Regulation of ISW2 by Concerted Action of Histone H4 Tail and Extranucleosomal DNA

REFERENCES

• Aalfs, J. D., and R. E. Kingston. 2000. What does “chromatin remodeling” mean? Trends Biochem. Sci. 25:548–555.
   PubMed Web of Science ®Google Scholar
• Angelov, D., J. M. Vitolo, V. Mutskov, S. Dimitrov, and J. J. Hayes. 2001. Preferential interaction of the core histone tail domains with linker DNA. Proc. Natl. Acad. Sci. USA 98:6599–6604.
   PubMedGoogle Scholar
• Baneres, J. L., A. Martin, and J. Parello. 1997. The N tails of histones H3 and H4 adopt a highly structured conformation in the nucleosome. J. Mol. Biol. 273:503–508.
   PubMedGoogle Scholar
• Bruno, M., A. Flaus, C. Stockdale, C. Rencurel, H. Ferreira, and T. Owen-Hughes. 2003. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol. Cell 12:1599–1606.
   PubMed Web of Science ®Google Scholar
• Cairns, B. R. 2001. Emerging roles for chromatin remodeling in cancer biology. Trends Cell Biol. 11:S15–S21.
   PubMedGoogle Scholar
• Clapier, C. R., G. Langst, D. F. Corona, P. B. Becker, and K. P. Nightingale. 2001. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21:875–883.
   PubMed Web of Science ®Google Scholar
• Clapier, C. R., K. P. Nightingale, and P. B. Becker. 2002. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30:649–655.
   PubMedGoogle Scholar
• Corona, D. F., C. R. Clapier, P. B. Becker, and J. W. Tamkun. 2002. Modulation of ISWI function by site-specific histone acetylation. EMBO Rep. 3:242–247.
   PubMedGoogle Scholar
• Dixon, W. J., J. J. Hayes, J. R. Levin, M. F. Weidner, B. A. Dombroski, and T. D. Tullius. 1991. Hydroxyl radical footprinting. Methods Enzymol. 208:380–413.
   PubMed Web of Science ®Google Scholar
• Eberharter, A., and P. B. Becker. 2004. ATP-dependent nucleosome remodelling: factors and functions. J. Cell Sci. 117:3707–3711.
   PubMed Web of Science ®Google Scholar
• Ebralidse, K. K., S. A. Grachev, and A. D. Mirzabekov. 1988. A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA. Nature 331:365–367.
   PubMed Web of Science ®Google Scholar
• Fan, H. Y., X. He, R. E. Kingston, and G. J. Narlikar. 2003. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell 11:1311–1322.
   PubMedGoogle Scholar
• Fazzio, T. G., M. E. Gelbart, and T. Tsukiyama. 2005. Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo. Mol. Cell. Biol. 25:9165–9174.
   PubMedGoogle Scholar
• Fazzio, T. G., and T. Tsukiyama. 2003. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Mol. Cell 12:1333–1340.
   PubMedGoogle Scholar
• Hamiche, A., J. G. Kang, C. Dennis, H. Xiao, and C. Wu. 2001. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl. Acad. Sci. USA 98:14316–14321.
   PubMed Web of Science ®Google Scholar
• Hansen, J. C., C. Tse, and A. P. Wolffe. 1998. Structure and function of the core histone N-termini: more than meets the eye. Biochemistry 37:17637–17641.
   PubMed Web of Science ®Google Scholar
• Ito, T., M. Bulger, M. J. Pazin, R. Kobayashi, and J. T. Kadonaga. 1997. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90:145–155.
   PubMedGoogle Scholar
• Kagalwala, M. N., B. J. Glaus, W. Dang, M. Zofall, and B. Bartholomew. 2004. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23:2092–2104.
   PubMedGoogle Scholar
• Kassabov, S. R., N. M. Henry, M. Zofall, T. Tsukiyama, and B. Bartholomew. 2002. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22:7524–7534.
   PubMedGoogle Scholar
• Langst, G., E. J. Bonte, D. F. Corona, and P. B. Becker. 1999. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97:843–852.
   PubMed Web of Science ®Google Scholar
• Lee, K. M., and J. J. Hayes. 1998. Linker DNA and H1-dependent reorganization of histone-DNA interactions within the nucleosome. Biochemistry 37:8622–8628.
   PubMedGoogle Scholar
• Lorch, Y., J. W. LaPointe, and R. D. Kornberg. 1987. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49:203–210.
   PubMed Web of Science ®Google Scholar
• Lowary, P. T., and J. Widom. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:19–42.
   PubMed Web of Science ®Google Scholar
• Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260.
   PubMed Web of Science ®Google Scholar
• Lusser, A., and J. T. Kadonaga. 2003. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192–1200.
   PubMed Web of Science ®Google Scholar
• Mizuguchi, G., X. Shen, J. Landry, W. H. Wu, S. Sen, and C. Wu. 2004. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303:343–348.
   PubMed Web of Science ®Google Scholar
• Reinke, H., and W. Horz. 2003. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11:1599–1607.
   PubMed Web of Science ®Google Scholar
• Saha, A., J. Wittmeyer, and B. R. Cairns. 2002. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16:2120–2134.
   PubMedGoogle Scholar
• Saha, A., J. Wittmeyer, and B. R. Cairns. 2005. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 12:747–755.
   PubMed Web of Science ®Google Scholar
• Schwanbeck, R., H. Xiao, and C. Wu. 2004. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279:39933–39941.
   PubMedGoogle Scholar
• Shogren-Knaak, M., H. Ishii, J. M. Sun, M. J. Pazin, J. R. Davie, and C. L. Peterson. 2006. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311:844–847.
   PubMed Web of Science ®Google Scholar
• Stefanovsky, V., S. I. Dimitrov, V. R. Russanova, D. Angelov, and I. G. Pashev. 1989. Laser-induced crosslinking of histones to DNA in chromatin and core particles: implications in studying histone-DNA interactions. Nucleic Acids Res. 17:10069–10081.
   PubMedGoogle Scholar
• Tsukiyama, T., C. Daniel, J. Tamkun, and C. Wu. 1995. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell 83:1021–1026.
   PubMedGoogle Scholar
• Tsukiyama, T., J. Palmer, C. C. Landel, J. Shiloach, and C. Wu. 1999. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13:686–697.
   PubMed Web of Science ®Google Scholar
• Tullius, T. D., B. A. Dombroski, M. E. Churchill, and L. Kam. 1987. Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods Enzymol. 155:537–558.
   PubMed Web of Science ®Google Scholar
• Usachenko, S. I., S. G. Bavykin, I. M. Gavin, and E. M. Bradbury. 1994. Rearrangement of the histone H2A C-terminal domain in the nucleosome. Proc. Natl. Acad. Sci. USA 91:6845–6849.
   PubMedGoogle Scholar
• Varga-Weisz, P. D., M. Wilm, E. Bonte, K. Dumas, M. Mann, and P. B. Becker. 1997. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388:598–602.
   PubMedGoogle Scholar
• Zheng, C., and J. J. Hayes. 2003. Structures and interactions of the core histone tail domains. Biopolymers 68:539–546.
   PubMed Web of Science ®Google Scholar
• Zheng, C., X. Lu, J. C. Hansen, and J. J. Hayes. 2005. Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array. J. Biol. Chem. 280:33552–33557.
   PubMedGoogle Scholar
• Zofall, M., J. Persinger, and B. Bartholomew. 2004. Functional role of extranucleosomal DNA and the entry site of the nucleosome in chromatin remodeling by ISW2. Mol. Cell. Biol. 24:10047–10057.
   PubMedGoogle Scholar
• Zofall, M., J. Persinger, S. R. Kassabov, and B. Bartholomew. 2006. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. 13:339–346.
   PubMed Web of Science ®Google Scholar