Dynamics of nucleosome remodelling by individual ACF complexes

Nature

Volumn 462, Issue 7276, 2009, Pages 1022-1027

  Blosser, Timothy R ^a   Yang, Janet G ^b   Stone, Michael D ^a,c   Narlikar, Geeta J ^b   Zhuang, Xiaowei ^a,c,d  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HARVARD UNIVERSITY   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; TRANSCRIPTION FACTOR SNF;

CHROMOSOME; DNA; GENETIC ENGINEERING; REAL TIME; TRANSLOCATION;

ARTICLE; BASE PAIRING; CHROMATIN ASSEMBLY AND DISASSEMBLY; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN TRANSPORT;

ADENOSINE TRIPHOSPHATE; CHROMATIN ASSEMBLY AND DISASSEMBLY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; MODELS, MOLECULAR; NUCLEOSOMES; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS;

EID: 72949099668     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08627     Document Type: Article

References (42)

1. Becker, P. B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247-273 (2002).
2. Narlikar, G. J., Fan, H. Y. & Kingston, R. E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475-487 (2002).
3. Flaus, A. & Owen-Hughes, T. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14, 165-173 (2004).
4. Smith, C. L. & Peterson, C. L. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65, 115-148 (2004).
5. Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273-304 (2009).
6. Saha, A., Wittmeyer, J. & Cairns, B. R. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16, 2120-2134 (2002).
7. Whitehouse, I., Stockdale, C., Flaus, A., Szczelkun, M. D. & Owen-Hughes, T. Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme. Mol. Cell. Biol. 23, 1935-1945 (2003).
8. Tsukiyama, T., Palmer, J., Landel, C. C., Shiloach, J. & Wu, C. Characterization of the Imitation Switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13, 686-697 (1999).
9. Hamiche, A., Sandaltzopoulos, R., Gdula, D. A. & Wu, C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97, 833-842 (1999).
10. Längst, G., Bonte, E. J., Corona, D. F. & Becker, P. B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97, 843-852 (1999).
11. Kassabov, S. R., Henry, N. M., Zofall, M., Tsukiyama, T. & Bartholomew, B. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22, 7524-7534 (2002).
12. Zhang, Y. et al. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol. Cell 24, 559-568 (2006).
13. Lia, G. et al. Direct observation of DNA distortion by the RSC complex. Mol. Cell 21, 417-425 (2006).
14. Shundrovsky, A., Smith, C. L., Lis, J. T., Peterson, C. L. & Wang, M. D. Probing SWI/ SNF remodeling of the nucleosome by unzipping single DNA molecules. Nature Struct. Mol. Biol. 13, 549-554 (2006).
15. Stryer, L. & Haugland, R. P. Energy transfer: a spectroscopic ruler. Proc. Natl Acad. Sci. USA 58, 719-726 (1967).
16. Ha, T. et al. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl Acad. Sci. USA 93, 6264-6268 (1996).
17. Zhuang, X. et al. A single molecule study of RNA catalysis and folding. Science 288, 2048-2051 (2000). (Pubitemid 30397686)
18. Ito, T., Bulger, M., Pazin, M. J., Kobayashi, R. & Kadonaga, J. T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90, 145-155 (1997).
19. Ito, T. et al. ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13, 1529-1539 (1999).
20. Bochar, D. A. et al. A family of chromatin remodeling factors related to Williams syndrome transcription factor. Proc. Natl Acad. Sci. USA 97, 1038-1043 (2000).
21. LeRoy, G., Loyola, A., Lane, W. S. & Reinberg, D. Purification and characterization of a human factor that assembles chromatin. J. Biol. Chem. 275, 14787-14790 (2000).
22. Poot, R. A. et al. HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J. 19, 3377-3387 (2000).
23. Yang, J. G., Madrid, T. S., Sevastopoulos, E. & Narlikar, G. J. The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing. Nature Struct. Mol. Biol. 13, 1078-1083 (2006).
24. Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19-42 (1998).
25. Abbondanzieri, E. A. et al. Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature 453, 184-189 (2008).
26. He, X., Fan, H. Y., Narlikar, G. J. & Kingston, R. E. Human ACF1 alters the remodeling strategy of SNF2h. J. Biol. Chem. 281, 28636-28647 (2006).
27. Stockdale, C., Flaus, A., Ferreira, H. & Owen-Hughes, T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J. Biol. Chem. 281, 16279-16288 (2006).
28. Schwanbeck, R., Xiao, H. & Wu, C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279, 39933-39941 (2004).
29. Zofall, M., Persinger, J., Kassabov, S. R. & Bartholomew, B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nature Struct. Mol. Biol. 13, 339-346 (2006).
30. Dang, W. & Bartholomew, B. Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Mol. Cell. Biol. 27, 8306-8317 (2007).
31. Li, G., Levitus, M., Bustamante, C. & Widom, J. Rapid spontaneous accessibility of nucleosomal DNA. Nature Struct. Mol. Biol. 12, 46-53 (2004).
32. Partensky, P. D. & Narlikar, G. J. Chromatin remodelers act globally, sequence positions nucleosomes locally. J. Mol. Biol. 391, 12-25 (2009).
33. 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
34. Fyodorov, D. V. & Kadonaga, J. T. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 896-900 (2002).
35. Gangaraju, V. K., Prasad, P., Srour, A., Kagalwala, M. N. & Bartholomew, B. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Mol. Cell 35, 58-69 (2009).
36. Raki, L. R. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature doi:10.1038/nature08621 (this issue).
37. Strohner, R. et al. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nature Struct. Mol. Biol. 12, 683-690 (2005).
38. Fitzgerald, D. J. et al. Reaction cycle of the yeast Isw2 chromatin remodeling complex. EMBO J. 23, 3836-3843 (2004).
39. Cairns, B. R. Chromatin remodeling: insights and intrigue from single-molecule studies. Nature Struct. Mol. Biol. 14, 989-996 (2007).
40. Luger, K., Rechsteiner, T. J. & Richmond, T. J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304, 3-19 (1999).
41. Aalfs, J. D., Narlikar, G. J. & Kingston, R. E. Functional differences between the human ATP-dependent nucleosome remodeling proteins BRG1 and SNF2H. J. Biol. Chem. 276, 34270-34278 (2001).
42. Rasnik, I., McKinney, S. A. & Ha, T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nature Methods 3, 891-893 (2006).