Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules (original) (raw)
References
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 Å resolution. J. Mol. Biol.319, 1097–1113 (2002). ArticleCAS Google Scholar
Kingston, R.E. & Narlikar, G.J. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev.13, 2339–2352 (1999). ArticleCAS Google Scholar
Kornberg, R.D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell98, 285–294 (1999). ArticleCAS Google Scholar
Vignali, M., Hassan, A.H., Neely, K.E. & Workman, J.L. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol.20, 1899–1910 (2000). ArticleCAS Google Scholar
Becker, P.B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem.71, 247–273 (2002). ArticleCAS Google Scholar
Winston, F. & Carlson, M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet.8, 387–391 (1992). ArticleCAS Google Scholar
Sudarsanam, P. & Winston, F. The Swi/Snf family nucleosome-remodeling complexes and transcriptional control. Trends Genet.16, 345–351 (2000). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Schnitzler, G.R. et al. Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Mol. Cell. Biol.21, 8504–8511 (2001). ArticleCAS Google Scholar
Aoyagi, S. et al. Nucleosome remodeling by the human SWI/SNF complex requires transient global disruption of histone-DNA interactions. Mol. Cell. Biol.22, 3653–3662 (2002). ArticleCAS Google Scholar
Narlikar, G.J., Phelan, M.L. & Kingston, R.E. Generation and interconversion of multiple distinct nucleosomal states as a mechanism for catalyzing chromatin fluidity. Mol. Cell8, 1219–1230 (2001). ArticleCAS Google Scholar
Kassabov, S.R., Zhang, B., Persinger, J. & Bartholomew, B. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol. Cell11, 391–403 (2003). ArticleCAS Google Scholar
Fan, H.Y., He, X., Kingston, R.E. & Narlikar, G.J. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell11, 1311–1322 (2003). ArticleCAS Google Scholar
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. USA95, 4947–4952 (1998). ArticleCAS Google Scholar
Schnitzler, G., Sif, S. & Kingston, R.E. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell94, 17–27 (1998). ArticleCAS Google Scholar
Lorch, Y., Cairns, B.R., Zhang, M. & Kornberg, R.D. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell94, 29–34 (1998). ArticleCAS Google Scholar
Jaskelioff, M., Gavin, I.M., Peterson, C.L. & Logie, C. SWI-SNF-mediated nucleosome remodeling: role of histone octamer mobility in the persistence of the remodeled state. Mol. Cell. Biol.20, 3058–3068 (2000). ArticleCAS Google Scholar
Flaus, A. & Owen-Hughes, T. Dynamic properties of nucleosomes during thermal and ATP-driven mobilization. Mol. Cell. Biol.23, 7767–7779 (2003). ArticleCAS Google Scholar
Zofall, M., Persinger, J., Kassabov, S.R. & Bartholomew, B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol.13, 339–346 (2006). ArticleCAS Google Scholar
Whitehouse, I. et al. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature400, 784–787 (1999). ArticleCAS Google Scholar
Koch, S.J., Shundrovsky, A., Jantzen, B.C. & Wang, M.D. Probing protein-DNA interactions by unzipping a single DNA double helix. Biophys. J.83, 1098–1105 (2002). ArticleCAS Google Scholar
Koch, S.J. & Wang, M.D. Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA. Phys. Rev. Lett.91, 028103 (2003). Article Google Scholar
Jiang, J. et al. Detection of high-affinity and sliding clamp modes for MSH2–MSH6 by single-molecule unzipping force analysis. Mol. Cell20, 771–781 (2005). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Thastrom, A., Bingham, L.M. & Widom, J. Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. J. Mol. Biol.338, 695–709 (2004). ArticleCAS Google Scholar
Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature389, 251–260 (1997). ArticleCAS Google Scholar
Brower-Toland, B.D. et al. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl. Acad. Sci. USA99, 1960–1965 (2002). ArticleCAS Google Scholar
Brower-Toland, B. & Wang, M.D. Use of optical trapping techniques to study single-nucleosome dynamics. Methods Enzymol.376, 62–72 (2004). ArticleCAS Google Scholar
Brower-Toland, B. et al. Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J. Mol. Biol.346, 135–146 (2005). ArticleCAS Google Scholar
Meersseman, G., Pennings, S. & Bradbury, E.M. Mobile nucleosomes—a general behavior. EMBO J.11, 2951–2959 (1992). ArticleCAS Google Scholar
Cote, J., Quinn, J., Workman, J.L. & Peterson, C.L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science265, 53–60 (1994). ArticleCAS Google Scholar
Bruno, M. et al. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol. Cell12, 1599–1606 (2003). ArticleCAS Google Scholar
Vicent, G.P. et al. DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol. Cell16, 439–452 (2004). ArticleCAS Google Scholar
Schafer, D.A., Gelles, J., Sheetz, M.P. & Landick, R. Transcription by single molecules of RNA polymerase observed by light microscopy. Nature352, 444–448 (1991). ArticleCAS Google Scholar
Lee, K.-M. & Narlikar, G. Assembly of nucleosomal templates by salt dialysis. in Current Protocols in Molecular Biology Vol. 3 (eds. Ausubel, F.A. et al.) 21.6.3 (Wiley, New York, 2001). Google Scholar
Smith, C.L., Horowitz-Scherer, R., Flanagan, J.F., Woodcock, C.L. & Peterson, C.L. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol.10, 141–145 (2003). ArticleCAS Google Scholar
Bockelmann, U., Essevaz-Roulet, B. & Heslot, F. DNA strand separation studied by single molecule force measurements. Phys. Rev. E58, 2386–2394 (1998). ArticleCAS Google Scholar
Orear, J. Notes on statistics for physicists. (Laboratory for Nuclear Studies report CLNS 82/511, Cornell University, New York, 1982).