Effects of Sin- versions of histone H4 on yeast chromatin structure and function

EMBO Journal

Volumn 16, Issue 8, 1997, Pages 2086-2095

  Wechser, Mark A ^a   Kladde, Michael P ^b   Alfieri, Jennifer A ^b   Peterson, Craig L ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Chromatin; Nucleosome; SIN1; SWI SNF; Transcription

Indexed keywords

DNA; HISTONE H3; HISTONE H4; METHYLTRANSFERASE; MICROCOCCAL NUCLEASE; MUTANT PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SUBSTITUTION; ARTICLE; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA SUPERCOILING; GENE EXPRESSION; GENE INDUCTION; GENE REPRESSION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN; REGULATOR GENE; YEAST;

CHROMATIN; CHROMOSOMES, FUNGAL; DNA, FUNGAL; DNA, SUPERHELICAL; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; HISTONES; MEMBRANE TRANSPORT PROTEINS; MICROCOCCAL NUCLEASE; MUTATION; PHOSPHATE TRANSPORT PROTEINS; RECOMBINANT FUSION PROTEINS; REGULATORY SEQUENCES, NUCLEIC ACID; SITE-SPECIFIC DNA-METHYLTRANSFERASE (ADENINE-SPECIFIC); TRANSCRIPTION, GENETIC; YEASTS;

EID: 0030893061     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.8.2086     Document Type: Article

References (49)

1. Adams, C.C. and Workman, J.L. (1993) Nucleosome displacement in transcription. Cell, 72, 305-308.
2. Almer, A. and Horz, W. (1986) Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the PHO5/PHO3 locus in yeast. EMBO J., 5, 2681-2687.
3. 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.
4. Arents, G. and Moudrianakis, E.N. (1993) Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc. Natl Acad. Sci. USA, 90, 10489-10443.
5. Arents, G., Burlingame, R.W., Wang, B.C., Love, W.E. and Moudrianakis, E.N. (1991) The nucleosomal core histone octamer at 3.1 Å resolution: a tripartite protein assembly and a left-handed superhelix. Proc. Natl Acad. Sci. USA, 88, 10148-10152.
6. Clark-Adams, C.D., Norris, D., Osley, M.A., Fassler, J.S. and Winston, F. (1988) Changes in histone gene dosage alter transcription in yeast. Genes Dev., 2, 150-159.
7. 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.
8. Fassler, J.S. and Winston, F. (1988) Isolation and analysis of a novel class of suppressor of Ty insertion mutations in Saccharomyces cerevisiae. Genetics, 118, 203-212.
9. Fisher-Adams, G. and Grunstein, M. (1995) Yeast histone H4 and H3 N-termini have different effects on the chromatin structure of the GAL1 promoter. EMBO J., 14, 1468-1477.
10. Germond, J.E., Hirt, B., Oudet, P., Gross-Bellark, M. and Chambon, P. (1975) Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc. Natl Acad. Sci. USA, 72, 1843-1847.
11. Gilbert, D.M., Losson, R. and Chambon, P. (1992) Ligand dependence of estrogen receptor induced changes in chromatin structure. Nucleic Acids Res., 20, 4525-1531.
12. Guarente, L. and Mason, T. (1983) Heme regulates transcription of the CYC1 gene of Saccharomyces cerevisiae via an upstream activation site. Cell, 32, 1279-1286.
13. Han, M. and Grunstein, M. (1988) Nucleosome loss activates yeast downstream promoters in vivo. Cell, 55, 1137-1145.
14. 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.
15. Higuchi, R., Krummel, B. and Saiki, R.K. (1988) A general method for in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res., 16, 7351-7367.
16. Holm, C., Meeks-Wagner, D.W., Fangman, W.L. and Botstein, D. (1986) A rapid, efficient method for isolating DNA from yeast. Gene, 42, 169-173.
17. Imbalzano, A.N., Kwon, H., Green, M.R. and Kingston, R.E. (1994) Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature, 370, 481-485.
18. Johnson, L.M., Fisher-Adams, G. and Grunstein, M. (1992) Identification of a non-basic domain in the histone H4 N-terminus required for repression of the yeast silent mating loci. EMBO J., 11, 2201-2209.
19. Kayne, P.S., Kim, U.-J., Han, M., Mullen, J.R., Yoshizaki, F. and Grunstein, M. (1988) Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell, 55, 27-39.
20. Kim, U.-J., Han, M., Kayne, P. and Grunstein, M. (1988) Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. EMBO J., 7, 2211-2219.
21. Kladde, M.P. and Simpson, R.T. (1994) Positioned nucleosomes inhibit Dam methylation in vivo. Proc. Natl Acad. Sci. USA, 91, 1361-1365.
22. Kladde, M.P. and Simpson, R.T. (1996) Chromatin structure mapping in vivo using methyltransferases. Methods Enzymol., 274, 214-233.
23. Kladde, M.P., Xu, M. and Simpson, R.T. (1996) Direct probing of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J., 15, 6290-6300.
24. Kruger, W. and Herskowitz, I. (1991) A negative regulator of HO gene transcription. SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol. Cell. Biol., 11, 4135-4146.
25. 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.
26. Kwon, H., Imbalzano, A.N., Khavari, P.A., Kingston, R.E. and Green, M.R. (1994) Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex. Nature, 370, 477-181.
27. Laybourn, P.J. and Kadonaga, J.T. (1991) The role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science, 254, 238-245.
28. Linder, C. and Thoma, F. (1994) Histone H1 expressed in Saccharomyces cerevisiae binds to chromatin and affects survival, growth, transcription, and plasmid stability but does not change nucleosome spacing. Mol. Cell. Biol., 14, 2822-2835.
29. Lorch, Y., LaPointe, J.W. and Kornberg, R.D. (1987) Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell, 49, 203-210.
30. Oshima, Y. (1982) The Molecular Biology of the Yeast Saccharomyces: Metabolism and Gene Expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. 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.
32. Patterton, H.G. and Simpson, R.T. (1994) Nucleosomal location of the STE6 TATA box and Mat alpha 2p-mediated repression. Mol. Cell Biol., 14, 4002-4010.
33. Peterson, C.L. and Tamkun, J.W. (1995) The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem. Sci., 20, 143-146.
34. Peterson, C.L., Kruger, W. and Herskowitz, L. (1991) A functional interaction between the C-terminal domain of RNA polymerase II and the negative regulator SIN1. Cell, 64, 1135-1143.
35. Rogers, D.T., Lemire, J.M. and Bostian, K.A. (1982) Acid phosphatase polypeptides in Saccharomyces cerevisiae are encoded by a differentially regulated multigene family. Proc. Natl Acad. Sci. USA, 79, 2157-2161.
36. Rose, M.D., Winston, F. and Hieter, P. (1990) Methods in Yeast Genetics: A Laboratory Course Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. Roth, S.Y., Dean, A. and Simpson, R.T. (1990) Yeast alpha2 repressor positions nucleosomes in TRP1/ARS1 chromatin. Mol. Cell Biol., 10, 2247-2260.
38. Roth, S.Y., Shimizu, M., Johnson, L., Grunstein, M. and Simpson, R.T. (1992) Stable nucleosome positioning and complete repression by the yeast α2 repressor are disrupted by amino-terminal mutations in histone H4. Genes Dev., 6, 411-425.
39. Rudolph, H. and Hinnen, A. (1987) The yeast PHO5 promoter: phosphate-control elements and sequences mediating mRNA start site selection. Proc. Natl Acad. Sci. USA, 84, 1340-1344.
40. Shimizu, M., Roth, S.Y. and Szent-Gyorgyi, C. (1991) Nucleosomes are positioned with base pair precision adjacent to the alpha2 operator in Saccharomyces cerevisiae. EMBO J., 10, 3033-3041.
41. 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.
42. Simpson, R.T., Thoma, F. and Brubaker, J.M. (1985) Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell, 42, 799-808.
43. 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.
44. 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.
45. Vogel, K. and Hinnen, A. (1990) The yeast phosphatase system. Mol. Microbiol., 4, 2013-2017.
46. Wang, J.C. (1982) The path of DNA in the nucleosome. Cell, 29, 724-726.
47. West, R.W., Yocum, R.R. and Ptashne, M. (1984) Saccharomyces cerevisiae GAL1-GAL10 divergent promoter region: location and function of the upstream activator sequence UASg. Mol. Cell. Biol., 4, 2467-2478.
48. Wolffe, A.P. (1994) Switched-on chromatin. Curr. Biol., 4, 525-528.
49. Worcel, A., Strogatz, S. and Riley, D. (1981) Structure of chromatin and the linking number of DNA. Proc. Natl Acad. Sci. USA, 78, 1461-1465.