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Article

The INO80 ATP-Dependent Chromatin Remodeling Complex Is a Nucleosome Spacing Factor

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Pages 662-673 | Received 03 Sep 2010, Accepted 28 Nov 2010, Published online: 20 Mar 2023

REFERENCES

  • Bakshi, R., et al. 2004. In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins. Biochem. Biophys. Res. Commun. 320:197–204.
  • Bao, Y., and X. Shen. 2007. INO80 subfamily of chromatin remodeling complexes. Mutat. Res. 618:18–29.
  • Barbaric, S., et al. 2007. Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo. J. Biol. Chem. 282:27610–27621.
  • Becker, P. B., and W. Horz. 2002. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:247–273.
  • Boyer, L. A., et al. 2000. Roles of the histone H2A-H2B dimers and the (H3-H4)(2) tetramer in nucleosome remodeling by the SWI-SNF complex. J. Biol. Chem. 275:11545–11552.
  • Cairns, B. R. 2004. Around the world of DNA damage INO80 days. Cell 119:733–735.
  • Clapier, C. R., et al. 2001. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21:875–883.
  • 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.
  • Dang, W., M. N. Kagalwala, and B. Bartholomew. 2006. Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA. Mol. Cell. Biol. 26:7388–7396.
  • Dechassa, M. L., et al. 2010. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol. Cell 38:590–602.
  • Downs, J. A., et al. 2004. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol. Cell 16:979–990.
  • Ebbert, R., A. Birkmann, and H. J. Schuller. 1999. The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol. Microbiol. 32:741–751.
  • Eberharter, A., R. Ferreira, and P. Becker. 2005. Dynamic chromatin: concerted nucleosome remodelling and acetylation. Biol. Chem. 386:745–751.
  • Eisen, J. A., K. S. Sweder, and P. C. Hanawalt. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23:2715–2723.
  • 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.
  • Flaus, A., and T. Owen-Hughes. 2004. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14:165–173.
  • Ford, J., O. Odeyale, and C. H. Shen. 2008. Activator-dependent recruitment of SWI/SNF and INO80 during INO1 activation. Biochem. Biophys. Res. Commun. 373:602–606.
  • Ford, J., et al. 2007. A SWI/SNF- and INO80-dependent nucleosome movement at the INO1 promoter. Biochem. Biophys. Res. Commun. 361:974–979.
  • Gangaraju, V. K., and B. Bartholomew. 2007. Mechanisms of ATP dependent chromatin remodeling. Mutat. Res. 618:3–17.
  • Gangaraju, V. K., and B. Bartholomew. 2007. Dependency of ISW1a chromatin remodeling on extranucleosomal DNA. Mol. Cell. Biol. 27:3217–3225.
  • Georgel, P. T., T. Tsukiyama, and C. Wu. 1997. Role of histone tails in nucleosome remodeling by Drosophila NURF. EMBO J. 16:4717–4726.
  • Guyon, J. R., et al. 1999. Stable remodeling of tailless nucleosomes by the human SWI-SNF complex. Mol. Cell. Biol. 19:2088–2097.
  • Hamiche, A., et al. 2001. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl. Acad. Sci. U. S. A. 98:14316–14321.
  • Hishida, T., et al. 2004. Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer. Proc. Natl. Acad. Sci. U. S. A. 101:9573–9577.
  • Ito, T., et al. 1997. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90:145–155.
  • Jonsson, Z. O., et al. 2004. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell 16:465–477.
  • Kagalwala, M. N., et al. 2004. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23:2092–2104.
  • Kassabov, S. R., et al. 2002. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22:7524–7534.
  • Kornberg, R. D., and Y. Lorch. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294.
  • 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.
  • 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.
  • Mizuguchi, G., et al. 2004. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303:343–348.
  • Morrison, A. J., et al. 2004. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell 119:767–775.
  • Morrison, A. J., and X. Shen. 2005. DNA repair in the context of chromatin. Cell Cycle 4:568–571.
  • Papamichos-Chronakis, M., and C. L. Peterson. 2008. The Ino80 chromatin-remodeling enzyme regulates replisome function and stability. Nat. Struct. Mol. Biol. 15:338–345.
  • Parsons, C. A., et al. 1992. Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions. Proc. Natl. Acad. Sci. U. S. A. 89:5452–5456.
  • Racki, L. R., et al. 2009. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 462:1016–1021.
  • Shen, X., et al. 2000. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406:541–544.
  • Shen, X., et al. 2003. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol. Cell 12:147–155.
  • Shen, X. 2004. Preparation and analysis of the INO80 complex. Methods Enzymol. 377:401–412.
  • Shimada, K., et al. 2008. Ino80 chromatin remodeling complex promotes recovery of stalled replication forks. Curr. Biol. 18:566–575.
  • Shogren-Knaak, M., et al. 2006. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311:844–847.
  • Smith, C. L., and C. L. Peterson. 2005. A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol. Cell. Biol. 25:5880–5892.
  • Steinboeck, F., et al. 2007. The nuclear actin-related protein of Saccharomyces cerevisiae, Arp4, directly interacts with the histone acetyltransferase Esa1p. J. Biochem. 141:661–668.
  • Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403:41–45.
  • Szerlong, H., et al. 2008. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat. Struct. Mol. Biol. 15:469–476.
  • Trujillo, K. M., and M. A. Osley. 2008. INO80 meets a fork in the road. Nat. Struct. Mol. Biol. 15:332–334.
  • Tsukiyama, T., et al. 1999. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13:686–697.
  • van Attikum, H., et al. 2004. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell 119:777–788.
  • Varga-Weisz, P. D., et al. 1997. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388:598–602.
  • Vary, J. C., Jr., et al. 2003. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23:80–91.
  • Vincent, J. A., T. J. Kwong, and T. Tsukiyama. 2008. ATP-dependent chromatin remodeling shapes the DNA replication landscape. Nat. Struct. Mol. Biol. 15:477–484.
  • Wippo, C. J., et al. 2009. Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability. Mol. Cell. Biol. 29:2960–2981.
  • Yu, E. Y., et al. 2007. Regulation of telomere structure and functions by subunits of the INO80 chromatin remodeling complex. Mol. Cell. Biol. 27:5639–5649.
  • Zofall, M., et al. 2006. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. 13:339–346.
  • 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.

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