Regulated nucleosome mobility and the histone code

Nature Structural and Molecular Biology

Volumn 11, Issue 11, 2004, Pages 1037-1043

  Cosgrove, Michael S ^a   Boeke, Jef D ^a   Wolberger, Cynthia ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; ARGININE; DNA; HISTONE; INOSITOL POLYPHOSPHATE; LYSINE; NONHISTONE PROTEIN; SERINE; THREONINE; TYROSINE; UBIQUITIN;

ACETYLATION; BINDING SITE; CHROMATIN; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; DNA SUPERCOILING; DNA TRANSCRIPTION; GENE MUTATION; HUMAN; HYDROLYSIS; METHYLATION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEOMICS; REVIEW; TRANSLATION REGULATION; UBIQUITINATION;

ADENOSINE TRIPHOSPHATE; ANIMALS; CHROMATIN; DNA; HISTONES; HUMANS; HYDROLYSIS; MODELS, BIOLOGICAL; NUCLEOSOMES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY;

EID: 7544241632     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb851     Document Type: Review

References (73)

1. Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475-487 (2002).
2. Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41-45 (2000).
3. Fischle, W., Wang, Y. & Allis, C.D. Binary switches and modification cassettes in histone biology and beyond. Nature 425, 475-479 (2003).
4. Cocklin, R.R. & Wang, M. Identification of methylation and acetylation sites on mouse histone H3 using matrix-assisted laser desorption/ionization time-of-flight and nanoelectrospray ionization tandem mass spectrometry. J. Protein Chem. 22, 327-334 (2003).
5. Zhang, K. et al. Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. Anal. Biochem. 306, 259-269 (2002).
6. Zhang, L., Eugeni, E.E., Parthun, M.R. & Freitas, M.A. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 112, 77-86 (2003).
7. Freitas, M.A., Sklenar, A.R. & Parthun, M.R. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J. Cell Biochem. 92, 691-700 (2004).
8. Hansen, J.C. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu. Rev. Biophys. Biomol. Struct. 31, 361-392 (2002).
9. Luger, K. Structure and dynamic behavior of nucleosomes. Curr. Opin. Genet. Dev. 13, 127-135 (2003).
10. Pennings, S., Meersseman, G. & Bradbury, E.M. Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220, 101-110 (1991).
11. Becker, P.B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247-273 (2002).
12. Becker, P.B. Nucleosome sliding: facts and fiction. EMBO J. 21, 4749-4753 (2002).
13. Eisen, J.A., Sweder, K.S. & Hanawalt, P.C. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23, 2715-2723 (1995).
14. Whitehouse, I. et al. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400, 784-787 (1999).
15. Langst, G. & Becker, P.B. ISWI induces nucleosome sliding on nicked DNA. Mol. Cell 8, 1085-1092 (2001).
16. Guschin, D. & Wolffe, A.P. SWItched-on mobility. Curr. Biol. 9, R742-R746 (1999).
17. Schnitzler, G., Sif, S. & Kingston, R.E. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell 94, 17-27 (1998).
18. Lorch, Y., Cairns, B.R., Zhang, M. & Kornberg, R.D. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 94, 29-34 (1998).
19. Imbalzano, A.N., Schnitzler, G.R. & Kingston, R.E. Nucleosome disruption by human SWI/SNF is maintained in the absence of continued ATP hydrolysis. J. Biol. Chem. 271, 20726-20733 (1996).
20. Cote, J., Peterson, C.L. & Workman, J.L. 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 (1998).
21. Owen-Hughes, T., Utley, R.T., Cote, J., Peterson, C.L. & Workman, J.L. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273, 513-516 (1996).
22. Bazett-Jones, D.P., Cote, J., Landel, C.C., Peterson, C.L. & Workman, J.L. The SWI/SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains. Mol. Cell. Biol. 19, 1470-1478 (1999).
23. Zeng, L. & Zhou, M.M. Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 513, 124-128 (2002).
24. Brehm, A., Tufteland, K.R., Aasland, R. & Becker, P.B. The many colours of chromodomains. Bioessays 26, 133-140 (2004).
25. White, C.L., Suto, R.K. & Luger, K. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20, 5207-5218 (2001).
26. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. & Richmond, T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319, 1097-1113 (2002).
27. Cuthbert, G.L. et al. Histone deimination antagonizes arginine methylation. Cell 118, 545-553 (2004).
28. Wang, Y. et al. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306, 279-283 (2004).
29. Roberts, S.M. & Winston, F. 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 (1997).
30. Pollard, K.J. & Peterson, C.L. Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol. Cell. Biol. 17, 6212-6222 (1997).
31. Syntichaki, P., Topalidou, I. & Thireos, G. The Gcn5 bromodomain co-ordinates nucleosome remodelling. Nature 404, 414-417 (2000).
32. Brownell, J.E. et al. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843-851 (1996).
33. Guyon, J.R., Narlikar, G.J., Sif, S. & Kingston, R.E. Stable remodeling of tailless nucleosomes by the human SWI-SNF complex. Mol. Cell. Biol. 19, 2088-2097 (1999).
34. Park, J.H., Cosgrove, M.S., Youngman, E., Wolberger, C. & Boeke, J.D. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32, 273-279 (2002).
35. Kruger, W. et al. 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 (1995).
36. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-260 (1997).
37. Perez-Martin, J. & Johnson, A.D. Mutations in chromatin components suppress a defect of Gcn5 protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 18, 1049-1054 (1998).
38. Muthurajan, U.M. et al. Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 23, 260-271 (2004).
39. Flaus, A., Rencurel, C., Ferreira, H., Wiechens, N. & Owen-Hughes, T. Sin mutations alter inherent nucleosome mobility. EMBO J. 23, 343-353 (2004).
40. Kadosh, D. & Struhl, K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89, 365-371 (1997).
41. Horn, P.J., Crowley, K.A., Carruthers, L.M., Hansen, J.C. & Peterson, C.L. The SIN domain of the histone octamer is essential for intramolecular folding of nucleosomal arrays. Nat. Struct. Biol. 9, 167-171 (2002).
42. Steger, D.J., Haswell, E.S., Miller, A.L., Wente, S.R. & O'Shea, E.K. Regulation of chromatin remodeling by inositol polyphosphates. Science 299, 114-116 (2003).
43. Shen, X., Xiao, H., Ranallo, R., Wu, W.H. & Wu, C. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science 299, 112-114 (2003).
44. Kruger, W. & Herskowitz, I. A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol. Cell. Biol. 11, 4135-4146 (1991).
45. Mizuguchi, G. et al. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303, 343-348 (2004).
46. Redon, C. et al. Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12, 162-169 (2002).
47. McKittrick, E., Gafken, P.R., Ahmad, K. & Henikoff, S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).
48. Noma, K., Allis, C.D. & Grewal, S.I. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 293, 1150-1155 (2001).
49. Dorigo, B., Schalch, T., Bystricky, K. & Richmond, T.J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327, 85-96 (2003).
50. Clapier, C.R., Nightingale, K.P. & Becker, P.B. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30, 649-655 (2002).
51. Hamiche, A., Kang, J.G., Dennis, C., Xiao, H. & Wu, C. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl. Acad. Sci. USA 98, 14316-14321 (2001).
52. Clapier, C.R., Langst, G., Corona, D.F., Becker, P.B. & Nightingale, K.P. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21, 875-883 (2001).
53. Langst, G. & Becker, P.B. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677, 58-63 (2004).
54. Hassan, A.H. et al. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111, 369-379 (2002).
55. Kasten, M. et al. Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J. 23, 1348-1359 (2004).
56. Nishioka, K. et al. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev. 16, 479-489 (2002).
57. Ahringer, J. NuRD and SIN3 histone deacetylase complexes in development. Trends Genet. 16, 351-356 (2000).
58. van Leeuwen, F., Gafken, P.R. & Gottschling, D.E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109, 745-756 (2002).
59. Li, G. & Widom, J. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11, 763-769 (2004).
60. Khorasanizadeh, S. The nucleosome: from genomic organization to genomic regulation. Cell 116, 259-272 (2004).
61. Fleming, A.B. & Pennings, S. Antagonistic remodelling by Swi-Snf and Tup1-Ssn6 of an extensive chromatin region forms the background for FLO1 gene regulation. EMBO J. 20, 5219-5231 (2001).
62. Maile, T., Kwoczynski, S., Katzenberger, R.J., Wassarman, D.A. & Sauer, F. TAF1 activates transcription by phosphorylation of serine 33 in histone H2B. Science 304, 1010-1014 (2004).
63. Sun, Z.W. & Allis, C.D. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418, 104-108 (2002).
64. Ng, H.H., Xu, R.M., Zhang, Y. & Struhl, K. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. J. Biol. Chem. 277, 34655-34657 (2002).
65. Briggs, S.D. et al. Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418, 498 (2002).
66. DiRenzo, J. et al. BRG-1 is recruited to estrogen-responsive promoters and cooperates with factors involved in histone acetylation. Mol. Cell. Biol. 20, 7541-7549 (2000).
67. Mizuguchi, G., Vassilev, A., Tsukiyama, T., Nakatani, Y. & Wu, C. ATP-dependent nucleosome remodeling and histone hyperacetylation synergistically facilitate transcription of chromatin. J. Biol. Chem. 276, 14773-14783 (2001).
68. Galarneau, L. et al. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol. Cell 5, 927-937 (2000).
69. Reid, J.L., Iyer, V.R., Brown, P.O. & Struhl, K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6, 1297-1307 (2000).
70. Kim, J. et al. Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity 10, 345-355 (1999).
71. Fazzio, T.G. et al. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21, 6450-6460 (2001).
72. Sif, S., Saurin, A.J., Imbalzano, A.N. & Kingston, R.E. Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes. Genes Dev. 15, 603-618 (2001).
73. Zhou, Y., Santoro, R. & Grummt, I. The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription. EMBO J. 21, 4632-4640 (2002).