Nucleosome sliding: Facts and fiction

EMBO Journal

Volumn 21, Issue 18, 2002, Pages 4749-4753

  Becker, Peter B ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

ATPase; Chromatin assembly; Chromosome structure; Nucleosome positioning; Remodelling

Indexed keywords

CATALYSIS; CHROMATIN STRUCTURE; DNA DAMAGE; DNA HELIX; DNA METHYLATION; DNA REPAIR; EUKARYOTE EVOLUTION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ASSEMBLY; PROTEIN FOLDING; REVIEW;

ADENOSINE TRIPHOSPHATE; ANIMALS; CHROMATIN; DNA-BINDING PROTEINS; MODELS, GENETIC; NUCLEOSOMES; PROMOTER REGIONS (GENETICS);

EUKARYOTA;

EID: 0037119967     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdf486     Document Type: Review

References (63)

1. Beard,P. (1978) Mobility of histones on the chromosomes of simian virus 40. Cell, 15, 955-967.
2. Beato,M. and Eisfeld,K. (1997) Transcription factor access to chromatin. Nucleic Acids Res., 25, 3559-3563.
3. Becker,P.B. and Hörz,W. (2002) ATP-dependent nucleosome remodeling. Annu. Rev. Biochem., 71, 247-273.
4. Becker,P.B., Ruppert,S. and Schütz,G. (1987) Genomic footprinting reveals cell type-specific binding of ubiquitous transcription factors. Cell, 51, 435-443.
5. Bednar,J., Horowitz,R.A., Grigoryev,S.A., Carruthers,L.M., Hansen,J.C., Koster,A.J. and Woodcock,C.L. (1998) Nucleosomes, linker DNA and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl Acad. Sci. USA, 95, 14173-14178.
6. Bozhenok,L., Wade,P.A. and Varga-Weisz,P. (2002) WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J., 21, 2231-2241.
7. Brehm,A., Langst,G., Kehle,J., Clapier,C.R., Imhof,A., Eberharter,A., Muller,J. and Becker,P.B. (2000) dMi-2 and ISWI chromatin remodelling factors have distinct nucleosome binding and mobilization properties. EMBO J., 19, 4332-4341
8. Buttinelli,M., Di Mauro,E. and Negri,R. (1993) Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo. Proc. Natl Acad. Sci. USA, 90, 9315-9319.
9. Clapier,C.R., Nightingale,K.P. and Becker,P.B. (2002) A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res., 30, 649-655.
10. Corona,D.F.V., Clapier,C.R., Becker,P.B. and Tamkun,J.W. (2002) Modulation of ISWI function by site-specific histone acetylation. EMBO rep., 3, 242-247.
11. Deuring,R. et al. (2000) The ISWI chromatin remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Mol. Cell, 5, 355-365.
12. Eberharter,A., Ferrari,S., Langst,G., Straub,T., Imhof, A., Varga-Weisz,P., Wilm,M. and Becker,P.B. (2001) Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J., 20, 3781-3788.
13. Eisen,J.A., Sweder,K.S. and Hanawalt,P.C. (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res., 23, 2715-2723.
14. Fedor,M.J., Lue,N.F. and Kornberg,R.D. (1988) Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J. Mol. Biol., 204, 109-127.
15. Flaus,A. and Owen-Hughes,T. (2001) Mechanisms for ATP-dependent chromatin remodelling. Curr. Opin. Genet. Dev., 11, 148-154.
16. Fletcher,T.M. and Hansen,J.C. (1996) The nucleosomal array: structure/ function relationships. Crit. Rev. Eukaryot. Gene Expr., 6, 149-188.
17. Fragoso,G.,John,S., Roberts,M.S. and Hager,G.L. (1995) Nucleosome positioning on the MMTV LTR results from frequency-biased occupancy of multiple frames. Genes Dev., 9, 1933-1947.
18. Francis,N.J., Saurin,A.J., Shao,Z. and Kingston,R.E. (2001) Reconstitution of a functional core polycomb repressive complex. Mol. Cell, 8, 545-556.
19. Gavin,I., Horn,P.J. and Peterson,C.L. (2001) SWI/SNF chromatin remodeling requires changes in DNA topology. Mol. Cell, 7, 97-104.
20. Goldmark,J.P., Fazzio,T.G., Estep,P.W., Church,G.M. and Tsukiyama,T. (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell, 103, 423-433.
21. Gregory,P.D., Wagner,K. and Hörz,W. (2001) Histone acetylation and chromatin remodeling. Exp. Cell Res., 265, 195-202.
22. Guschin,D., Wade,P.A., Kikyo,N. and Wolffe,A.P. (2000) ATP- Dependent histone octamer mobilization and histone deacetylation mediated by the Mi-2 chromatin remodeling complex. Biochemistry, 39, 5238-5245.
23. Hamiche,A., Sandaltzopoulos,R., Gdula,D.A. and Wu,C. (1999) ATP- dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell, 97, 833-842.
24. Hassan,A.H., Neely,K.E. and Workman,J.L. (2001) Histone acetyl-transferase complexes stabilize SWI/SNF binding to promoter nucleosomes. Cell, 104, 817-827.
25. Havas,K., Flaus,A., Phelan,M., Kingston,R., Wade,P.A., Lilley,D.M. and Owen-Hughes,T. (2000) Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell, 103, 1133-1142.
26. Horn,P.J., Carruthers,L.M., Logie,C., Hill,D.A., Solomon,M.J., Wade,P.A., Imbalzano,A.N., Hansen,J.C. and Peterson,C.L. (2002) Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nat. Struct. Biol., 9, 263-267.
27. Ito,T., Bulger,M., Pazin,M.J., Kobayashi,R. and Kadonaga,J.T. (1997a) ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell, 90, 145-155.
28. Ito,T., Tyler,J.K. and Kadonaga,J.T. (1997b) Chromatin assembly factors: a dual function in nucleosome formation and mobilization? Genes Cells, 2, 593-600.
29. Ito,T., Levenstein,M.E., Fyodorov,D.V., Kutach,A.K., Kobayashi,R. and Kadonaga,J.T. (1999) ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev., 13, 1529-1539.
30. Jaskelioff,M., Gavin,I.M., Peterson,C.L. and Logie,C. (2000) SWI-SNF-mediated nucleosome remodeling: role of histone octamer mobility in the persistence of the remodeled state. Mol. Cell. Biol., 20, 3058-3068.
31. Jenuwein,T. and Allis,C.D. (2001) Translating the histone code. Science, 293, 1074-1080.
32. Kang,J.G., Hamiche,A. and Wu,C. (2002) GAL4 directs nucleosome sliding induced by NURF. EMBO J., 21, 1406-1413.
33. Kent,N.A., Karabetsou,N., Politis,P.K. and Mellor,J. (2001) In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev., 15, 619-626.
34. Kornberg,R.D. and Stryer,L. (1988) Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res., 16, 6677-6690.
35. Längst,G. and Becker,P.B. (2001a) ISWI induces nucleosome sliding on nicked DNA. Mol. Cell, 8, 1085-1092.
36. Längst,G. and Becker,P.B. (2001b) Nucleosome mobilization and positioning by ISWI-containing chromatin remodeling factors. J. Cell Sci., 114, 2561-2568.
37. Längst,G., Bonte,E.J., Corona,D.F.V. and Becker,P.B. (1999) Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell, 97, 843-852.
38. Liu,R., Liu,H., Chen,X., Kirby,M., Brown,P.O. and Zhao,K. (2001) Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell, 106, 309-318.
39. Lomvardas,S. and Thanos,D. (2001) Nucleosome sliding via TBP DNA binding in vivo. Cell, 106, 685-696.
40. Lorch,Y., Zhang,M. and Kornberg,R.D. (1999) Histone octamer transfer by a chromatin-remodeling complex. Cell, 96, 389-392.
41. Luger,K. and Richmond,T.J. (1998) DNA binding within the nucleosome core. Curr. Opin. Struct. Biol., 8, 33-40.
42. Meersseman,G., Pennings,S. and Bradbury,E.M. (1992) Mobile nucleosomes-a general behaviour. EMBO J., 11, 2951-2959.
43. Muchardt,C., Reyes,J.C., Bourachot,B., Leguoy,E. and Yaniv,M. (1996) The hbrm and BRG-1 proteins, components of the human SNF/SWI complex, are phosphorylated and excluded from the condensed chromosomes during mitosis. EMBO J., 15, 3394-3402.
44. Narlikar,G.J., Phelan,M.L. and Kingston,R.E. (2001) Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity. Mol. Cell, 8, 1219-1230.
45. Narlikar,G.J., Fan,H.Y. and Kingston,R.E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell, 108, 475-487.
46. Pennings,S., Meersseman,G. and Bradbury,M.E. (1991) Mobility on nucleosomes on 5S rDNA. J. Mol. Biol., 220, 101-110.
47. Pennings,S., Meersseman,G. and Bradbury,E.M. (1994) Linker histones H1 and H5 prevent the mobility of positioned nucleosomes. Proc. Natl Acad. Sci. USA, 91, 10275-10279.
48. Peterson,C.L. and Logie,C. (2000) Recruitment of chromatin remodeling machines. J. Cell. Biochem., 78, 179-185.
49. Phelan,M.L., Schnitzler,G.R. and Kingston,R.E. (2000) Octamer transfer and creation of stably remodeled nucleosomes by human SWI-SNF and its isolated ATPases. Mol. Cell. Biol., 20, 6380-6389.
50. Schiessel,H., Widom,J., Bruinsma,R.F. and Gelbart,W.M. (2001) Polymer reptation and nucleosome repositioning. Phys. Rev. Lett., 86, 4414-4417.
51. Schnitzler,G.R., Cheung,C.L., Hafner,J.H., Saurin,A.J., Kingston,R.E. and Lieber,C.M. (2001) Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Mol. Cell. Biol., 21, 8504-8511.
52. Tanaka,S., Livingstone-Zatchej,M. and Thoma,F. (1996) Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context. J. Mol. Biol., 257, 919-934.
53. Tsukiyama,T. and Wu,C. (1995) Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell, 83, 1011-1020.
54. Tsukiyama,T., Daniel, C., Tamkun,J. and Wu,C. (1995) ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kD subunit of the nucleosome remodeling factor. Cell, 83, 1021-1026.
55. Tsukiyama,T., Palmer,J., Landel,C.C., Shiloach,J. and Wu,C. (1999) Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev., 13, 686-697.
56. Van Holde,K.E. and Yager,T.D. (1985) Nucleosome motion: evidence and models. In Nicolini,C. and Ts'o,P.O.P. (eds), Structure and Function of the Genetic Apparatus. Plenum Press, New York, NY, pp. 35-53.
57. Varga-Weisz,P.D., Blank,T.A. and Becker,P.B. (1995) Energy- dependent chromatin accessibility and nucleosome mobility in a cell-free system. EMBO J., 14, 2209-2216.
58. Varga-Weisz,P.D., Wilm,M., Bonte,E., Dumas,K., Mann,M. and Becker,P.B. (1997) Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature, 388, 598-602.
59. Wade,P.A., Gegonne,A., Jones,P.L., Ballestar,E., Aubry,F. and Wolffe,A.P. (1999) Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat. Genet., 23, 62-66.
60. Wallrath,L.L., Quinn,L., Granok,H. and Elgin,S.C.R. (1994) Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. BioEssays, 16, 165-170.
61. Widom,J. (1999) Equilibrium and dynamic nucleosome stability. Methods Mol. Biol., 119, 61-77.
62. Woodcock,C.L. and Dimitrov,S. (2001) Higher-order structure of chromatin and chromosomes. Curr. Opin. Genet. Dev., 11, 130-135.
63. Xiao,H., Sandaltzopoulos,R., Wang,H., Hamiche,A., Ranallo,R., Lee,K., Fu,D. and Wu,C. (2001) Dual functions of the largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol. Cell, 8, 531-543.