53
Views
105
CrossRef citations to date
0
Altmetric
Transcriptional Regulation

Yeast Isw1p Forms Two Separable Complexes In Vivo

, , , , , & show all
Pages 80-91 | Received 12 Jun 2002, Accepted 07 Oct 2002, Published online: 27 Mar 2023

REFERENCES

  • Adams, A., D. Gottschling, and T. Stearns. 1997. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
  • Angus-Hill, M. L., A. Schlichter, D. Roberts, H. Erdjument-Bromage, P. Tempst, and B. R. Cairns. 2001. A rsc3/rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler rsc in gene expression and cell cycle control. Mol. Cell 7: 741–751.
  • Bochar, D. A., J. Savard, W. Wang, D. W. Lafleur, P. Moore, J. Cote, and R. Shiekhattar. 2000. A family of chromatin remodeling factors related to Williams syndrome transcription factor. Proc. Natl. Acad. Sci. USA 97: 1038–1043.
  • Boeke, J. D., J. Trueheart, G. Natsoulis, and G. R. Fink. 1987. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154: 164–175.
  • Bozhenok, L., P. A. Wade, and P. Varga-Weisz. 2002. WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J. 21: 2231–2241.
  • Cairns, B. R. 1998. Chromatin remodeling machines: similar motors, ulterior motives. Trends Biochem. Sci. 23: 20–25.
  • Cairns, B. R., A. Schlichter, H. Erdjument-Bromage, P. Tempst, R. D. Kornberg, and F. Winston. 1999. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4: 715–723.
  • Capili, A. D., D. C. Schultz, I. F. Rauscher, and K. L. Borden. 2001. Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J. 20: 165–177.
  • Corona, D. F., A. Eberharter, A. Budde, R. Deuring, S. Ferrari, P. Varga-Weisz, M. Wilm, J. Tamkun, and P. B. Becker. 2000. Two histone fold proteins, CHRAC-14 and CHRAC-16, are developmentally regulated subunits of chromatin accessibility complex (CHRAC). EMBO J. 19: 3049–3059.
  • Corona, D. F., G. Langst, C. R. Clapier, E. J. Bonte, S. Ferrari, J. W. Tamkun, and P. B. Becker. 1999. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell 3: 239–245.
  • Costanzo, M. C., M. E. Crawford, J. E. Hirschman, J. E. Kranz, P. Olsen, L. S. Robertson, M. S. Skrzypek, B. R. Braun, K. L. Hopkins, P. Kondu, C. Lengieza, J. E. Lew-Smith, M. Tillberg, and J. I. Garrels. 2001. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 29: 75–79.
  • Costanzo, M. C., J. D. Hogan, M. E. Cusick, B. P. Davis, A. M. Fancher, P. E. Hodges, P. Kondu, C. Lengieza, J. E. Lew-Smith, C. Lingner, K. J. Roberg-Perez, M. Tillberg, J. E. Brooks, and J. I. Garrels. 2000. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28: 73–76.
  • Deuring, R., L. Fanti, J. A. Armstrong, M. Sarte, O. Papoulas, M. Verardo, S. Moseley, M. Berloco, T. Tsukiyama, C. Wu, S. Pimpinelli, and J. W. Tamkun. 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.
  • Eberharter, A., S. Ferrari, G. Langst, T. Straub, A. Imhof, P. Varga-Weisz, M. Wilm, and P. B. Becker. 2001. Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J. 20: 3781–3788.
  • Elfring, L. K., R. Deuring, C. M. McCallum, C. L. Peterson, and J. W. Tamkun. 1994. Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2. Mol. Cell. Biol. 14: 2225–2234.
  • Fazzio, T. G., C. Kooperberg, J. P. Goldmark, C. Neal, R. Basom, J. Delrow, and T. Tsukiyama. 2001. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21: 6450–6460.
  • Fyodorov, D. V., and J. T. Kadonaga. 2001. The many faces of chromatin remodeling: SWItching beyond transcription. Cell 106: 523–525.
  • Gelbart, M. E., T. Rechsteiner, T. J. Richmond, and T. Tsukiyama. 2001. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Mol. Cell. Biol. 21: 2098–2106.
  • Gelius, B., P. Wade, A. Wolffe, O. Wrange, and A. K. Ostlund Farrants. 1999. Characterization of a chromatin remodelling activity in Xenopus oocytes. Eur. J. Biochem. 262: 426–434.
  • Goldmark, J. P., T. G. Fazzio, P. W. Estep, G. M. Church, and T. Tsukiyama. 2000. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103: 423–433.
  • Goldstein, A. L., and J. H. McCusker. 1999. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15: 1541–1553.
  • Gottlieb, B., H. Lehvaslaiho, L. K. Beitel, R. Lumbroso, L. Pinsky, and M. Trifiro. 1998. The androgen receptor gene mutations database. Nucleic Acids Res. 26: 234–238.
  • Güldener, U., S. Heck, T. Fielder, J. Beinhauer, and J. H. Hegemann. 1996. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24: 2519–2524.
  • Guschin, D., T. M. Geiman, N. Kikyo, D. J. Tremethick, A. P. Wolffe, and P. A. Wade. 2000. Multiple ISWI ATPase complexes from Xenopus laevis. Functional conservation of an ACF/CHRAC homolog. J. Biol. Chem. 275: 35248–35255.
  • Hamiche, A., R. Sandaltzopoulos, D. A. Gdula, and C. Wu. 1999. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97: 833–842.
  • Henikoff, S., and J. G. Henikoff. 1994. Protein family classification based on searching a database of blocks. Genomics 19: 97–107.
  • Hughes, T. R., M. J. Marton, A. R. Jones, C. J. Roberts, R. Stoughton, C. D. Armour, H. A. Bennett, E. Coffey, H. Dai, Y. D. He, M. J. Kidd, A. M. King, M. R. Meyer, D. Slade, P. Y. Lum, S. B. Stepaniants, D. D. Shoemaker, D. Gachotte, K. Chakraburtty, J. Simon, M. Bard, and S. H. Friend. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109–126.
  • Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98: 4569–4574.
  • Ito, T., M. E. Levenstein, D. V. Fyodorov, A. K. Kutach, R. Kobayashi, and J. T. Kadonaga. 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.
  • Kent, N. A., N. Karabetsou, P. K. Politis, and J. Mellor. 2001. In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev. 15: 619–626.
  • Kingston, R. E., and G. J. Narlikar. 1999. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13: 2339–2352.
  • Kooperberg, C., T. G. Fazzio, J. J. Delrow, and T. T. Tsukiyama. 2002. Improved background correction for spotted DNA microarrays. J. Comput. Biol. 9: 57–68.
  • Kornberg, R. D. 1974. Chromatin structure: a repeating unit of histones and DNA. Science 184: 868–871.
  • 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.
  • Lazzaro, M. A., and D. J. Picketts. 2001. Cloning and characterization of the murine Imitation Switch (ISWI) genes: differential expression patterns suggest distinct developmental roles for Snf2h and Snf2l. J. Neurochem. 77: 1145–1156.
  • LeRoy, G., A. Loyola, W. S. Lane, and D. Reinberg. 2000. Purification and characterization of a human factor that assembles and remodels chromatin. J. Biol. Chem. 275: 14787–14790.
  • LeRoy, G., G. Orphanides, W. S. Lane, and D. Reinberg. 1998. Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282: 1900–1904.
  • 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.
  • Okabe, I., L. C. Bailey, O. Attree, S. Srinivasan, J. M. Perkel, B. C. Laurent, M. Carlson, D. L. Nelson, and R. L. Nussbaum. 1992. Cloning of human and bovine homologs of SNF2/SWI2: a global activator of transcription in yeast S. cerevisiae. Nucleic Acids Res. 20: 4649–4655.
  • Poot, R. A., G. Dellaire, B. B. Hulsmann, M. A. Grimaldi, D. F. Corona, P. B. Becker, W. A. Bickmore, and P. D. Varga-Weisz. 2000. HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J. 19: 3377–3387.
  • Qiu, C., K. Sawada, X. Zhang, and X. Cheng. 2002. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol. 9: 217–224.
  • Rigaut, G., A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17: 1030–1032.
  • Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • Sawa, H., H. Kouike, and H. Okano. 2000. Components of the SWI/SNF complex are required for asymmetric cell division in C. elegans. Mol. Cell 6: 617–624.
  • Schneider, B. L., W. Seufert, B. Steiner, Q. H. Yang, and A. B. Futcher. 1995. Use of polymerase chain reaction epitope tagging for protein tagging in Saccharomyces cerevisiae. Yeast 11: 1265–1274.
  • Strohner, R., A. Nemeth, P. Jansa, U. Hofmann-Rohrer, R. Santoro, G. Langst, and I. Grummt. 2001. NoRC—a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J. 20: 4892–4900.
  • Thomas, B. J., and R. Rothstein. 1989. The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene. Genetics 123: 725–738.
  • 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.
  • Varga-Weisz, P. D., and P. B. Becker. 1998. Chromatin-remodeling factors: machines that regulate? Curr. Opin. Cell Biol. 10: 346–353.
  • Wolffe, A. P., and J. C. Hansen. 2001. Nuclear visions: functional flexibility from structural instability. Cell 104: 631–634.
  • Xiao, H., R. Sandaltzopoulos, H. M. Wang, A. Hamiche, R. Ranallo, K. M. Lee, D. Fu, and C. Wu. 2001. Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol. Cell 8: 531–543.
  • Yang, Y. H., S. Dudoit, P. Luu, and T. P. Speed. 2001. Normalization for cDNA microarray data, p. 141–152. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (ed.), Microarrays: optical technologies and informatics. Proceedings of SPIE, vol. 4266. International Society for Optical Engineering, San Diego, Calif.
  • Zhao, X., E. G. Muller, and R. Rothstein. 1998. A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Mol. Cell 2: 329–340.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.