21
Views
51
CrossRef citations to date
0
Altmetric
Article

Isw1 Functions in Parallel with the NuA4 and Swr1 Complexes in Stress-Induced Gene Repression

, , , &
Pages 6117-6129 | Received 13 Apr 2006, Accepted 31 May 2006, Published online: 27 Mar 2023

REFERENCES

  • Babiarz, J. E., J. E. Halley, and J. Rine. 2006. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A. Z in Saccharomyces cerevisiae. Genes Dev. 20:700–710.
  • Baldi, P., and A. D. Long. 2001. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17:509–519.
  • Basehoar, A. D., S. J. Zanton, and B. F. Pugh. 2004. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699–709.
  • Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57:289–300.
  • Bird, A. W., D. Y. Yu, M. G. Pray-Grant, Q. Qiu, K. E. Harmon, P. C. Megee, P. A. Grant, M. M. Smith, and M. F. Christman. 2002. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419:411–415.
  • Bittner, C. B., D. T. Zeisig, B. B. Zeisig, and R. K. Slany. 2004. Direct physical and functional interaction of the NuA4 complex components Yaf9p and Swc4p. Eukaryot. Cell 3:976–983.
  • Boudreault, A. A., D. Cronier, W. Selleck, N. Lacoste, R. T. Utley, S. Allard, J. Savard, W. S. Lane, S. Tan, and J. Cote. 2003. Yeast enhancer of polycomb defines global Esa1-dependent acetylation of chromatin. Genes Dev. 17:1415–1428.
  • Cai, Y., J. Jin, L. Florens, S. K. Swanson, T. Kusch, B. Li, J. L. Workman, M. P. Washburn, R. C. Conaway, and J. W. Conaway. 2005. The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J. Biol. Chem. 280:13665–13670.
  • Carrozza, M. J., R. T. Utley, J. L. Workman, and J. Cote. 2003. The diverse functions of histone acetyltransferase complexes. Trends Genet. 19:321–329.
  • Ceol, C. J., and H. R. Horvitz. 2004. A new class of C. elegans synMuv genes implicates a Tip60/NuA4-like HAT complex as a negative regulator of Ras signaling. Dev. Cell 6:563–576.
  • Choy, J. S., and S. J. Kron. 2002. NuA4 subunit Yng2 function in intra-S-phase DNA damage response. Mol. Cell. Biol. 22:8215–8225.
  • Cosma, M. P. 2002. Ordered recruitment: gene-specific mechanism of transcription activation. Mol. Cell 10:227–236.
  • Dion, M. F., S. J. Altschuler, L. F. Wu, and O. J. Rando. 2005. Genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. USA 102:5501–5506.
  • Ehrenhofer-Murray, A. E. 2004. Chromatin dynamics at DNA replication, transcription and repair. Eur. J. Biochem. 271:2335–2349.
  • Eisen, A., R. T. Utley, A. Nourani, S. Allard, P. Schmidt, W. S. Lane, J. C. Lucchesi, and J. Cote. 2001. The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J. Biol. Chem. 276:3484–3491.
  • 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.
  • Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genomewide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863–14868.
  • 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.
  • Fazzio, T. G., and T. Tsukiyama. 2003. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Mol. Cell 12:1333–1340.
  • Fuchs, M., J. Gerber, R. Drapkin, S. Sif, T. Ikura, V. Ogryzko, W. S. Lane, Y. Nakatani, and D. M. Livingston. 2001. The p400 complex is an essential E1A transformation target. Cell 106:297–307.
  • Galarneau, L., A. Nourani, A. A. Boudreault, Y. Zhang, L. Heliot, S. Allard, J. Savard, W. S. Lane, D. J. Stillman, and J. Cote. 2000. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol. Cell 5:927–937.
  • Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241–4257.
  • 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.
  • Gorner, W., E. Durchschlag, M. T. Martinez-Pastor, F. Estruch, G. Ammerer, B. Hamilton, H. Ruis, and C. Schuller. 1998. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev. 12:586–597.
  • Gorzer, I., C. Schuller, E. Heidenreich, L. Krupanska, K. Kuchler, and U. Wintersberger. 2003. The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes. Mol. Microbiol. 50:1155–1171.
  • Guldener, 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.
  • Henikoff, S., and K. Ahmad. 2005. Assembly of variant histones into chromatin. Annu. Rev. Cell Dev. Biol. 21:133–153.
  • Huisinga, K. L., and B. F. Pugh. 2004. A genomewide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13:573–585.
  • Iizuka, M., and M. M. Smith. 2003. Functional consequences of histone modifications. Curr. Opin. Genet. Dev. 13:154–160.
  • Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science 293:1074–1080.
  • Kamakaka, R. T., and S. Biggins. 2005. Histone variants: deviants? Genes Dev. 19:295–310.
  • Kelly, T. J., S. Qin, D. E. Gottschling, and M. R. Parthun. 2000. Type B histone acetyltransferase Hat1p participates in telomeric silencing. Mol. Cell. Biol. 20:7051–7058.
  • Keogh, M. C., T. A. Mennella, C. Sawa, S. Berthelet, N. J. Krogan, A. Wolek, V. Podolny, L. R. Carpenter, J. F. Greenblatt, K. Baetz, and S. Buratowski. 2006. The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev. 20:660–665.
  • Kobor, M. S., S. Venkatasubrahmanyam, M. D. Meneghini, J. W. Gin, J. L. Jennings, A. J. Link, H. D. Madhani, and J. Rine. 2004. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A. Z into euchromatin. PLoS Biol. 2:E131.
  • Krogan, N. J., K. Baetz, M. C. Keogh, N. Datta, C. Sawa, T. C. Kwok, N. J. Thompson, M. G. Davey, J. Pootoolal, T. R. Hughes, A. Emili, S. Buratowski, P. Hieter, and J. F. Greenblatt. 2004. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc. Natl. Acad. Sci. USA 101:13513–13518.
  • Krogan, N. J., M. C. Keogh, N. Datta, C. Sawa, O. W. Ryan, H. Ding, R. A. Haw, J. Pootoolal, A. Tong, V. Canadien, D. P. Richards, X. Wu, A. Emili, T. R. Hughes, S. Buratowski, and J. F. Greenblatt. 2003. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell 12:1565–1576.
  • Kurdistani, S. K., and M. Grunstein. 2003. Histone acetylation and deacetylation in yeast. Nat. Rev. Mol. Cell. Biol. 4:276–284.
  • Le Masson, I., D. Y. Yu, K. Jensen, A. Chevalier, R. Courbeyrette, Y. Boulard, M. M. Smith, and C. Mann. 2003. Yaf9, a novel NuA4 histone acetyltransferase subunit, is required for the cellular response to spindle stress in yeast. Mol. Cell. Biol. 23:6086–6102.
  • Li, B., S. G. Pattenden, D. Lee, J. Gutierrez, J. Chen, C. Seidel, J. Gerton, and J. L. Workman. 2005. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc. Natl. Acad. Sci. USA 102:18385–18390.
  • Liu, C. L., T. Kaplan, M. Kim, S. Buratowski, S. L. Schreiber, N. Friedman, and O. J. Rando. 2005. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3:e328.
  • Meneghini, M. D., M. Wu, and H. D. Madhani. 2003. Conserved histone variant H2A. Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112:725–736.
  • Millar, C. B., F. Xu, K. Zhang, and M. Grunstein. 2006. Acetylation of H2AZ Lys 14 is associated with genomewide gene activity in yeast. Genes Dev. 20:711–722.
  • 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.
  • Morillon, A., N. Karabetsou, A. Nair, and J. Mellor. 2005. Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell 18:723–734.
  • Morillon, A., N. Karabetsou, J. O'Sullivan, N. Kent, N. Proudfoot, and J. Mellor. 2003. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell 115:425–435.
  • Narlikar, G. J., H. Y. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487.
  • Nourani, A., R. T. Utley, S. Allard, and J. Cote. 2004. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J. 23:2597–2607.
  • Peterson, C. L., and M. A. Laniel. 2004. Histones and histone modifications. Curr. Biol. 14:R546–R551.
  • Pokholok, D. K., C. T. Harbison, S. Levine, M. Cole, N. M. Hannett, T. I. Lee, G. W. Bell, K. Walker, P. A. Rolfe, E. Herbolsheimer, J. Zeitlinger, F. Lewitter, D. K. Gifford, and R. A. Young. 2005. Genomewide map of nucleosome acetylation and methylation in yeast. Cell 122:517–527.
  • Raisner, R. M., P. D. Hartley, M. D. Meneghini, M. Z. Bao, C. L. Liu, S. L. Schreiber, O. J. Rando, and H. D. Madhani. 2005. Histone variant H2A. Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123:233–248.
  • Reid, J. L., V. R. Iyer, P. O. Brown, and K. Struhl. 2000. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6:1297–1307.
  • Reid, J. L., Z. Moqtaderi, and K. Struhl. 2004. Eaf3 regulates the global pattern of histone acetylation in Saccharomyces cerevisiae. Mol. Cell. Biol. 24:757–764.
  • Robinson, M. D., J. Grigull, N. Mohammad, and T. R. Hughes. 2002. FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 3:35.
  • Santisteban, M. S., T. Kalashnikova, and M. M. Smith. 2000. Histone H2A. Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 103:411–422.
  • Shen, X., G. Mizuguchi, A. Hamiche, and C. Wu. 2000. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406:541–544.
  • Shia, W. J., S. Osada, L. Florens, S. K. Swanson, M. P. Washburn, and J. L. Workman. 2005. Characterization of the yeast trimeric-SAS acetyltransferase complex. J. Biol. Chem. 280:11987–11994.
  • Smith, C. L., and C. L. Peterson. 2005. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65:115–148.
  • 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. 2002. The in vivo functions of ATP-dependent chromatin-remodelling factors. Nat. Rev. Mol. Cell. Biol. 3:422–429.
  • 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.
  • Vary, J. C., Jr., V. K. Gangaraju, J. Qin, C. C. Landel, C. Kooperberg, B. Bartholomew, and T. Tsukiyama. 2003. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23:80–91.
  • Zhang, H., D. O. Richardson, D. N. Roberts, R. Utley, H. Erdjument-Bromage, P. Tempst, J. Cote, and B. R. Cairns. 2004. The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol. Cell. Biol. 24:9424–9436.
  • Zhang, H., D. N. Roberts, and B. R. Cairns. 2005. Genomewide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123:219–231.
  • 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.