Chd1 and yFACT Act in Opposition in Regulating Transcription

REFERENCES

• Ausubel, F. M., R. Brent, R. E. Kingston, D. E. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1987. Current protocols in molecular biology. Wiley and Sons, New York, NY.
   Google Scholar
• Belotserkovskaya, R., S. Oh, V. A. Bondarenko, G. Orphanides, V. M. Studitsky, and D. Reinberg. 2003. FACT facilitates transcription-dependent nucleosome alteration. Science 301:1090–1093.
   PubMed Web of Science ®Google Scholar
• Bhoite, L. T., and D. J. Stillman. 1998. Residues in the Swi5 zinc finger protein that mediate cooperative DNA-binding with the Pho2 homeodomain protein. Mol. Cell. Biol. 18:6436–6446.
   PubMedGoogle Scholar
• Biswas, D., R. Dutta-Biswas, D. Mitra, Y. Shibata, B. D. Strahl, T. Formosa, and D. J. Stillman. 2006. Opposing roles for Set2 and yFACT in regulating TBP binding at promoters. EMBO J. 25:4479–4489.
   PubMed Web of Science ®Google Scholar
• Biswas, D., A. N. Imbalzano, P. Eriksson, Y. Yu, and D. J. Stillman. 2004. Role for Nhp6, Gcn5, and the Swi/Snf complex in stimulating formation of the TATA-binding protein-TFIIA-DNA complex. Mol. Cell. Biol. 24:8312–8321.
   PubMedGoogle Scholar
• Biswas, D., Y. Yu, M. Prall, T. Formosa, and D. J. Stillman. 2005. The yeast FACT complex has a role in transcriptional initiation. Mol. Cell. Biol. 25:5812–5822.
   PubMed Web of Science ®Google Scholar
• Brehm, A., K. R. Tufteland, R. Aasland, and P. B. Becker. 2004. The many colours of chromodomains. Bioessays 26:133–140.
   PubMed Web of Science ®Google Scholar
• Brewster, N. K., G. C. Johnston, and R. A. Singer. 2001. A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription. Mol. Cell. Biol. 21:3491–3502.
   PubMed Web of Science ®Google Scholar
• Briggs, S. D., M. Bryk, B. D. Strahl, W. L. Cheung, J. K. Davie, S. Y. Dent, F. Winston, and C. D. Allis. 2001. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15:3286–3295.
   PubMed Web of Science ®Google Scholar
• Cairns, B. R. 2005. Chromatin remodeling complexes: strength in diversity, precision through specialization. Curr. Opin. Genet. Dev. 15:185–190.
   PubMed Web of Science ®Google Scholar
• Costa, P. J., and K. M. Arndt. 2000. Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics 156:535–547.
   PubMed Web of Science ®Google Scholar
• de la Cruz, X., S. Lois, S. Sanchez-Molina, and M. A. Martinez-Balbas. 2005. Do protein motifs read the histone code? Bioessays 27:164–175.
   PubMed Web of Science ®Google Scholar
• Dryhurst, D., A. A. Thambirajah, and J. Ausio. 2004. New twists on H2A.Z: a histone variant with a controversial structural and functional past. Biochem. Cell Biol. 82:490–497.
   PubMedGoogle Scholar
• Dudley, A. M., C. Rougeulle, and F. Winston. 1999. The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev. 13:2940–2945.
   PubMedGoogle Scholar
• Duroux, M., A. Houben, K. Ruzicka, J. Friml, and K. D. Grasser. 2004. The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome. Plant J. 40:660–671.
   PubMed Web of Science ®Google Scholar
• Eriksson, P., D. Biswas, Y. Yu, J. M. Stewart, and D. J. Stillman. 2004. TATA-binding protein mutants that are lethal in the absence of the Nhp6 high-mobility-group protein. Mol. Cell. Biol. 24:6419–6429.
   PubMedGoogle Scholar
• Flanagan, J. F., B. J. Blus, Y. Kim, K. L. Clines, F. Rastinejad, and S. Khorasanizadeh. 2007. Molecular implications of evolutionary differences in CHD double chromodomains. J. Mol. Biol. 369:334–342.
   PubMed Web of Science ®Google Scholar
• Flanagan, J. F., L. Z. Mi, M. Chruszcz, M. Cymborowski, K. L. Clines, Y. Kim, W. Minor, F. Rastinejad, and S. Khorasanizadeh. 2005. Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature 438:1181–1185.
   PubMed Web of Science ®Google Scholar
• Formosa, T. 2003. Changing the DNA landscape: putting a SPN on chromatin. Curr. Top. Microbiol. Immunol. 274:171–201.
   PubMedGoogle Scholar
• Formosa, T., P. Eriksson, J. Wittmeyer, J. Ginn, Y. Yu, and D. J. Stillman. 2001. Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. EMBO J. 20:3506–3517.
   PubMed Web of Science ®Google Scholar
• Formosa, T., S. Ruone, M. D. Adams, A. E. Olsen, P. Eriksson, Y. Yu, A. R. Rhoades, P. D. Kaufman, and D. J. Stillman. 2002. Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway. Polymerase passage may degrade chromatin structure. Genetics 162:1557–1571.
   PubMedGoogle Scholar
• Fragiadakis, G. S., D. Tzamarias, and D. Alexandraki. 2004. Nhp6 facilitates Aft1 binding and Ssn6 recruitment, both essential for FRE2 transcriptional activation. EMBO J. 23:333–342.
   PubMedGoogle Scholar
• Havas, K., I. Whitehouse, and T. Owen-Hughes. 2001. ATP-dependent chromatin remodeling activities. Cell Mol. Life Sci. 58:673–682.
   PubMedGoogle Scholar
• Imbalzano, A. N., H. Kwon, M. R. Green, and R. E. Kingston. 1994. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370:481–485.
   PubMed Web of Science ®Google Scholar
• Kassavetis, G. A., and D. F. Steiner. 2006. NHP6 is a transcriptional initiation fidelity factor for RNA polymerase III transcription in vitro and in vivo. J. Biol. Chem. 281:7445–7451.
   PubMedGoogle Scholar
• Kelley, D. E., D. G. Stokes, and R. P. Perry. 1999. CHD1 interacts with SSRP1 and depends on both its chromodomain and its ATPase/helicase-like domain for proper association with chromatin. Chromosoma 108:10–25.
   PubMed Web of Science ®Google Scholar
• Keogh, M. C., S. K. Kurdistani, S. A. Morris, S. H. Ahn, V. Podolny, S. R. Collins, M. Schuldiner, K. Chin, T. Punna, N. J. Thompson, C. Boone, A. Emili, J. S. Weissman, T. R. Hughes, B. D. Strahl, M. Grunstein, J. F. Greenblatt, S. Buratowski, and N. J. Krogan. 2005. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123:593–605.
   PubMed Web of Science ®Google Scholar
• Keogh, M. C., V. Podolny, and S. Buratowski. 2003. Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol. Cell. Biol. 23:7005–7018.
   PubMed Web of Science ®Google Scholar
• Krogan, N. J., M. Kim, S. H. Ahn, G. Zhong, M. S. Kobor, G. Cagney, A. Emili, A. Shilatifard, S. Buratowski, and J. F. Greenblatt. 2002. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22:6979–6992.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Lusser, A., D. L. Urwin, and J. T. Kadonaga. 2005. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat. Struct. Mol. Biol. 12:160–166.
   PubMed Web of Science ®Google Scholar
• Mason, P. B., and K. Struhl. 2003. The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol. Cell. Biol. 23:8323–8333.
   PubMed Web of Science ®Google Scholar
• Mason, P. B., and K. Struhl. 2005. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell 17:831–840.
   PubMed Web of Science ®Google Scholar
• Mellor, J., and A. Morillon. 2004. ISWI complexes in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1677:100–112.
   PubMedGoogle Scholar
• Okuda, M., M. Horikoshi, and Y. Nishimura. 2006. Structural Polymorphism of Chromodomains in Chd1. J. Mol. Biol. 365:1047–1062.
   PubMedGoogle Scholar
• Orphanides, G., G. LeRoy, C. H. Chang, D. S. Luse, and D. Reinberg. 1998. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92:105–116.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., W. H. Wu, W. S. Lane, M. Hampsey, and D. Reinberg. 1999. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400:284–288.
   PubMed Web of Science ®Google Scholar
• Ozer, J., L. E. Lezina, J. Ewing, S. Audi, and P. M. Lieberman. 1998. Association of transcription factor IIA with TATA binding protein is required for transcriptional activation of a subset of promoters and cell cycle progression in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:2559–2570.
   PubMedGoogle Scholar
• Prather, D. M., E. Larschan, and F. Winston. 2005. Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 25:2650–2659.
   PubMedGoogle Scholar
• Pray-Grant, M. G., J. A. Daniel, D. Schieltz, J. R. Yates III, and P. A. Grant. 2005. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433:434–438.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Rhoades, A. R., S. Ruone, and T. Formosa. 2004. Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6. Mol. Cell. Biol. 24:3907–3917.
   PubMedGoogle Scholar
• Robinson, K. M., and M. C. Schultz. 2003. Replication-independent assembly of nucleosome arrays in a novel yeast chromatin reconstitution system involves antisilencing factor Asf1p and chromodomain protein Chd1p. Mol. Cell. Biol. 23:7937–7946.
   PubMed Web of Science ®Google Scholar
• Ruone, S., A. R. Rhoades, and T. Formosa. 2003. Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. J. Biol. Chem. 278:45288–45295.
   PubMed Web of Science ®Google Scholar
• Saunders, A., J. Werner, E. D. Andrulis, T. Nakayama, S. Hirose, D. Reinberg, and J. T. Lis. 2003. Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science 301:1094–1096.
   PubMed Web of Science ®Google Scholar
• Schroeder, S. C., B. Schwer, S. Shuman, and D. Bentley. 2000. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev 14:2435–2440.
   PubMed Web of Science ®Google Scholar
• Sherman, F. 1991. Getting started with yeast. Methods Enzymol. 194:1–21.
   PubMedGoogle Scholar
• Shimojima, T., M. Okada, T. Nakayama, H. Ueda, K. Okawa, A. Iwamatsu, H. Handa, and S. Hirose. 2003. Drosophila FACT contributes to Hox gene expression through physical and functional interactions with GAGA factor. Genes Dev. 17:1605–1616.
   PubMedGoogle Scholar
• Simic, R., D. L. Lindstrom, H. G. Tran, K. L. Roinick, P. J. Costa, A. D. Johnson, G. A. Hartzog, and K. M. Arndt. 2003. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22:1846–1856.
   PubMed Web of Science ®Google Scholar
• Sims, R. J., III, C. F. Chen, H. Santos-Rosa, T. Kouzarides, S. S. Patel, and D. Reinberg. 2005. Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. J. Biol. Chem. 280:41789–41792.
   PubMed Web of Science ®Google Scholar
• Squazzo, S. L., P. J. Costa, D. L. Lindstrom, K. E. Kumer, R. Simic, J. L. Jennings, A. J. Link, K. M. Arndt, and G. A. Hartzog. 2002. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J. 21:1764–1774.
   PubMed Web of Science ®Google Scholar
• Stockdale, C., A. Flaus, H. Ferreira, and T. Owen-Hughes. 2006. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J. Biol. Chem. 281:16279–16288.
   PubMed Web of Science ®Google Scholar
• Stolinski, L. A., D. M. Eisenmann, and K. M. Arndt. 1997. Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:4490–4500.
   PubMedGoogle Scholar
• Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403:41–45.
   PubMed Web of Science ®Google Scholar
• Szerlong, H., A. Saha, and B. R. Cairns. 2003. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 22:3175–3187.
   PubMedGoogle Scholar
• Thomas, B. J., and R. Rothstein. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619–630.
   PubMed Web of Science ®Google Scholar
• Tran, H. G., D. J. Steger, V. R. Iyer, and A. D. Johnson. 2000. The chromo domain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 19:2323–2331.
   PubMed Web of Science ®Google 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
• Wang, W. 2003. The SWI/SNF family of ATP-dependent chromatin remodelers: similar mechanisms for diverse functions. Curr. Top. Microbiol. Immunol. 274:143–169.
   PubMedGoogle Scholar
• Wittmeyer, J., and T. Formosa. 1997. The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein. Mol. Cell. Biol. 17:4178–4190.
   PubMed Web of Science ®Google Scholar
• Wittmeyer, J., L. Joss, and T. Formosa. 1999. Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. Biochemistry 38:8961–8971.
   PubMed Web of Science ®Google Scholar
• Wittschieben, B. O., G. Otero, T. de Bizemont, J. Fellows, H. Erdjument-Bromage, R. Ohba, Y. Li, C. D. Allis, P. Tempst, and J. Q. Svejstrup. 1999. A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme. Mol. Cell 4:123–128.
   PubMed Web of Science ®Google Scholar
• Woodage, T., M. A. Basrai, A. D. Baxevanis, P. Hieter, and F. S. Collins. 1997. Characterization of the CHD family of proteins. Proc. Natl. Acad. Sci. USA 94:11472–11477.
   PubMed Web of Science ®Google Scholar
• Xella, B., C. Goding, E. Agricola, E. Di Mauro, and M. Caserta. 2006. The ISWI and CHD1 chromatin remodelling activities influence ADH2 expression and chromatin organization. Mol. Microbiol. 59:1531–1541.
   PubMed Web of Science ®Google Scholar
• Yang, X. J. 2004. Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays 26:1076–1087.
   PubMed Web of Science ®Google Scholar
• Zhang, H., D. N. Roberts, and B. R. Cairns. 2005. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123:219–231.
   PubMed Web of Science ®Google Scholar
• Zhang, L., S. Schroeder, N. Fong, and D. L. Bentley. 2005. Altered nucleosome occupancy and histone H3K4 methylation in response to ‘transcriptional stress.’ EMBO J. 24:2379–2390.
   PubMedGoogle Scholar