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Article

Requirement of Nhp6 Proteins for Transcription of a Subset of tRNA Genes and Heterochromatin Barrier Function in Saccharomyces cerevisiae

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Pages 1545-1557 | Received 03 May 2006, Accepted 04 Dec 2006, Published online: 27 Mar 2023

REFERENCES

  • Andrau, J. C., and M. Werner. 2001. B"-associated factor(s) involved in RNA polymerase III preinitiation complex formation and start-site selection. Eur. J. Biochem. 268:5167–5175.
  • Bachman, N., M. E. Gelbart, T. Tsukiyama, and J. D. Boeke. 2005. TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes Dev. 19:955–964.
  • Baker, R. E., S. Camier, A. Sentenac, and B. D. Hall. 1987. Gene size differentially affects the binding of yeast transcription factor τ to two intragenic regions. Proc. Natl. Acad. Sci. USA 84:8768–8772.
  • Bianchi, M. E., and A. Agresti. 2005. HMG proteins: dynamic players in gene regulation and differentiation. Curr. Opin. Genet. Dev. 15:496–506.
  • 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.
  • Biswas, D., Y. Yu, D. Mitra, and D. J. Stillman. 2006. Genetic interactions between Nhp6 and Gcn5 with Mot1 and the Ccr4-Not complex that regulate binding of TATA-binding protein in Saccharomyces cerevisiae. Genetics 172:837–849.
  • 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.
  • Bolchi, A., S. Ottonello, and S. Petrucco. 2005. A general one-step method for the cloning of PCR products. Biotechnol. Appl. Biochem. 42:205–209.
  • Bolton, E. C., and J. D. Boeke. 2003. Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Res. 13:254–263.
  • Bonneaud, N., O. Ozier-Kalogeropoulos, G. Y. Li, M. Labouesse, L. Minvielle-Sebastia, and F. Lacroute. 1991. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 7:609–615.
  • Braglia, P., R. Percudani, and G. Dieci. 2005. Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J. Biol. Chem. 280:19551–19562.
  • Burnol, A. F., F. Margottin, P. Schultz, M.-C. Marsolier, P. Oudet, and A. Sentenac. 1993. Basal promoter and enhancer element of yeast U6 snRNA gene. J. Mol. Biol. 233:644–658.
  • Bustin, M., and R. Reeves. 1996. High-mobility-group chromosomal proteins: architectural components that facilitate chromatin function. Prog. Nucleic Acid Res. Mol. Biol. 54:35–100.
  • Chédin, S., M. L. Ferri, G. Peyroche, J. C. Andrau, S. Jourdain, O. Lefebvre, M. Werner, C. Carles, and A. Sentenac. 1998. The yeast RNA polymerase III transcription machinery: a paradigm for eukaryotic gene activation. Cold Spring Harbor Symp. Quant. Biol. 63:381–389.
  • Costigan, C., D. Kolodrubetz, and M. Snyder. 1994. NHP6A and NHP6B, which encode HMG1-like proteins, are candidates for downstream components of the yeast SLT2 mitogen-activated protein kinase pathway. Mol. Cell. Biol. 14:2391–2403.
  • Devine, S. E., and J. D. Boeke. 1996. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. Genes Dev. 10:620–633.
  • Dieci, G., L. Duimio, F. Coda-Zabetta, K. U. Sprague, and S. Ottonello. 1993. A novel RNA polymerase III transcription factor fraction that is not required for template commitment. J. Biol. Chem. 268:11199–11207.
  • Dieci, G., R. Percudani, S. Giuliodori, L. Bottarelli, and S. Ottonello. 2000. TFIIIC-independent in vitro transcription of yeast tRNA genes. J. Mol. Biol. 299:601–613.
  • Dieci, G., and A. Sentenac. 2003. Detours and shortcuts to transcription reinitiation. Trends Biochem. Sci. 28:202–209.
  • Dieci, G., and A. Sentenac. 1996. Facilitated recycling pathway for RNA polymerase III. Cell 84:245–252.
  • Donze, D., C. R. Adams, J. Rine, and R. T. Kamakaka. 1999. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13:698–708.
  • Donze, D., and R. T. Kamakaka. 2001. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20:520–531.
  • Dumay-Odelot, H., J. Acker, R. Arrebola, A. Sentenac, and C. Marck. 2002. Multiple roles of the τ131 subunit of yeast transcription factor IIIC (TFIIIC) in TFIIIB assembly. Mol. Cell. Biol. 22:298–308.
  • 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.
  • Ferrari, R., C. Rivetti, J. Acker, and G. Dieci. 2004. Distinct roles of transcription factors TFIIIB and TFIIIC in RNA polymerase III transcription reinitiation. Proc. Natl. Acad. Sci. USA 101:13442–13447.
  • 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.
  • Geiduschek, E. P., and G. A. Kassavetis. 2001. The RNA polymerase III transcription apparatus. J. Mol. Biol. 310:1–26.
  • Ghaemmaghami, S., W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O'Shea, and J. S. Weissman. 2003. Global analysis of protein expression in yeast. Nature 425:737–741.
  • Giuliodori, S., R. Percudani, P. Braglia, R. Ferrari, E. Guffanti, S. Ottonello, and G. Dieci. 2003. A composite upstream sequence motif potentiates tRNA gene transcription in yeast. J. Mol. Biol. 333:1–20.
  • Grove, A., G. A. Kassavetis, T. E. Johnson, and E. P. Geiduschek. 1999. The RNA polymerase III-recruiting factor TFIIIB induces a DNA bend between the TATA box and the transcriptional start site. J. Mol. Biol. 285:1429–1440.
  • Hani, J., and H. Feldmann. 1998. tRNA genes and retroelements in the yeast genome. Nucleic Acids Res. 26:689–696.
  • Harismendy, O., C. G. Gendrel, P. Soularue, X. Gidrol, A. Sentenac, M. Werner, and O. Lefebvre. 2003. Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J. 22:4738–4747.
  • Huet, J., N. Manaud, G. Dieci, G. Peyroche, C. Conesa, O. Lefebvre, A. Ruet, M. Riva, and A. Sentenac. 1996. RNA polymerase III and class III transcription factors from Saccharomyces cerevisiae. Methods Enzymol. 273:249–267.
  • Hull, M. W., J. Erickson, M. Johnston, and D. R. Engelke. 1994. tRNA genes as transcriptional repressor elements. Mol. Cell. Biol. 14:1266–1277.
  • Jambunathan, N., A. W. Martinez, E. C. Robert, N. B. Agochukwu, M. E. Ibos, S. L. Dugas, and D. Donze. 2005. Multiple bromodomain genes are involved in restricting the spread of heterochromatic silencing at the Saccharomyces cerevisiae HMR-tRNA boundary. Genetics 171:913–922.
  • Kassavetis, G. A., B. R. Braun, L. H. Nguyen, and P. E. Geiduschek. 1990. S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors. Cell 60:235–245.
  • Kassavetis, G. A., C. A. P. Joazeiro, M. Pisano, E. P. Geiduschek, T. Colbert, S. Hahn, and J. A. Blanco. 1992. The role of the TATA binding protein in the assembly and function of the multisubunit yeast RNA polymerase III transcription factor TFIIIB. Cell 71:1055–1064.
  • Kassavetis, G. A., E. Soragni, R. Driscoll, and E. P. Geiduschek. 2005. Reconfiguring the connectivity of a multiprotein complex: fusions of yeast TATA-binding protein with Brf1, and the function of transcription factor IIIB. Proc. Natl. Acad. Sci. USA 102:15406–15411.
  • 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.
  • Kirchner, J., C. M. Connolly, and S. B. Sandmeyer. 1995. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267:1488–1491.
  • Kolodrubetz, D., M. Kruppa, and A. Burgum. 2001. Gene dosage affects the expression of the duplicated NHP6 genes of Saccharomyces cerevisiae. Gene 272:93–101.
  • Komarnitsky, P., E. J. Cho, and S. Buratowski. 2000. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:2452–2460.
  • Krieg, R., R. Stucka, S. Clark, and H. Feldmann. 1991. The use of a synthetic tRNA gene as a novel approach to study in vivo transcription and chromatin structure in yeast. Nucleic Acids Res. 19:3849–3855.
  • Kruppa, M., R. D. Moir, D. Kolodrubetz, and I. M. Willis. 2001. Nhp6, an HMG1 protein, functions in SNR6 transcription by RNA polymerase III in S. cerevisiae. Mol. Cell 7:309–318.
  • Kumar, A., A. Grove, G. A. Kassavetis, and E. P. Geiduschek. 1998. Transcription factor IIIB: the architecture of its DNA complex, and its roles in initiation of transcription by RNA polymerase III. Cold Spring Harbor Symp. Quant. Biol. 63:121–129.
  • Léveillard, T., G. A. Kassavetis, and E. P. Geiduschek. 1991. Saccharomyces cerevisiae transcription factors IIIB and IIIC bend the DNA of a tRNA(Gln) gene. J. Biol. Chem. 266:5162–5168.
  • Lopez, S., M. Livingstone-Zatchej, S. Jourdain, F. Thoma, A. Sentenac, and M.-C. Marsolier. 2001. High-mobility-group proteins NHP6A and NHP6B participate in activation of the RNA polymerase III SNR6 gene. Mol. Cell. Biol. 21:3096–3104.
  • Martin, M. P., V. L. Gerlach, and D. A. Brow. 2001. A novel upstream RNA polymerase III promoter element becomes essential when the chromatin structure of the yeast U6 RNA gene is altered. Mol. Cell. Biol. 21:6429–6439.
  • Moqtaderi, Z., and K. Struhl. 2004. Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol. Cell. Biol. 24:4118–4127.
  • Moreira, J. M., and S. Holmberg. 2000. Chromatin-mediated transcriptional regulation by the yeast architectural factors NHP6A and NHP6B. EMBO J. 19:6804–6813.
  • Paull, T. T., M. Carey, and R. C. Johnson. 1996. Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. Genes Dev. 10:2769–2781.
  • Percudani, R., A. Pavesi, and S. Ottonello. 1997. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol. 268:322–330.
  • 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.
  • Roberts, D. N., A. J. Stewart, J. T. Huff, and B. R. Cairns. 2003. The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc. Natl. Acad. Sci. USA 100:14695–14700.
  • 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.
  • Rüth, J., C. Conesa, G. Dieci, O. Lefebvre, A. Düsterhoft, S. Ottonello, and A. Sentenac. 1996. A suppressor of mutations in the class III transcription system encodes a component of yeast TFIIIB. EMBO J. 15:1941–1949.
  • Sethy-Coraci, I., R. D. Moir, A. Lopez-de-Leon, and I. M. Willis. 1998. A differential response of wild type and mutant promoters to TFIIIB70 overexpression in vivo and in vitro. Nucleic Acids Res. 26:2344–2352.
  • Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
  • Simms, T. A., E. C. Miller, N. P. Buisson, N. Jambunathan, and D. Donze. 2004. The Saccharomyces cerevisiae TRT2 tRNAThr gene upstream of STE6 is a barrier to repression in MATα cells and exerts a potential tRNA position effect in MATa cells. Nucleic Acids Res. 32:5206–5213.
  • Thomas, J. O., and A. A. Travers. 2001. HMG1 and 2, and related ‘architectural’ DNA-binding proteins. Trends Biochem. Sci. 26:167–174.
  • White, R. J. 2002. RNA polymerase III transcription, 3rd edition. Landes Bioscience, Austin, TX.
  • Yu, Y., P. Eriksson, L. T. Bhoite, and D. J. Stillman. 2003. Regulation of TATA-binding protein binding by the SAGA complex and the Nhp6 high-mobility group protein. Mol. Cell. Biol. 23:1910–1921.

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