A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter

Cell

Volumn 87, Issue 3, 1996, Pages 459-470

  Zhu, Zhiwu ^a   Thiele, Dennis J ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COPPER ION; METAL; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE); TRANSCRIPTION FACTOR;

ARTICLE; CANDIDA GLABRATA; CHROMATIN STRUCTURE; DETOXIFICATION; DNA BINDING; DNA FOOTPRINTING; METAL BINDING; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION;

CANDIDA GLABRATA;

EID: 0030297549     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81366-5     Document Type: Article

References (46)

1. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (1987). Current Protocols in Molecular Biology (New York: John Wiley & Sons).
2. Bernardi, F., Koller, T., and Thoma, F. (1991). The ade6 gene of the fission yeast Schizosaccharomyces pombe has the same chromatin structure in the chromosome and in plasmids. Yeast 7, 547-558.
3. Company, M., Adler, C., and Errede, B. (1988). Identification of a Ty1 regulatory sequence responsive to STE7 and STE12. Mol. Cell. Biol. 8, 2545-2554.
4. Dickerson, R.E., Goodsell, D., and Kopa, M.L. (1996). MPD and DNA bending in crystals and in solution. J. Mol. Biol. 256, 108-125.
5. Fascher, K.D., Schmits, J., and Horz, W. (1990). Role of transactivating proteins in the generation of active chromatin at the PHO5 promoter in S. cerevisiae. EMBO J. 9, 2523-2528.
6. Felsenfeld, G. (1992). Chromatin as an essential part of the transcriptional mechanism. Nature 355, 219-224.
7. Ganter, B., Tan, S., and Richmond, T.J. (1993). Genomic footprinting of the promoter regions of STE2 and STE3 genes in the yeast Saccharomyces cerevisiae. J. Mol. Biol. 234, 975-987.
8. Garrity, P.A. and Wold, B.J. (1992). Effects of different DNA polymerases in ligation-mediated PCR: enhanced genomic sequencing and in vivo footprinting. Proc. Natl. Acad. Sci. USA 89, 1021-1025.
9. Grimm, S., and Baeuerle, P.A. (1993). The inducible transcription factor NF-κB: structure-function relationship of its protein subunits. Biochem. J. 290, 297-308.
10. Gross, D.S., and Garrard, W.T. (1988). Nuclease hypersensitive sites in chromatin. Ann. Rev. Biochem. 57, 159-197.
11. Halliwell, B. and Gutteridge, M.C. (1990). Role of free radicals and catalytic metal ions in human disease: an overview. Methods Enzymol. 186, 1-85.
12. Hayes, J.J., Bashkin, J., Tullius, T.D., and Wolffe, A.P. (1991). The histone core exerts a dominant constraint on the structure of DNA in a nucleosome. Biochemistry 30, 8434-8440.
13. Hayes, J.J., and Wolffe, A.P. (1992). The interaction of transcription factors with nucleosomal DNA. BioEssays 14, 597-603.
14. Iyer, V., and Struhl, K. (1995). Poly (dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14, 2570-2579.
15. Kingston, R.E., Bunker, C.A., and Imbalzano, A.N. (1996). Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev. 10, 905-920.
16. Koch, K., and Thiele, D.J. (1996). Autoactivation by a Candida glabrata copper metalloregulatory transcription factor requires critical minor groove interactions. Mol. Cell. Biol. 16, 724-734.
17. Kornberg, R.D., and Lorch, Y. (1995). Interplay between chromatin structure and transcription. Curr. Opin. Cell Biol. 7, 371-375.
18. Lee, H.J., Masuda, E.S., Arai, N., Arai, K., and Yokota, T. (1995). Definition of cis-regulatory elements of the mouse interleukin-5 gene promoter. J. Biol. Chem. 270, 17541-17550.
19. Lewin, B. (1994). Chromatin and gene expression: constant questions, but changing answers. Cell 79, 397-406.
20. Lu, Q., Wallrath, L.L., and Elgin, S.C.R. (1995). The role of a positioned nucleosome at the Drosophila melanogaster hsp26 promoter. EMBO J. 14, 4738-4746.
21. McGhee, J., and Felsenfeld, G. (1983). Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. Cell 32, 1205-1215.
22. Nelson, H.C.M., Finch, J.T., Luisi, B.F., and Klug, A. (1987). The structure of an oligo(dA) • oligo(dT) tract and its biological implications. Nature 330, 221-226.
23. Noll, M., and Kornberg, R.D. (1977). Action of microccocal nuclease on chromatin and location of histone H1. J. Mol. Biol. 109, 393-404.
24. Paranjape, S.M., Kamakaka, R.T., and Kadonaga, J.T. (1994). Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu. Rev. Biochem. 63, 265-297.
25. Perez-Ortin, J.E., Estruch, F., Matallana, E., and Franco, L. (1987). Fine analysis of the chromatin structure of the yeast SUC2 gene and of its changes upon derepression. Comparison between the chromosomal and plasmid-inserted copies. Nucleic Acids Res. 15, 6937-6954.
26. Peterson, C.L., and Tamkun, J.W. (1995). The SWI-SNF complex: a chromatin remodeling machine? Trends Biol. Sci. 20, 143-146.
27. Polach, K.J., and Widom, J. (1995). Mechanism of protein access to specific DNA sequence in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254, 130-149.
28. Puhl, H.L., Gudibande, S.R., and Behe, M.J. (1991). Poly [d(A • T)] and other synthetic polydeoxynucleotides containing oligoadenosine tracts form nucleosomes easily. J. Mol. Biol. 222, 1149-1160.
29. Richmond, T.J., Finch, J.T., Rushton, B., Rhodes, D., and Klug, A. (1984). Structure of the nucleosome core particle at 7 Å resolution. Nature 311, 532-537.
30. Sabova, L., Zeman, I., Supek, F., and Kolarov, J. (1993). Transcriptional control of AAC3 gene encoding mitochondrial ADP/ATP translocator in Saccharomyces cerevisiae by oxygen, heme, and ROX1 factor. Eur. J. Biochem. 273, 547-553.
31. Shopland, L.S., Hirayoshi, K., Fernandes, M., and Lis, J.T. (1995). 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, 2756-2769.
32. Simpson, R.T., and Stafford, D.W. (1983). Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. USA 80, 51-55.
33. Strauss, E.C., Andrews, N.C., Higgs, D.R., and Orkin, S.H. (1992). In vivo footprinting of the human α-globin locus upstream regulatory element by guanine and adenine ligation-mediated polymerase chain reaction. Mol. Cell. Biol. 12, 2135-2142.
34. Struhl, K. (1996). Chromatin structure and RNA polymerase II connection: implications for transcription. Cell 84, 179-182.
35. Tsai, M.-J., and O'Malley, B.W. (1994). Molecular mechanisms of action of steroid/thyroid receptor superfamily members. Annu. Rev. Biochem. 63, 451-486.
36. Truss, M., Barstch, J., Schelbert, A., Hache, R.J.G., and Beato, M. (1994). Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J. 14, 1737-1751.
37. Tsukiyama, T., and Wu, C. (1995). Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83, 1011-1020.
38. Wallrath, L.L., Lu, Q., Granok, H., and Elgin, S.C.R. (1994). Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. BioEssays 16, 165-170.
39. Wilson, C.J., Cho, 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.
40. Wolffe, A.P., and Pruss, D. (1996). Targeting chromatin disruption: Transcription regulators that acetylate histones. Cell 84, 817-819.
41. Wu, C. (1980). The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286, 854-860.
42. Wu, C. (1995). Heat shock transcription factors: structure and regulation. Annu. Rev. Cell Dev. Biol. 11, 441-469.
43. Zhou, P., Szczypka, M.S., Sosinowski, T., and Thiele, D.J. (1992). Expression of a yeast metallothionein gene family is activated by a single metalloregulatory transcription factor. Mol. Cell. Biol. 12, 3766-3775.
44. Zhou, P., and Thiele, D.J. (1993). Rapid transcriptional autoregulation of a yeast metalloregulatory factor is essential for high-level copper detoxification. Genes Dev. 7, 1824-1835.
45. Zhu, Z., Szczypka, M.S., and Thiele, D.J. (1995). Transcriptional regulation and function of yeast metallothionein. In Genetic Response to Metals, B. Sarkar, ed. (New York: Marcel Dekker, Inc.), pp. 379-395.
46. Zitomer, R.S., and Lowry, C.V. (1992). Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiol. Rev. 56, 1-11.