serotype 2. J Mol Biol. 1981 Jun 25;149(2):189–221. doi: 10.1016/0022-2836(81)90298-9. [DOI] [PubMed] [Google Scholar]
  10. Baniahmad A., Ha I., Reinberg D., Tsai S., Tsai M. J., O'Malley B. W. Interaction of human thyroid hormone receptor beta with transcription factor TFIIB may mediate target gene derepression and activation by thyroid hormone. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8832–8836. doi: 10.1073/pnas.90.19.8832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Baniahmad A., Leng X., Burris T. P., Tsai S. Y., Tsai M. J., O'Malley B. W. The tau 4 activation domain of the thyroid hormone receptor is required for release of a putative corepressor(s) necessary for transcriptional silencing. Mol Cell Biol. 1995 Jan;15(1):76–86. doi: 10.1128/mcb.15.1.76. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Baniahmad A., Steiner C., Köhne A. C., Renkawitz R. Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site. Cell. 1990 May 4;61(3):505–514. doi: 10.1016/0092-8674(90)90532-j. [DOI] [PubMed] [Google Scholar]
  13. Bannister A. J., Kouzarides T. The CBP co-activator is a histone acetyltransferase. Nature. 1996 Dec 19;384(6610):641–643. doi: 10.1038/384641a0. [DOI] [PubMed] [Google Scholar]
  14. Barberis A., Superti-Furga G., Busslinger M. Mutually exclusive interaction of the CCAAT-binding factor and of a displacement protein with overlapping sequences of a histone gene promoter. Cell. 1987 Jul 31;50(3):347–359. doi: 10.1016/0092-8674(87)90489-2. [DOI] [PubMed] [Google Scholar]
  15. Bauknecht T., See R. H., Shi Y. A novel C/EBP beta-YY1 complex controls the cell-type-specific activity of the human papillomavirus type 18 upstream regulatory region. J Virol. 1996 Nov;70(11):7695–7705. doi: 10.1128/jvi.70.11.7695-7705.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Baumhueter S., Courtois G., Crabtree G. R. A variant nuclear protein in dedifferentiated hepatoma cells binds to the same functional sequences in the beta fibrinogen gene promoter as HNF-1. EMBO J. 1988 Aug;7(8):2485–2493. doi: 10.1002/j.1460-2075.1988.tb03095.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Bender T. P., Thompson C. B., Kuehl W. M. Differential expression of c-myb mRNA in murine B lymphomas by a block to transcription elongation. Science. 1987 Sep 18;237(4821):1473–1476. doi: 10.1126/science.3498214. [DOI] [PubMed] [Google Scholar]
  18. Bentley D. L., Groudine M. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells. Nature. 1986 Jun 12;321(6071):702–706. doi: 10.1038/321702a0. [DOI] [PubMed] [Google Scholar]
  19. Bentley D. L. Regulation of transcriptional elongation by RNA polymerase II. Curr Opin Genet Dev. 1995 Apr;5(2):210–216. doi: 10.1016/0959-437x(95)80010-7. [DOI] [PubMed] [Google Scholar]
  20. Bessis A., Champtiaux N., Chatelin L., Changeux J. P. The neuron-restrictive silencer element: a dual enhancer/silencer crucial for patterned expression of a nicotinic receptor gene in the brain. Proc Natl Acad Sci U S A. 1997 May 27;94(11):5906–5911. doi: 10.1073/pnas.94.11.5906. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Bird A. The essentials of DNA methylation. Cell. 1992 Jul 10;70(1):5–8. doi: 10.1016/0092-8674(92)90526-i. [DOI] [PubMed] [Google Scholar]
  22. Björklund S., Kim Y. J. Mediator of transcriptional regulation. Trends Biochem Sci. 1996 Sep;21(9):335–337. doi: 10.1016/s0968-0004(96)10051-7. [DOI] [PubMed] [Google Scholar]
  23. Bode J., Kohwi Y., Dickinson L., Joh T., Klehr D., Mielke C., Kohwi-Shigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science. 1992 Jan 10;255(5041):195–197. doi: 10.1126/science.1553545. [DOI] [PubMed] [Google Scholar]
  24. Bossu J. P., Chartier F. L., Fruchart J. C., Auwerx J., Staels B., Laine B. Two regulatory elements of similar structure and placed in tandem account for the repressive activity of the first intron of the human apolipoprotein A-II gene. Biochem J. 1996 Sep 1;318(Pt 2):547–553. doi: 10.1042/bj3180547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Boyes J., Bird A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 1992 Jan;11(1):327–333. doi: 10.1002/j.1460-2075.1992.tb05055.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Brand A. H., Breeden L., Abraham J., Sternglanz R., Nasmyth K. Characterization of a "silencer" in yeast: a DNA sequence with properties opposite to those of a transcriptional enhancer. Cell. 1985 May;41(1):41–48. doi: 10.1016/0092-8674(85)90059-5. [DOI] [PubMed] [Google Scholar]
  27. Buratowski S., Hahn S., Guarente L., Sharp P. A. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell. 1989 Feb 24;56(4):549–561. doi: 10.1016/0092-8674(89)90578-3. [DOI] [PubMed] [Google Scholar]
  28. Buratowski S. The basics of basal transcription by RNA polymerase II. Cell. 1994 Apr 8;77(1):1–3. doi: 10.1016/0092-8674(94)90226-7. [DOI] [PubMed] [Google Scholar]
  29. Cadena D. L., Dahmus M. E. Messenger RNA synthesis in mammalian cells is catalyzed by the phosphorylated form of RNA polymerase II. J Biol Chem. 1987 Sep 15;262(26):12468–12474. [PubMed] [Google Scholar]
  30. Cai H. N., Levine M. The gypsy insulator can function as a promoter-specific silencer in the Drosophila embryo. EMBO J. 1997 Apr 1;16(7):1732–1741. doi: 10.1093/emboj/16.7.1732. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Cedar H., Razin A. DNA methylation and development. Biochim Biophys Acta. 1990 May 24;1049(1):1–8. doi: 10.1016/0167-4781(90)90076-e. [DOI] [PubMed] [Google Scholar]
  32. Chambers R. S., Kane C. M. Purification and characterization of an RNA polymerase II phosphatase from yeast. J Biol Chem. 1996 Oct 4;271(40):24498–24504. doi: 10.1074/jbc.271.40.24498. [DOI] [PubMed] [Google Scholar]
  33. Chaudhary S., Crossland L. Identification of tissue-specific, dehydration-responsive elements in the Trg-31 promoter. Plant Mol Biol. 1996 Mar;30(6):1247–1257. doi: 10.1007/BF00019556. [DOI] [PubMed] [Google Scholar]
  34. Chen J. D., Evans R. M. A transcriptional co-repressor that interacts with nuclear hormone receptors. Nature. 1995 Oct 5;377(6548):454–457. doi: 10.1038/377454a0. [DOI] [PubMed] [Google Scholar]
  35. Chi T., Carey M. Assembly of the isomerized TFIIA--TFIID--TATA ternary complex is necessary and sufficient for gene activation. Genes Dev. 1996 Oct 15;10(20):2540–2550. doi: 10.1101/gad.10.20.2540. [DOI] [PubMed] [Google Scholar]
  36. Chong J. A., Tapia-Ramírez J., Kim S., Toledo-Aral J. J., Zheng Y., Boutros M. C., Altshuller Y. M., Frohman M. A., Kraner S. D., Mandel G. REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell. 1995 Mar 24;80(6):949–957. doi: 10.1016/0092-8674(95)90298-8. [DOI] [PubMed] [Google Scholar]
  37. Clark A. R., Docherty K. Negative regulation of transcription in eukaryotes. Biochem J. 1993 Dec 15;296(Pt 3):521–541. doi: 10.1042/bj2960521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Cohen-Kupiec R., Blank C., Leigh J. A. Transcriptional regulation in Archaea: in vivo demonstration of a repressor binding site in a methanogen. Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1316–1320. doi: 10.1073/pnas.94.4.1316. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Conaway R. C., Conaway J. W. General initiation factors for RNA polymerase II. Annu Rev Biochem. 1993;62:161–190. doi: 10.1146/annurev.bi.62.070193.001113. [DOI] [PubMed] [Google Scholar]
  40. Corces V. G. Chromatin insulators. Keeping enhancers under control. Nature. 1995 Aug 10;376(6540):462–463. doi: 10.1038/376462a0. [DOI] [PubMed] [Google Scholar]
  41. Cortes P., Flores O., Reinberg D. Factors involved in specific transcription by mammalian RNA polymerase II: purification and analysis of transcription factor IIA and identification of transcription factor IIJ. Mol Cell Biol. 1992 Jan;12(1):413–421. doi: 10.1128/mcb.12.1.413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Cowell I. G. Repression versus activation in the control of gene transcription. Trends Biochem Sci. 1994 Jan;19(1):38–42. doi: 10.1016/0968-0004(94)90172-4. [DOI] [PubMed] [Google Scholar]
  43. Dietrich-Goetz W., Kennedy I. M., Levins B., Stanley M. A., Clements J. B. A cellular 65-kDa protein recognizes the negative regulatory element of human papillomavirus late mRNA. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):163–168. doi: 10.1073/pnas.94.1.163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Dirks R. P., Klok E. J., van Genesen S. T., Schoenmakers J. G., Lubsen N. H. The sequence of regulatory events controlling the expression of the gamma D-crystallin gene during fibroblast growth factor-mediated rat lens fiber cell differentiation. Dev Biol. 1996 Jan 10;173(1):14–25. doi: 10.1006/dbio.1996.0003. [DOI] [PubMed] [Google Scholar]
  45. Dombret H., Font M. P., Sigaux F. A dominant transcriptional silencer located 5' to the human T-cell receptor V beta 2.2 gene segment which is activated in cell lines of thymic phenotype. Nucleic Acids Res. 1996 Jul 15;24(14):2782–2789. doi: 10.1093/nar/24.14.2782. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Donda A., Schulz M., Bürki K., De Libero G., Uematsu Y. Identification and characterization of a human CD4 silencer. Eur J Immunol. 1996 Feb;26(2):493–500. doi: 10.1002/eji.1830260232. [DOI] [PubMed] [Google Scholar]
  47. Dong J. M., Lim L. The human neuronal alpha 1-chimaerin gene contains a position-dependent negative regulatory element in the first exon. Neurochem Res. 1996 Sep;21(9):1023–1030. doi: 10.1007/BF02532412. [DOI] [PubMed] [Google Scholar]
  48. Doyle H. J., Kraut R., Levine M. Spatial regulation of zerknüllt: a dorsal-ventral patterning gene in Drosophila. Genes Dev. 1989 Oct;3(10):1518–1533. doi: 10.1101/gad.3.10.1518. [DOI] [PubMed] [Google Scholar]
  49. Dunaway M., Dröge P. Transactivation of the Xenopus rRNA gene promoter by its enhancer. Nature. 1989 Oct 19;341(6243):657–659. doi: 10.1038/341657a0. [DOI] [PubMed] [Google Scholar]
  50. Dynlacht B. D., Hoey T., Tjian R. Isolation of coactivators associated with the TATA-binding protein that mediate transcriptional activation. Cell. 1991 Aug 9;66(3):563–576. doi: 10.1016/0092-8674(81)90019-2. [DOI] [PubMed] [Google Scholar]
  51. Emili A., Greenblatt J., Ingles C. J. Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein. Mol Cell Biol. 1994 Mar;14(3):1582–1593. doi: 10.1128/mcb.14.3.1582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Evans R. M. The steroid and thyroid hormone receptor superfamily. Science. 1988 May 13;240(4854):889–895. doi: 10.1126/science.3283939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Fabre E., Hurt E. C. Nuclear transport. Curr Opin Cell Biol. 1994 Jun;6(3):335–342. doi: 10.1016/0955-0674(94)90023-x. [DOI] [PubMed] [Google Scholar]
  54. Feng J. Q., Chen D., Cooney A. J., Tsai M. J., Harris M. A., Tsai S. Y., Feng M., Mundy G. R., Harris S. E. The mouse bone morphogenetic protein-4 gene. Analysis of promoter utilization in fetal rat calvarial osteoblasts and regulation by COUP-TFI orphan receptor. J Biol Chem. 1995 Nov 24;270(47):28364–28373. doi: 10.1074/jbc.270.47.28364. [DOI] [PubMed] [Google Scholar]
  55. Fondell J. D., Brunel F., Hisatake K., Roeder R. G. Unliganded thyroid hormone receptor alpha can target TATA-binding protein for transcriptional repression. Mol Cell Biol. 1996 Jan;16(1):281–287. doi: 10.1128/mcb.16.1.281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Frenkel B., Mijnes J., Aronow M. A., Zambetti G., Banerjee C., Stein J. L., Lian J. B., Stein G. S. Position and orientation-selective silencer in protein-coding sequences of the rat osteocalcin gene. Biochemistry. 1993 Dec 14;32(49):13636–13643. doi: 10.1021/bi00212a031. [DOI] [PubMed] [Google Scholar]
  57. Furth P. A., Choe W. T., Rex J. H., Byrne J. C., Baker C. C. Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions. Mol Cell Biol. 1994 Aug;14(8):5278–5289. doi: 10.1128/mcb.14.8.5278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Furuichi Y., LaFiandra A., Shatkin A. J. 5'-Terminal structure and mRNA stability. Nature. 1977 Mar 17;266(5599):235–239. doi: 10.1038/266235a0. [DOI] [PubMed] [Google Scholar]
  59. Garcia-Ramirez M., Rocchini C., Ausio J. Modulation of chromatin folding by histone acetylation. J Biol Chem. 1995 Jul 28;270(30):17923–17928. doi: 10.1074/jbc.270.30.17923. [DOI] [PubMed] [Google Scholar]
  60. Gasser S. M., Amati B. B., Cardenas M. E., Hofmann J. F. Studies on scaffold attachment sites and their relation to genome function. Int Rev Cytol. 1989;119:57–96. doi: 10.1016/s0074-7696(08)60649-x. [DOI] [PubMed] [Google Scholar]
  61. Gerber H. P., Hagmann M., Seipel K., Georgiev O., West M. A., Litingtung Y., Schaffner W., Corden J. L. RNA polymerase II C-terminal domain required for enhancer-driven transcription. Nature. 1995 Apr 13;374(6523):660–662. doi: 10.1038/374660a0. [DOI] [PubMed] [Google Scholar]
  62. Gidoni D., Dynan W. S., Tjian R. Multiple specific contacts between a mammalian transcription factor and its cognate promoters. 1984 Nov 29-Dec 5Nature. 312(5993):409–413. doi: 10.1038/312409a0. [DOI] [PubMed] [Google Scholar]
  63. Giffin W., Torrance H., Saffran H., MacLeod H. L., Haché R. J. Repression of mouse mammary tumor virus transcription by a transcription factor complex. Binding of individual components to separated DNA strands. J Biol Chem. 1994 Jan 14;269(2):1449–1459. [PubMed] [Google Scholar]
  64. Goodbourn S. Negative regulation of transcriptional initiation in eukaryotes. Biochim Biophys Acta. 1990 Jun 1;1032(1):53–77. doi: 10.1016/0304-419x(90)90012-p. [DOI] [PubMed] [Google Scholar]
  65. Goodman P. A., Medina-Martinez O., Fernandez-Mejia C. Identification of the human insulin negative regulatory element as a negative glucocorticoid response element. Mol Cell Endocrinol. 1996 Jul 1;120(2):139–146. doi: 10.1016/0303-7207(96)03830-0. [DOI] [PubMed] [Google Scholar]
  66. Goto K., Heymont J. L., Klein-Nulend J., Kronenberg H. M., Demay M. B. Identification of an osteoblastic silencer element in the first intron of the rat osteocalcin gene. Biochemistry. 1996 Aug 20;35(33):11005–11011. doi: 10.1021/bi960723o. [DOI] [PubMed] [Google Scholar]
  67. Gray S., Szymanski P., Levine M. Short-range repression permits multiple enhancers to function autonomously within a complex promoter. Genes Dev. 1994 Aug 1;8(15):1829–1838. doi: 10.1101/gad.8.15.1829. [DOI] [PubMed] [Google Scholar]
  68. Greenblatt J., Nodwell J. R., Mason S. W. Transcriptional antitermination. Nature. 1993 Jul 29;364(6436):401–406. doi: 10.1038/364401a0. [DOI] [PubMed] [Google Scholar]
  69. Greenblatt J. RNA polymerase II holoenzyme and transcriptional regulation. Curr Opin Cell Biol. 1997 Jun;9(3):310–319. doi: 10.1016/s0955-0674(97)80002-6. [DOI] [PubMed] [Google Scholar]
  70. Grunstein M. Histone acetylation in chromatin structure and transcription. Nature. 1997 Sep 25;389(6649):349–352. doi: 10.1038/38664. [DOI] [PubMed] [Google Scholar]
  71. Gumucio D. L., Shelton D. A., Bailey W. J., Slightom J. L., Goodman M. Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the epsilon-globin gene. Proc Natl Acad Sci U S A. 1993 Jul 1;90(13):6018–6022. doi: 10.1073/pnas.90.13.6018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  72. Gunster M. J., Satijn D. P., Hamer K. M., den Blaauwen J. L., de Bruijn D., Alkema M. J., van Lohuizen M., van Driel R., Otte A. P. Identification and characterization of interactions between the vertebrate polycomb-group protein BMI1 and human homologs of polyhomeotic. Mol Cell Biol. 1997 Apr;17(4):2326–2335. doi: 10.1128/mcb.17.4.2326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Haecker S. A., Muramatsu T., Sensenbaugh K. R., Sanders M. M. Repression of the ovalbumin gene involves multiple negative elements including a ubiquitous transcriptional silencer. Mol Endocrinol. 1995 Sep;9(9):1113–1126. doi: 10.1210/mend.9.9.7491104. [DOI] [PubMed] [Google Scholar]
  74. Han K., Manley J. L. Transcriptional repression by the Drosophila even-skipped protein: definition of a minimal repression domain. Genes Dev. 1993 Mar;7(3):491–503. doi: 10.1101/gad.7.3.491. [DOI] [PubMed] [Google Scholar]
  75. Haniel A., Welge-Lüssen U., Kühn K., Pöschl E. Identification and characterization of a novel transcriptional silencer in the human collagen type IV gene COL4A2. J Biol Chem. 1995 May 12;270(19):11209–11215. doi: 10.1074/jbc.270.19.11209. [DOI] [PubMed] [Google Scholar]
  76. He Y., Borellini F., Koch W. H., Huang K. X., Glazer R. I. Transcriptional regulation of c-Fes in myeloid leukemia cells. Biochim Biophys Acta. 1996 May 2;1306(2-3):179–186. doi: 10.1016/0167-4781(96)00005-x. [DOI] [PubMed] [Google Scholar]
  77. Heinzel T., Lavinsky R. M., Mullen T. M., Söderstrom M., Laherty C. D., Torchia J., Yang W. M., Brard G., Ngo S. D., Davie J. R. A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression. Nature. 1997 May 1;387(6628):43–48. doi: 10.1038/387043a0. [DOI] [PubMed] [Google Scholar]
  78. Hengartner C. J., Thompson C. M., Zhang J., Chao D. M., Liao S. M., Koleske A. J., Okamura S., Young R. A. Association of an activator with an RNA polymerase II holoenzyme. Genes Dev. 1995 Apr 15;9(8):897–910. doi: 10.1101/gad.9.8.897. [DOI] [PubMed] [Google Scholar]
  79. Hoeben R. C., Fallaux F. J., Cramer S. J., van den Wollenberg D. J., van Ormondt H., Briët E., van der Eb A. J. Expression of the blood-clotting factor-VIII cDNA is repressed by a transcriptional silencer located in its coding region. Blood. 1995 May 1;85(9):2447–2454. [PubMed] [Google Scholar]
  80. Homberger H. P. Bent DNA is a structural feature of scaffold-attached regions in Drosophila melanogaster interphase nuclei. Chromosoma. 1989 Aug;98(2):99–104. doi: 10.1007/BF00291044. [DOI] [PubMed] [Google Scholar]
  81. Horikoshi M., Carey M. F., Kakidani H., Roeder R. G. Mechanism of action of a yeast activator: direct effect of GAL4 derivatives on mammalian TFIID-promoter interactions. Cell. 1988 Aug 26;54(5):665–669. doi: 10.1016/s0092-8674(88)80011-4. [DOI] [PubMed] [Google Scholar]
  82. Huang W., Bateman E. Transcription of the Acanthamoeba TATA-binding protein gene. A single transcription factor acts both as an activator and a repressor. J Biol Chem. 1997 Feb 7;272(6):3852–3859. doi: 10.1074/jbc.272.6.3852. [DOI] [PubMed] [Google Scholar]
  83. Hurlin P. J., Quéva C., Koskinen P. J., Steingrímsson E., Ayer D. E., Copeland N. G., Jenkins N. A., Eisenman R. N. Mad3 and Mad4: novel Max-interacting transcriptional repressors that suppress c-myc dependent transformation and are expressed during neural and epidermal differentiation. EMBO J. 1996 Apr 15;15(8):2030–2030. [PMC free article] [PubMed] [Google Scholar]
  84. Hörlein A. J., När A. M., Heinzel T., Torchia J., Gloss B., Kurokawa R., Ryan A., Kamei Y., Söderström M., Glass C. K. Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor. Nature. 1995 Oct 5;377(6548):397–404. doi: 10.1038/377397a0. [DOI] [PubMed] [Google Scholar]
  85. Inostroza J. A., Mermelstein F. H., Ha I., Lane W. S., Reinberg D. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. Cell. 1992 Aug 7;70(3):477–489. doi: 10.1016/0092-8674(92)90172-9. [DOI] [PubMed] [Google Scholar]
  86. Izaurralde E., Käs E., Laemmli U. K. Highly preferential nucleation of histone H1 assembly on scaffold-associated regions. J Mol Biol. 1989 Dec 5;210(3):573–585. doi: 10.1016/0022-2836(89)90133-2. [DOI] [PubMed] [Google Scholar]
  87. Jones K. A., Yamamoto K. R., Tjian R. Two distinct transcription factors bind to the HSV thymidine kinase promoter in vitro. Cell. 1985 Sep;42(2):559–572. doi: 10.1016/0092-8674(85)90113-8. [DOI] [PubMed] [Google Scholar]
  88. Kamachi Y., Kondoh H. Overlapping positive and negative regulatory elements determine lens-specific activity of the delta 1-crystallin enhancer. Mol Cell Biol. 1993 Sep;13(9):5206–5215. doi: 10.1128/mcb.13.9.5206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Kaufmann J., Verrijzer C. P., Shao J., Smale S. T. CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 1996 Apr 1;10(7):873–886. doi: 10.1101/gad.10.7.873. [DOI] [PubMed] [Google Scholar]
  90. Kellum R., Schedl P. A position-effect assay for boundaries of higher order chromosomal domains. Cell. 1991 Mar 8;64(5):941–950. doi: 10.1016/0092-8674(91)90318-s. [DOI] [PubMed] [Google Scholar]
  91. Kerppola T. K., Kane C. M. RNA polymerase: regulation of transcript elongation and termination. FASEB J. 1991 Oct;5(13):2833–2842. doi: 10.1096/fasebj.5.13.1916107. [DOI] [PubMed] [Google Scholar]
  92. Kim M. K., Lesoon-Wood L. A., Weintraub B. D., Chung J. H. A soluble transcription factor, Oct-1, is also found in the insoluble nuclear matrix and possesses silencing activity in its alanine-rich domain. Mol Cell Biol. 1996 Aug;16(8):4366–4377. doi: 10.1128/mcb.16.8.4366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Kim Y. J., Björklund S., Li Y., Sayre M. H., Kornberg R. D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell. 1994 May 20;77(4):599–608. doi: 10.1016/0092-8674(94)90221-6. [DOI] [PubMed] [Google Scholar]
  94. Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
  95. Kingston R. E., Bunker C. A., Imbalzano A. N. Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev. 1996 Apr 15;10(8):905–920. doi: 10.1101/gad.10.8.905. [DOI] [PubMed] [Google Scholar]
  96. Koleske A. J., Young R. A. An RNA polymerase II holoenzyme responsive to activators. Nature. 1994 Mar 31;368(6470):466–469. doi: 10.1038/368466a0. [DOI] [PubMed] [Google Scholar]
  97. Koleske A. J., Young R. A. The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem Sci. 1995 Mar;20(3):113–116. doi: 10.1016/s0968-0004(00)88977-x. [DOI] [PubMed] [Google Scholar]
  98. Kraner S. D., Chong J. A., Tsay H. J., Mandel G. Silencing the type II sodium channel gene: a model for neural-specific gene regulation. Neuron. 1992 Jul;9(1):37–44. doi: 10.1016/0896-6273(92)90218-3. [DOI] [PubMed] [Google Scholar]
  99. Kretzner L., Blackwood E. M., Eisenman R. N. Myc and Max proteins possess distinct transcriptional activities. Nature. 1992 Oct 1;359(6394):426–429. doi: 10.1038/359426a0. [DOI] [PubMed] [Google Scholar]
  100. Kurokawa R., Söderström M., Hörlein A., Halachmi S., Brown M., Rosenfeld M. G., Glass C. K. Polarity-specific activities of retinoic acid receptors determined by a co-repressor. Nature. 1995 Oct 5;377(6548):451–454. doi: 10.1038/377451a0. [DOI] [PubMed] [Google Scholar]
  101. Laherty C. D., Yang W. M., Sun J. M., Davie J. R., Seto E., Eisenman R. N. Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression. Cell. 1997 May 2;89(3):349–356. doi: 10.1016/s0092-8674(00)80215-9. [DOI] [PubMed] [Google Scholar]
  102. Le Cam A., Legraverend C. Transcriptional repression, a novel function for 3' untranslated regions. Eur J Biochem. 1995 Aug 1;231(3):620–627. [PubMed] [Google Scholar]
  103. Lee C. G., Zamore P. D., Green M. R., Hurwitz J. RNA annealing activity is intrinsically associated with U2AF. J Biol Chem. 1993 Jun 25;268(18):13472–13478. [PubMed] [Google Scholar]
  104. Lee D. Y., Hayes J. J., Pruss D., Wolffe A. P. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell. 1993 Jan 15;72(1):73–84. doi: 10.1016/0092-8674(93)90051-q. [DOI] [PubMed] [Google Scholar]
  105. Lerner M. R., Boyle J. A., Mount S. M., Wolin S. L., Steitz J. A. Are snRNPs involved in splicing? Nature. 1980 Jan 10;283(5743):220–224. doi: 10.1038/283220a0. [DOI] [PubMed] [Google Scholar]
  106. Li L., Suzuki T., Mori N., Greengard P. Identification of a functional silencer element involved in neuron-specific expression of the synapsin I gene. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1460–1464. doi: 10.1073/pnas.90.4.1460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Lis J., Wu C. Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell. 1993 Jul 16;74(1):1–4. doi: 10.1016/0092-8674(93)90286-y. [DOI] [PubMed] [Google Scholar]
  108. Liu B., Maul R. S., Kaetzel D. M., Jr Repression of platelet-derived growth factor A-chain gene transcription by an upstream silencer element. Participation by sequence-specific single-stranded DNA-binding proteins. J Biol Chem. 1996 Oct 18;271(42):26281–26290. doi: 10.1074/jbc.271.42.26281. [DOI] [PubMed] [Google Scholar]
  109. Liu F., Bateman E. An upstream promoter element of the Acanthamoeba castellanii TBP gene binds a DNA sequence specific transcription activating protein, TPBF. Nucleic Acids Res. 1993 Sep 11;21(18):4321–4329. doi: 10.1093/nar/21.18.4321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Lu H., Flores O., Weinmann R., Reinberg D. The nonphosphorylated form of RNA polymerase II preferentially associates with the preinitiation complex. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10004–10008. doi: 10.1073/pnas.88.22.10004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Lu H., Zawel L., Fisher L., Egly J. M., Reinberg D. Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II. Nature. 1992 Aug 20;358(6388):641–645. doi: 10.1038/358641a0. [DOI] [PubMed] [Google Scholar]
  112. Ma J., Saito H., Oka T., Vijay I. K. Negative regulatory element involved in the hormonal regulation of GlcNAc-1-P transferase gene in mouse mammary gland. J Biol Chem. 1996 May 10;271(19):11197–11203. doi: 10.1074/jbc.271.19.11197. [DOI] [PubMed] [Google Scholar]
  113. Majello B., De Luca P., Lania L. Sp3 is a bifunctional transcription regulator with modular independent activation and repression domains. J Biol Chem. 1997 Feb 14;272(7):4021–4026. doi: 10.1074/jbc.272.7.4021. [DOI] [PubMed] [Google Scholar]
  114. Manley J. L. Polyadenylation of mRNA precursors. Biochim Biophys Acta. 1988 May 6;950(1):1–12. doi: 10.1016/0167-4781(88)90067-x. [DOI] [PubMed] [Google Scholar]
  115. Maue R. A., Kraner S. D., Goodman R. H., Mandel G. Neuron-specific expression of the rat brain type II sodium channel gene is directed by upstream regulatory elements. Neuron. 1990 Feb;4(2):223–231. doi: 10.1016/0896-6273(90)90097-y. [DOI] [PubMed] [Google Scholar]
  116. Maxon M. E., Goodrich J. A., Tjian R. Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. Genes Dev. 1994 Mar 1;8(5):515–524. doi: 10.1101/gad.8.5.515. [DOI] [PubMed] [Google Scholar]
  117. McCrae M. A., Woodland H. R. Stability of non-polyadenylated viral mRNAs injected into frog oocytes. Eur J Biochem. 1981 Jun 1;116(3):467–470. doi: 10.1111/j.1432-1033.1981.tb05359.x. [DOI] [PubMed] [Google Scholar]
  118. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  119. Meehan R. R., Lewis J. D., McKay S., Kleiner E. L., Bird A. P. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell. 1989 Aug 11;58(3):499–507. doi: 10.1016/0092-8674(89)90430-3. [DOI] [PubMed] [Google Scholar]
  120. Meisterernst M., Roy A. L., Lieu H. M., Roeder R. G. Activation of class II gene transcription by regulatory factors is potentiated by a novel activity. Cell. 1991 Sep 6;66(5):981–993. doi: 10.1016/0092-8674(91)90443-3. [DOI] [PubMed] [Google Scholar]
  121. Merino A., Madden K. R., Lane W. S., Champoux J. J., Reinberg D. DNA topoisomerase I is involved in both repression and activation of transcription. Nature. 1993 Sep 16;365(6443):227–232. doi: 10.1038/365227a0. [DOI] [PubMed] [Google Scholar]
  122. Mieda M., Haga T., Saffen D. W. Promoter region of the rat m4 muscarinic acetylcholine receptor gene contains a cell type-specific silencer element. J Biol Chem. 1996 Mar 1;271(9):5177–5182. doi: 10.1074/jbc.271.9.5177. [DOI] [PubMed] [Google Scholar]
  123. Mizzen C. A., Yang X. J., Kokubo T., Brownell J. E., Bannister A. J., Owen-Hughes T., Workman J., Wang L., Berger S. L., Kouzarides T. The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell. 1996 Dec 27;87(7):1261–1270. doi: 10.1016/s0092-8674(00)81821-8. [DOI] [PubMed] [Google Scholar]
  124. Moffat G. J., McLaren A. W., Wolf C. R. Functional characterization of the transcription silencer element located within the human Pi class glutathione S-transferase promoter. J Biol Chem. 1996 Aug 23;271(34):20740–20747. doi: 10.1074/jbc.271.34.20740. [DOI] [PubMed] [Google Scholar]
  125. Mori N., Schoenherr C., Vandenbergh D. J., Anderson D. J. A common silencer element in the SCG10 and type II Na+ channel genes binds a factor present in nonneuronal cells but not in neuronal cells. Neuron. 1992 Jul;9(1):45–54. doi: 10.1016/0896-6273(92)90219-4. [DOI] [PubMed] [Google Scholar]
  126. Morse R. H. Transcribed chromatin. Trends Biochem Sci. 1992 Jan;17(1):23–26. doi: 10.1016/0968-0004(92)90422-6. [DOI] [PubMed] [Google Scholar]
  127. Murasawa S., Matsubara H., Mori Y., Kijima K., Maruyama K., Inada M. Identification of a negative cis-regulatory element and trans-acting protein that inhibit transcription of the angiotensin II type 1a receptor gene. J Biol Chem. 1995 Oct 13;270(41):24282–24286. doi: 10.1074/jbc.270.41.24282. [DOI] [PubMed] [Google Scholar]
  128. Müller J. Transcriptional silencing by the Polycomb protein in Drosophila embryos. EMBO J. 1995 Mar 15;14(6):1209–1220. doi: 10.1002/j.1460-2075.1995.tb07104.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. Nagasawa T., Takeda T., Minemura K., DeGroot L. J. Oct-1, silencer sequence, and GC box regulate thyroid hormone receptor beta1 promoter. Mol Cell Endocrinol. 1997 Jun 20;130(1-2):153–165. doi: 10.1016/s0303-7207(97)00085-3. [DOI] [PubMed] [Google Scholar]
  130. Nakajima N., Horikoshi M., Roeder R. G. Factors involved in specific transcription by mammalian RNA polymerase II: purification, genetic specificity, and TATA box-promoter interactions of TFIID. Mol Cell Biol. 1988 Oct;8(10):4028–4040. doi: 10.1128/mcb.8.10.4028. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Nan X., Campoy F. J., Bird A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell. 1997 Feb 21;88(4):471–481. doi: 10.1016/s0092-8674(00)81887-5. [DOI] [PubMed] [Google Scholar]
  132. Natesan S., Gilman M. Z. DNA bending and orientation-dependent function of YY1 in the c-fos promoter. Genes Dev. 1993 Dec;7(12B):2497–2509. doi: 10.1101/gad.7.12b.2497. [DOI] [PubMed] [Google Scholar]
  133. Nye J. A., Petersen J. M., Gunther C. V., Jonsen M. D., Graves B. J. Interaction of murine ets-1 with GGA-binding sites establishes the ETS domain as a new DNA-binding motif. Genes Dev. 1992 Jun;6(6):975–990. doi: 10.1101/gad.6.6.975. [DOI] [PubMed] [Google Scholar]
  134. O'Brien T., Hardin S., Greenleaf A., Lis J. T. Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature. 1994 Jul 7;370(6484):75–77. doi: 10.1038/370075a0. [DOI] [PubMed] [Google Scholar]
  135. Oelgeschläger T., Chiang C. M., Roeder R. G. Topology and reorganization of a human TFIID-promoter complex. Nature. 1996 Aug 22;382(6593):735–738. doi: 10.1038/382735a0. [DOI] [PubMed] [Google Scholar]
  136. Ogryzko V. V., Schiltz R. L., Russanova V., Howard B. H., Nakatani Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell. 1996 Nov 29;87(5):953–959. doi: 10.1016/s0092-8674(00)82001-2. [DOI] [PubMed] [Google Scholar]
  137. Oh C. K., Neurath M., Cho J. J., Semere T., Metcalfe D. D. Two different negative regulatory elements control the transcription of T-cell activation gene 3 in activated mast cells. Biochem J. 1997 Apr 15;323(Pt 2):511–519. doi: 10.1042/bj3230511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Ohkuma Y., Roeder R. G. Regulation of TFIIH ATPase and kinase activities by TFIIE during active initiation complex formation. Nature. 1994 Mar 10;368(6467):160–163. doi: 10.1038/368160a0. [DOI] [PubMed] [Google Scholar]
  139. Opstelten R. J., Clement J. M., Wanka F. Direct repeats at nuclear matrix-associated DNA regions and their putative control function in the replicating eukaryotic genome. Chromosoma. 1989 Dec;98(6):422–427. doi: 10.1007/BF00292787. [DOI] [PubMed] [Google Scholar]
  140. Ortiz E. M., Dusetti N. J., Dagorn J. C., Iovanna J. L. Characterization of a silencer regulatory element in the rat PAP I gene which confers tissue-specific expression and is promoter-dependent. Arch Biochem Biophys. 1997 Apr 1;340(1):111–116. doi: 10.1006/abbi.1997.9886. [DOI] [PubMed] [Google Scholar]
  141. Oskouian B., Rangan V. S., Smith S. Transcriptional regulation of the rat fatty acid synthase gene: identification and functional analysis of positive and negative effectors of basal transcription. Biochem J. 1996 Jul 1;317(Pt 1):257–265. doi: 10.1042/bj3170257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Park K. Y., Roe J. H. Negative regulation of bovine growth hormone gene by YY1 binding to NRE's. Biochem Biophys Res Commun. 1996 Nov 21;228(3):745–751. doi: 10.1006/bbrc.1996.1726. [DOI] [PubMed] [Google Scholar]
  143. Paro R., Hogness D. S. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):263–267. doi: 10.1073/pnas.88.1.263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Penning T. M. 3 alpha-hydroxysteroid dehydrogenase: three dimensional structure and gene regulation. J Endocrinol. 1996 Sep;150 (Suppl):S175–S187. [PubMed] [Google Scholar]
  145. Perri S., Ganem D. A host factor that binds near the termini of hepatitis B virus pregenomic RNA. J Virol. 1996 Oct;70(10):6803–6809. doi: 10.1128/jvi.70.10.6803-6809.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Peters B., Merezhinskaya N., Diffley J. F., Noguchi C. T. Protein-DNA interactions in the epsilon-globin gene silencer. J Biol Chem. 1993 Feb 15;268(5):3430–3437. [PubMed] [Google Scholar]
  147. Peterson M. G., Inostroza J., Maxon M. E., Flores O., Admon A., Reinberg D., Tjian R. Structure and functional properties of human general transcription factor IIE. Nature. 1991 Dec 5;354(6352):369–373. doi: 10.1038/354369a0. [DOI] [PubMed] [Google Scholar]
  148. Platt T. Transcription termination and the regulation of gene expression. Annu Rev Biochem. 1986;55:339–372. doi: 10.1146/annurev.bi.55.070186.002011. [DOI] [PubMed] [Google Scholar]
  149. Proudfoot N. Poly(A) signals. Cell. 1991 Feb 22;64(4):671–674. doi: 10.1016/0092-8674(91)90495-k. [DOI] [PubMed] [Google Scholar]
  150. Ptashne M., Johnson A. D., Pabo C. O. A genetic switch in a bacterial virus. Sci Am. 1982 Nov;247(5):128-30, 132, 134-40. doi: 10.1038/scientificamerican1182-128. [DOI] [PubMed] [Google Scholar]
  151. Pugh B. F., Tjian R. Mechanism of transcriptional activation by Sp1: evidence for coactivators. Cell. 1990 Jun 29;61(7):1187–1197. doi: 10.1016/0092-8674(90)90683-6. [DOI] [PubMed] [Google Scholar]
  152. Qian S., Capovilla M., Pirrotta V. The bx region enhancer, a distant cis-control element of the Drosophila Ubx gene and its regulation by hunchback and other segmentation genes. EMBO J. 1991 Jun;10(6):1415–1425. doi: 10.1002/j.1460-2075.1991.tb07662.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  153. Reijnen M. J., Hamer K. M., den Blaauwen J. L., Lambrechts C., Schoneveld I., van Driel R., Otte A. P. Polycomb and bmi-1 homologs are expressed in overlapping patterns in Xenopus embryos and are able to interact with each other. Mech Dev. 1995 Sep;53(1):35–46. doi: 10.1016/0925-4773(95)00422-x. [DOI] [PubMed] [Google Scholar]
  154. Riggs K. J., Saleque S., Wong K. K., Merrell K. T., Lee J. S., Shi Y., Calame K. Yin-yang 1 activates the c-myc promoter. Mol Cell Biol. 1993 Dec;13(12):7487–7495. doi: 10.1128/mcb.13.12.7487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  155. Rincón-Limas D. E., Amaya-Manzanares F., Niño-Rosales M. L., Yu Y., Yang T. P., Patel P. I. Ubiquitous and neuronal DNA-binding proteins interact with a negative regulatory element of the human hypoxanthine phosphoribosyltransferase gene. Mol Cell Biol. 1995 Dec;15(12):6561–6571. doi: 10.1128/mcb.15.12.6561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  156. Roberts S. G., Green M. R. Transcription. Dichotomous regulators. Nature. 1995 May 11;375(6527):105–106. doi: 10.1038/375105a0. [DOI] [PubMed] [Google Scholar]
  157. Roberts S. G., Ha I., Maldonado E., Reinberg D., Green M. R. Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation. Nature. 1993 Jun 24;363(6431):741–744. doi: 10.1038/363741a0. [DOI] [PubMed] [Google Scholar]
  158. Roeder R. G. The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly. Trends Biochem Sci. 1991 Nov;16(11):402–408. doi: 10.1016/0968-0004(91)90164-q. [DOI] [PubMed] [Google Scholar]
  159. Roeder R. G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 1996 Sep;21(9):327–335. [PubMed] [Google Scholar]
  160. Rogers J., Wall R. A mechanism for RNA splicing. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1877–1879. doi: 10.1073/pnas.77.4.1877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Rougvie A. E., Lis J. T. Postinitiation transcriptional control in Drosophila melanogaster. Mol Cell Biol. 1990 Nov;10(11):6041–6045. doi: 10.1128/mcb.10.11.6041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  162. Ryder K., Silver S., DeLucia A. L., Fanning E., Tegtmeyer P. An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen. Cell. 1986 Mar 14;44(5):719–725. doi: 10.1016/0092-8674(86)90838-x. [DOI] [PubMed] [Google Scholar]
  163. Santoro C., Mermod N., Andrews P. C., Tjian R. A family of human CCAAT-box-binding proteins active in transcription and DNA replication: cloning and expression of multiple cDNAs. Nature. 1988 Jul 21;334(6179):218–224. doi: 10.1038/334218a0. [DOI] [PubMed] [Google Scholar]
  164. Satijn D. P., Gunster M. J., van der Vlag J., Hamer K. M., Schul W., Alkema M. J., Saurin A. J., Freemont P. S., van Driel R., Otte A. P. RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor. Mol Cell Biol. 1997 Jul;17(7):4105–4113. doi: 10.1128/mcb.17.7.4105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  165. Sauer F., Fondell J. D., Ohkuma Y., Roeder R. G., Jäckle H. Control of transcription by Krüppel through interactions with TFIIB and TFIIE beta. Nature. 1995 May 11;375(6527):162–164. doi: 10.1038/375162a0. [DOI] [PubMed] [Google Scholar]
  166. Schoch S., Cibelli G., Thiel G. Neuron-specific gene expression of synapsin I. Major role of a negative regulatory mechanism. J Biol Chem. 1996 Feb 9;271(6):3317–3323. doi: 10.1074/jbc.271.6.3317. [DOI] [PubMed] [Google Scholar]
  167. Schoenherr C. J., Anderson D. J. The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science. 1995 Mar 3;267(5202):1360–1363. doi: 10.1126/science.7871435. [DOI] [PubMed] [Google Scholar]
  168. Schoenherr C. J., Paquette A. J., Anderson D. J. Identification of potential target genes for the neuron-restrictive silencer factor. Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9881–9886. doi: 10.1073/pnas.93.18.9881. [DOI] [PMC free article] [PubMed] [Google Scholar]
  169. Selby M. J., Bain E. S., Luciw P. A., Peterlin B. M. Structure, sequence, and position of the stem-loop in tar determine transcriptional elongation by tat through the HIV-1 long terminal repeat. Genes Dev. 1989 Apr;3(4):547–558. doi: 10.1101/gad.3.4.547. [DOI] [PubMed] [Google Scholar]
  170. Serizawa H., Conaway R. C., Conaway J. W. Multifunctional RNA polymerase II initiation factor delta from rat liver. Relationship between carboxyl-terminal domain kinase, ATPase, and DNA helicase activities. J Biol Chem. 1993 Aug 15;268(23):17300–17308. [PubMed] [Google Scholar]
  171. Seto E., Shi Y., Shenk T. YY1 is an initiator sequence-binding protein that directs and activates transcription in vitro. Nature. 1991 Nov 21;354(6350):241–245. doi: 10.1038/354241a0. [DOI] [PubMed] [Google Scholar]
  172. Shi Y., Lee J. S., Galvin K. M. Everything you have ever wanted to know about Yin Yang 1...... Biochim Biophys Acta. 1997 Apr 18;1332(2):F49–F66. doi: 10.1016/s0304-419x(96)00044-3. [DOI] [PubMed] [Google Scholar]
  173. Shi Y., Seto E., Chang L. S., Shenk T. Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein. Cell. 1991 Oct 18;67(2):377–388. doi: 10.1016/0092-8674(91)90189-6. [DOI] [PubMed] [Google Scholar]
  174. Shibata H., Nawaz Z., Tsai S. Y., O'Malley B. W., Tsai M. J. Gene silencing by chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI) is mediated by transcriptional corepressors, nuclear receptor-corepressor (N-CoR) and silencing mediator for retinoic acid receptor and thyroid hormone receptor (SMRT). Mol Endocrinol. 1997 Jun;11(6):714–724. doi: 10.1210/mend.11.6.0002. [DOI] [PubMed] [Google Scholar]
  175. Shimizu M., Li W., Shindo H., Mitchell A. P. Transcriptional repression at a distance through exclusion of activator binding in vivo. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):790–795. doi: 10.1073/pnas.94.3.790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  176. Shimokawa T., Fujimoto H. Identification of a transcriptional silencer in the protein-coding region of the mouse major inducible Hsp70 gene. Biochem Biophys Res Commun. 1996 Apr 25;221(3):843–848. doi: 10.1006/bbrc.1996.0684. [DOI] [PubMed] [Google Scholar]
  177. Shrivastava A., Calame K. An analysis of genes regulated by the multi-functional transcriptional regulator Yin Yang-1. Nucleic Acids Res. 1994 Dec 11;22(24):5151–5155. doi: 10.1093/nar/22.24.5151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. Simon J. Locking in stable states of gene expression: transcriptional control during Drosophila development. Curr Opin Cell Biol. 1995 Jun;7(3):376–385. doi: 10.1016/0955-0674(95)80093-x. [DOI] [PubMed] [Google Scholar]
  179. Smale S. T., Baltimore D. The "initiator" as a transcription control element. Cell. 1989 Apr 7;57(1):103–113. doi: 10.1016/0092-8674(89)90176-1. [DOI] [PubMed] [Google Scholar]
  180. Smale S. T., Schmidt M. C., Berk A. J., Baltimore D. Transcriptional activation by Sp1 as directed through TATA or initiator: specific requirement for mammalian transcription factor IID. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4509–4513. doi: 10.1073/pnas.87.12.4509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  181. Spana C., Corces V. G. DNA bending is a determinant of binding specificity for a Drosophila zinc finger protein. Genes Dev. 1990 Sep;4(9):1505–1515. doi: 10.1101/gad.4.9.1505. [DOI] [PubMed] [Google Scholar]
  182. Staknis D., Reed R. SR proteins promote the first specific recognition of Pre-mRNA and are present together with the U1 small nuclear ribonucleoprotein particle in a general splicing enhancer complex. Mol Cell Biol. 1994 Nov;14(11):7670–7682. doi: 10.1128/mcb.14.11.7670. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. Steinmetzer K., Brantl S. Plasmid pIP501 encoded transcriptional repressor CopR binds asymmetrically at two consecutive major grooves of the DNA. J Mol Biol. 1997 Jun 27;269(5):684–693. doi: 10.1006/jmbi.1997.1083. [DOI] [PubMed] [Google Scholar]
  184. Sterling K., Bresnick E. Oct-1 transcription factor is a negative regulator of rat CYP1A1 expression via an octamer sequence in its negative regulatory element. Mol Pharmacol. 1996 Feb;49(2):329–337. [PubMed] [Google Scholar]
  185. Stillman D. J., Dorland S., Yu Y. Epistasis analysis of suppressor mutations that allow HO expression in the absence of the yeast SW15 transcriptional activator. Genetics. 1994 Mar;136(3):781–788. doi: 10.1093/genetics/136.3.781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  186. Stringer K. F., Ingles C. J., Greenblatt J. Direct and selective binding of an acidic transcriptional activation domain to the TATA-box factor TFIID. Nature. 1990 Jun 28;345(6278):783–786. doi: 10.1038/345783a0. [DOI] [PubMed] [Google Scholar]
  187. Strömstedt P. E., Poellinger L., Gustafsson J. A., Carlstedt-Duke J. The glucocorticoid receptor binds to a sequence overlapping the TATA box of the human osteocalcin promoter: a potential mechanism for negative regulation. Mol Cell Biol. 1991 Jun;11(6):3379–3383. doi: 10.1128/mcb.11.6.3379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  188. Svaren J., Hörz W. Regulation of gene expression by nucleosomes. Curr Opin Genet Dev. 1996 Apr;6(2):164–170. doi: 10.1016/s0959-437x(96)80046-3. [DOI] [PubMed] [Google Scholar]
  189. Söderström M., Vo A., Heinzel T., Lavinsky R. M., Yang W. M., Seto E., Peterson D. A., Rosenfeld M. G., Glass C. K. Differential effects of nuclear receptor corepressor (N-CoR) expression levels on retinoic acid receptor-mediated repression support the existence of dynamically regulated corepressor complexes. Mol Endocrinol. 1997 Jun;11(6):682–692. doi: 10.1210/mend.11.6.0018. [DOI] [PubMed] [Google Scholar]
  190. Takimoto M., Quinn J. P., Farina A. R., Staudt L. M., Levens D. fos/jun and octamer-binding protein interact with a common site in a negative element of the human c-myc gene. J Biol Chem. 1989 May 25;264(15):8992–8999. [PubMed] [Google Scholar]
  191. Tanese N., Pugh B. F., Tjian R. Coactivators for a proline-rich activator purified from the multisubunit human TFIID complex. Genes Dev. 1991 Dec;5(12A):2212–2224. doi: 10.1101/gad.5.12a.2212. [DOI] [PubMed] [Google Scholar]
  192. Tapia-Ramírez J., Eggen B. J., Peral-Rubio M. J., Toledo-Aral J. J., Mandel G. A single zinc finger motif in the silencing factor REST represses the neural-specific type II sodium channel promoter. Proc Natl Acad Sci U S A. 1997 Feb 18;94(4):1177–1182. doi: 10.1073/pnas.94.4.1177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  193. Turner B. M., Birley A. J., Lavender J. Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell. 1992 Apr 17;69(2):375–384. doi: 10.1016/0092-8674(92)90417-b. [DOI] [PubMed] [Google Scholar]
  194. Usheva A., Maldonado E., Goldring A., Lu H., Houbavi C., Reinberg D., Aloni Y. Specific interaction between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein. Cell. 1992 May 29;69(5):871–881. doi: 10.1016/0092-8674(92)90297-p. [DOI] [PubMed] [Google Scholar]
  195. Vidal M., Strich R., Esposito R. E., Gaber R. F. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306–6316. doi: 10.1128/mcb.11.12.6306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  196. Wahle E., Keller W. The biochemistry of 3'-end cleavage and polyadenylation of messenger RNA precursors. Annu Rev Biochem. 1992;61:419–440. doi: 10.1146/annurev.bi.61.070192.002223. [DOI] [PubMed] [Google Scholar]
  197. Walker S., Hayes S., O'Hare P. Site-specific conformational alteration of the Oct-1 POU domain-DNA complex as the basis for differential recognition by Vmw65 (VP16). Cell. 1994 Dec 2;79(5):841–852. doi: 10.1016/0092-8674(94)90073-6. [DOI] [PubMed] [Google Scholar]
  198. Walsh A. A., Tullis K., Rice R. H., Denison M. S. Identification of a novel cis-acting negative regulatory element affecting expression of the CYP1A1 gene in rat epidermal cells. J Biol Chem. 1996 Sep 13;271(37):22746–22753. doi: 10.1074/jbc.271.37.22746. [DOI] [PubMed] [Google Scholar]
  199. Wandersee N. J., Ferris R. C., Ginder G. D. Intronic and flanking sequences are required to silence enhancement of an embryonic beta-type globin gene. Mol Cell Biol. 1996 Jan;16(1):236–246. doi: 10.1128/mcb.16.1.236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  200. Wang Z. Y., Masaharu N., Qiu Q. Q., Takimoto Y., Deuel T. F. An S1 nuclease-sensitive region in the first intron of human platelet-derived growth factor A-chain gene contains a negatively acting cell type-specific regulatory element. Nucleic Acids Res. 1994 Feb 11;22(3):457–464. doi: 10.1093/nar/22.3.457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  201. Wasylyk B., Hahn S. L., Giovane A. The Ets family of transcription factors. Eur J Biochem. 1993 Jan 15;211(1-2):7–18. doi: 10.1007/978-3-642-78757-7_2. [DOI] [PubMed] [Google Scholar]
  202. 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. 1997 Jul;17(7):3799–3808. doi: 10.1128/mcb.17.7.3799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  203. Wickens M. How the messenger got its tail: addition of poly(A) in the nucleus. Trends Biochem Sci. 1990 Jul;15(7):277–281. doi: 10.1016/0968-0004(90)90054-f. [DOI] [PubMed] [Google Scholar]
  204. Williams T. M., Moolten D., Burlein J., Romano J., Bhaerman R., Godillot A., Mellon M., Rauscher F. J., 3rd, Kant J. A. Identification of a zinc finger protein that inhibits IL-2 gene expression. Science. 1991 Dec 20;254(5039):1791–1794. doi: 10.1126/science.1840704. [DOI] [PubMed] [Google Scholar]
  205. Wolffe A. P. Histones, nucleosomes and the roles of chromatin structure in transcriptional control. Biochem Soc Trans. 1997 May;25(2):354–358. doi: 10.1042/bst0250354. [DOI] [PubMed] [Google Scholar]
  206. Wolffe A. P., Pruss D. Targeting chromatin disruption: Transcription regulators that acetylate histones. Cell. 1996 Mar 22;84(6):817–819. doi: 10.1016/s0092-8674(00)81059-4. [DOI] [PubMed] [Google Scholar]
  207. Wood I. C., Roopra A., Buckley N. J. Neural specific expression of the m4 muscarinic acetylcholine receptor gene is mediated by a RE1/NRSE-type silencing element. J Biol Chem. 1996 Jun 14;271(24):14221–14225. doi: 10.1074/jbc.271.24.14221. [DOI] [PubMed] [Google Scholar]
  208. Workman J. L., Buchman A. R. Multiple functions of nucleosomes and regulatory factors in transcription. Trends Biochem Sci. 1993 Mar;18(3):90–95. doi: 10.1016/0968-0004(93)90160-o. [DOI] [PubMed] [Google Scholar]
  209. Wu G. D., Lai E. J., Huang N., Wen X. Oct-1 and CCAAT/enhancer-binding protein (C/EBP) bind to overlapping elements within the interleukin-8 promoter. The role of Oct-1 as a transcriptional repressor. J Biol Chem. 1997 Jan 24;272(4):2396–2403. [PubMed] [Google Scholar]
  210. Yager T. D., von Hippel P. H. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry. 1991 Jan 29;30(4):1097–1118. doi: 10.1021/bi00218a032. [DOI] [PubMed] [Google Scholar]
  211. Yamamoto K. R. Steroid receptor regulated transcription of specific genes and gene networks. Annu Rev Genet. 1985;19:209–252. doi: 10.1146/annurev.ge.19.120185.001233. [DOI] [PubMed] [Google Scholar]
  212. Yang X. J., Ogryzko V. V., Nishikawa J., Howard B. H., Nakatani Y. A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A. Nature. 1996 Jul 25;382(6589):319–324. doi: 10.1038/382319a0. [DOI] [PubMed] [Google Scholar]
  213. Ye J., Cippitelli M., Dorman L., Ortaldo J. R., Young H. A. The nuclear factor YY1 suppresses the human gamma interferon promoter through two mechanisms: inhibition of AP1 binding and activation of a silencer element. Mol Cell Biol. 1996 Sep;16(9):4744–4753. doi: 10.1128/mcb.16.9.4744. [DOI] [PMC free article] [PubMed] [Google Scholar]
  214. Zamir I., Harding H. P., Atkins G. B., Hörlein A., Glass C. K., Rosenfeld M. G., Lazar M. A. A nuclear hormone receptor corepressor mediates transcriptional silencing by receptors with distinct repression domains. Mol Cell Biol. 1996 Oct;16(10):5458–5465. doi: 10.1128/mcb.16.10.5458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  215. Zamir I., Zhang J., Lazar M. A. Stoichiometric and steric principles governing repression by nuclear hormone receptors. Genes Dev. 1997 Apr 1;11(7):835–846. doi: 10.1101/gad.11.7.835. [DOI] [PubMed] [Google Scholar]
  216. Zamore P. D., Patton J. G., Green M. R. Cloning and domain structure of the mammalian splicing factor U2AF. Nature. 1992 Feb 13;355(6361):609–614. doi: 10.1038/355609a0. [DOI] [PubMed] [Google Scholar]
  217. Zawel L., Reinberg D. Common themes in assembly and function of eukaryotic transcription complexes. Annu Rev Biochem. 1995;64:533–561. doi: 10.1146/annurev.bi.64.070195.002533. [DOI] [PubMed] [Google Scholar]
  218. Zawel L., Reinberg D. Initiation of transcription by RNA polymerase II: a multi-step process. Prog Nucleic Acid Res Mol Biol. 1993;44:67–108. doi: 10.1016/s0079-6603(08)60217-2. [DOI] [PubMed] [Google Scholar]
  219. Zhang C. C., Müller J., Hoch M., Jäckle H., Bienz M. Target sequences for hunchback in a control region conferring Ultrabithorax expression boundaries. Development. 1991 Dec;113(4):1171–1179. doi: 10.1242/dev.113.4.1171. [DOI] [PubMed] [Google Scholar]
  220. Zhou Q., Lieberman P. M., Boyer T. G., Berk A. J. Holo-TFIID supports transcriptional stimulation by diverse activators and from a TATA-less promoter. Genes Dev. 1992 Oct;6(10):1964–1974. doi: 10.1101/gad.6.10.1964. [DOI] [PubMed] [Google Scholar]
  221. Zlatanova J. S., van Holde K. E. Chromatin loops and transcriptional regulation. Crit Rev Eukaryot Gene Expr. 1992;2(3):211–224. [PubMed] [Google Scholar]