Continuous and widespread roles for the Swi-Snf complex in transcription

EMBO Journal

Volumn 18, Issue 8, 1999, Pages 2254-2264

  Biggar, Stephen R ^a   Crabtree, Gerald R ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Chromatin remodeling; GAL1; Gcn5; Histone acetylation; Swi Snf

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION REGULATION;

EID: 0033561043     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.8.2254     Document Type: Article

References (69)

1. Almer, A., Rudolph, H., Hinnen, A. and Horz, W. (1986) Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J., 5, 2689-2696.
2. Axelrod, J.D., Reagan, M.S. and Majors, J. (1993) GAL4 disrupts a repressing nucleosome during activation of GALI transcription in vivo. Genes Dev., 7, 857-869.
3. Berger, S.L., Pina, B., Silverman, N., Marcus, G.A., Agapite, J., Regier, J.L., Triezenberg, S.J. and Guarente, L. (1992) Genetic isolation of ADA2: a potential transcriptional adaptor required for function of certain acidic activation domains. Cell, 70, 251-265.
4. Brownell, J.E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D.G., Roth, S.Y. and Allis, C.D. (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell, 84, 843-851.
5. Burns, L.G. and Peterson, C.L. (1997) The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo. Mol. Cell. Biol., 17, 4811-4819.
6. Cairns, B.R. et al. (1996) RSC, an essential, abundant chromatin-remodeling complex. Cell, 87, 1249-1260.
7. Candau, R., Zhou, J.X., Allis, C.D. and Berger, S.L. (1997) Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivo. EMBO J., 16, 555-565.
8. Carlson, M. and Botstein, D. (1982) Two differentially regulated mRNAs with different 5′ ends encode secreted with intracellular forms of yeast invertase. Cell, 28, 145-154.
9. Cereghino, G.P. and Scheffler, I.E. (1996) Genetic analysis of glucose regulation in Saccharomyces cerevisiae: control of transcription versus mRNA turnover. EMBO J., 15, 363-374.
10. Cooper, J.P., Roth, S.Y. and Simpson, R.T. (1994) The global transcriptional regulators, SSN6 and TUP1, play distinct roles in the establishment of a repressive chromatin structure. Genes Dev., 8, 1400-1410.
11. Cote, J., Quinn, J., Workman, J.L. and Peterson, C.L. (1994) Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/ SNF complex. Science, 265, 53-60.
12. Cote, J., Peterson, C.L. and Workman, J.L. (1998) Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enhancing subsequent transcription factor binding. Proc. Natl Acad. Sci. USA, 95, 4947-4952.
13. Fiorentino, D.F. and Crabtree, G.R. (1997) Characterization of Saccharomyces cerevisiae dna2 mutants suggests a role for the helicase late in S phase. Mol. Biol. Cell, 8, 2519-2537.
14. Flick, J.S. and Johnston, M. (1990) Two systems of glucose repression of the GALI promoter in Saccharomyces cerevisiae. Mol. Cell. Biol., 10, 4757-4769.
15. Gaudreau, L., Schmid, A., Blaschke, D., Ptashne, M. and Horz, W. (1997) RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter Cell, 89, 55-62.
16. Gavin, I.M. and Simpson, R.T. (1997) Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure. EMBO J., 16, 6263-6271.
17. Grant, P.A. et al. (1997) Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev., 11, 1640-1650.
18. Guthrie, C. and Fink, G. (1991) Guide to Yeast Genetics and Molecular Biology. Academic Press, Inc., San Diego, CA.
19. Han, M. and Grunstein, M. (1988) Nucleosome loss activates yeast downstream promoters in vivo. Cell, 55, 1137-1145.
20. Han, M., Kim, U.J., Kayne, P. and Grunstein, M. (1988) Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J., 7, 2221-2228.
21. Herrick, D., Parker, R. and Jacobson, A. (1990) Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae. Mol. Cell. Biol., 10, 2269-2284.
22. Hirschhorn, J.N., Brown, S.A., Clark, C.D. and Winston, F. (1992) Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev., 6, 2288-2298.
23. i in single Saccharomyces cerevisiae cells with imaging of fura2. J. Biol. Chem., 265, 13391-13399.
24. Juan, L.J., Utley, R.T., Adams, C.C., Vettese-Dadey, M. and Workman, J.L. (1994) Differential repression of transcription factor binding by histone H1 is regulated by the core histone amino termini. EMBO J., 13, 6031-6040.
25. Kim, Y.J., Bjorklund, S., Li, Y., Sayre, M.H. and Kornberg, R.D. (1994) A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell, 77, 599-608.
26. Knezetic, J.A., Jacob, G.A. and Luse, D.S. (1988) Assembly of RNA polymerase II preinitiation complexes before assembly of nucleosomes allows efficient initiation of transcription on nucleosomal templates. Mol. Cell. Biol., 8, 3114-3121.
27. Kruger, W. and Herskowitz, I. (1991) A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol. Cell. Biol., 11, 4135-4146.
28. Kruger, W., Peterson, C.L., Sil, A., Coburn, C., Arents, G., Moudrianakis, E.N. and Herskowitz, I. (1995) Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev., 9, 2770-2779.
29. Kuo, M.H., Brownell, J.E., Sobel, R.E., Ranalli, T.A., Cook, R.G., Edmondson, D.G., Roth, S.Y. and Allis, C.D. (1996) Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature, 383, 269-272.
30. Laurent, B.C. and Carlson, M. (1992) Yeast SNF2/SWI2, SNF5 and SNF6 proteins function coordinately with the gene-specific transcriptional activators GAL4 and Bicoid [published erratum appears in Genes Dev., 1992 Nov; 6 (11): 2233]. Genes Dev., 6, 1707-1715.
31. Laurent, B.C., Treich, I. and Carlson, M. (1993) The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev., 7, 583-591.
32. Lee, D.Y., Hayes, J.J., Pruss, D. and Wolffe, A7.P. (1993) A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell, 72, 73-84.
33. Logie, C. and Peterson, C.L. (1997) Catalytic activity of the yeast SWI/ SNF complex on reconstituted nucleosome arrays. EMBO J., 16, 6772-6782.
34. Lorch, Y., LaPointe, J.W. and Komberg, R.D. (1987) Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell, 49, 203-210.
35. Lutfiyya, L.L. and Johnston, M. (1996) Two zinc-finger-containing repressers are responsible for glucose repression of SUC2 expression. Mol. Cell. Biol., 16, 4790-4797.
36. Marcus, G.A., Silverman, N., Berger, S.L., Horiuchi, J. and Guarente, L. (1994) Functional similarity and physical association between GCN5 and ADA2: putative transcriptional adaptors. EMBO J., 13, 4807-4815.
37. Matsui, T. (1987) Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly. Mol. Cell. Biol., 7, 1401-1408.
38. Melcher, K. and Johnston, S.A. (1995) GAL4 interacts with TATA-binding protein and coactivators. Mol. Cell. Biol., 15, 2839-2848.
39. Melton, D.A., Krieg, P.A., Rebagliati, M.R., Maniatis, T., Zinn, K. and Green, M.R. (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res., 12, 7035-7056.
40. Mizzen, C.A. et al. (1996) The TAF (II)250 subunit of TFIID has histone acetyltransferase activity. Cell, 87, 1261-1270.
41. Moqtaderi, Z., Bai, Y., Poon, D., Weil, P.A. and Struhl, K. (1996) TBP-associated factors are not generally required for transcriptional activation in yeast Nature, 383, 188-191.
42. Neigeborn, L. and Carlson, M. (1984) Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics, 108, 845-858.
43. Orphanides, G., LeRoy, G., Chang, C.H., Luse, D.S. and Reinberg, D. (1998) FACT, a factor that facilitates transcript elongation through nucleosomes. Cell, 92, 105-116.
44. Owen-Hughes, T., Utley, R.T., Cote, J., Peterson, C.L. and Workman, J.L. (1996) Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science, 273, 513-516.
45. Pennisi, E. (1997) Opening the way to gene activity. Science, 275, 155-157.
46. Peterson, C.L. and Tamkun, J.W. (1995) The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem. Sci., 20, 143-146.
47. Pina, B., Bruggemeier, U. and Beato, M. (1990) Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell, 60, 719-731.
48. Pollard, K.J. and Peterson, C.L. (1997) Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol. Cell. Biol., 17, 6212-6222.
49. Roberts, S.M. and Winston, F. (1997) Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics, 147, 451-465.
50. Roth, S.Y., Shimizu, M., Johnson, L., Grunstein, M. and Simpson, R.T. (1992) Stable nucleosome positioning and complete repression by the yeast alpha 2 repressor are disrupted by amino-terminal mutations in histone H4. Genes Dev., 6, 411-425.
51. Ryan, M.P., Jones, R. and Morse, R.H. (1998) SWI-SNF complex participation in transcriptional activation at a step subsequent to activator binding. Mol. Cell. Biol., 18, 1774-1782.
52. Schmitt, M.E., Brown, T.A. and Trumpower, B.L. (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res., 18, 3091-3092.
53. Schnitzler, G., Sif, S. and Kingston, R.E. (1998) Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell, 94, 17-27.
54. Sikorski, R.S. and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122, 19-27.
55. Stern, M., Jensen, R. and Herskowitz, I. (1984) Five SWI genes are required for expression of the HO gene in yeast. J. Mol. Biol., 178, 853-868.
56. Sternberg, P.W., Stern, M.J., Clark, I. and Herskowitz, I. (1987) Activation of the yeast HO gene by release from multiple negative controls. Cell, 48, 567-577.
57. Studitsky, V.M., Clark, D.J. and Felsenfeld, G. (1994) A histone octamer can step around a transcribing polymerase without leaving the template. Cell, 76, 371-382.
58. Studitsky, V.M., Kassavetis, G.A., Geiduschek, E.P. and Felsenfeld, G. (1997) Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science, 278, 1960-1963.
59. Taylor, I.C., Workman, J.L., Schuetz, T.J. and Kingston, R.E. (1991) Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev., 5, 1285-1298.
60. Thompson, C.M. and Young, R.A. (1995) General requirement for RNA polymerase II holoenzymes in vivo. Proc. Natl Acad. Sci. USA, 92, 4587-4590.
61. Turner, B.M. (1991) Histone acetylation and control of gene expression. J. Cell Sci., 99, 13-20.
62. Vallier, L.G. and Carlson, M. (1994) Synergistic release from glucose repression by mig1 and ssn mutations in Saccharomyces cerevisiae. Genetics, 137, 49-54.
63. Vettese-Dadey, M., Grant, P.A., Hebbes, T.R., Crane-Robinson, C., Allis, C.D. and Workman, J.L. (1996) Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J., 15, 2508-2518.
64. West, R.W.,Jr, Yocum, R.R. and Ptashne, M. (1984) Saccharomyces cerevisiae GAL1-GAL10 divergent promoter region: location and function of the upstream activating sequence UASG. Mol. Cell. Biol., 4, 2467-2478.
65. Wilson, C.J., Chao, D.M., Imbalzano, A.N., Schnitzler, G.R., Kingston, R.E. and Young, R.A. (1996) RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell, 84, 235-244.
66. Wolffe, A.P. (1994) Transcription: in tune with the histones. Cell, 77, 13-16.
67. Workman, J.L. and Roeder, R.G. (1987) Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell, 51, 613-622.
68. Workman, J.L., Roeder, R.G. and Kingston, R.E. (1990) An upstream transcription factor, USF (MLTF), facilitates the formation of preinitiation complexes during in vitro chromatin assembly. EMBO J., 9, 1299-1308.
69. Workman, J.L., Taylor, I.C. and Kingston, R.E. (1991) Activation domains of stably bound GAL4 derivatives alleviate repression of promoters by nucleosomes. Cell, 64, 533-544.