Genome-wide location of yeast RNA polymerase III transcription machinery

EMBO Journal

Volumn 22, Issue 18, 2003, Pages 4738-4747

  Harismendy, Olivier ^a   Gendrel, Christiane Gabrielle ^a   Soularue, Pascal ^b   Gidrol, Xavier ^b   Sentenac, André ^a   Werner, Michel ^a   Lefebvre, Olivier ^a  

^a CEA SACLAY   (France)

^b DIF   (France)

Author keywords

ChIP on chip; Microarray; Transcription; tRNA gene; Yeast

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; FUNGAL ENZYME; FUNGAL RNA; PRP1 RNA; RNA 5S; SMALL NUCLEAR RNA; SMALL NUCLEAR RNA U6; SMALL NUCLEOLAR RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FUNGAL GENE; FUNGUS GROWTH; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENE TARGETING; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; RNA TRANSCRIPTION; RNA TRANSLATION; YEAST;

BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; RNA POLYMERASE III; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION FACTORS, TFIII; TRANSCRIPTION, GENETIC;

FUNGI;

EID: 0141625270     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg466     Document Type: Article

References (63)

1. Andrau, J.-C., Sentenac, A. and Wemer, M. (1999) Mutagenesis of yeast TFIIIB70 reveals C-terminal residues critical for interaction with TBP and C34. J. Mol. Biol., 288, 511-520.
2. Bartholomew, B., Kassavetis, G.A., Braun, B.B. and Geiduschek. (1990) The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent. EMBO J., 9, 2197-2205.
3. Bartholomew, B., Kassavetis, G.A. and Geiduschek, E.P. (1991) Two components of Saccharomyces cerevisiae transcription factor IIIB (TFIIIB) are stereospecifically located upstream of a tRNA gene and interact with the second-largest subunit of TFIIIC. Mol. Cell. Biol., 11, 5181-5189.
4. Bartholomew, B., Durkovich, D., Kassavetis, G.A. and Geiduschek, E.P. (1993) Orientation and topography of RNA polymerase III in transcription complexes. Mol. Cell. Biol., 13, 942-952.
5. Braun, B.R., Riggs, D.L., Kassavetis, G.A. and Geiduschek, E.P. (1989) Multiple states of protein-DNA interaction in the assembly of transcription complexes on Saccharomyces cerevisiae 5S ribosomal RNA genes. Proc. Natl Acad. Sci. USA, 86, 2530-2534.
6. Braun, B.R., Bartholomew, B., Kassavetis, G.A. and Geiduschek, E.P. (1992) Topography of transcription factor complexes on the Saccharomyces cerevisiae 5S RNA gene. J. Mol. Biol., 228, 1063-1077.
7. Briand, J.F., Navarro, F., Gadal, O. and Thuriaux, P. (2001) Cross talk between tRNA and rRNA synthesis in Saccharomyces cerevisiae. Mol. Cell. Biol., 21, 189-195.
8. Brow, D.A. and Guthrie, C. (1990) Transcription of a yeast U6 snRNA gene requires a polymerase III promoter element in a novel position. Genes Dev., 4, 1345-1356.
9. Brun, I., Sentenac, A. and Wemer, M. (1997) Dual role of the C34 subunit of RNA polymerase III in transcription initiation. EMBO J., 16, 5730-5741.
10. Burnol, A.-F., Margottin, F., Huet, J., Almouzni, G., Prioleau, M.-N., Méchali, M. and Sentenac, A. (1993a) TFIIIC relieves repression of U6 snRNA transcription by chromatin. Nature, 362, 475-477.
11. Bumol, A.-F., Margottin, F., Schultz, P., Marsolier, M.-C., Oudet, P. and Sentenac, A. (1993b) Basal promoter and enhancer element of yeast U6 snRNA gene. J. Mol. Biol., 233, 644-658.
12. Challice, J.M. and Segall, J. (1989) Transcription of the 5S rRNA gene of Saccharomyces cerevisiae requires a promoter element at +1 and a 14-base pair internal control region. J. Biol. Chem., 264, 20060-20067.
13. Chédin, S., Ferri, L., Peyroche, G., Andrau, J.-C., Jourdain, S., Lefebvre, O., Wemer, M., Carles, C. and Sentenac, A. (1998) The Yeast RNA Polymerase III Transcription Machinery. A Paradigm for Eukaryotic Gene Activation. Vol. 63. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 381-389.
14. Clarke, E.M., Peterson, C.L., Brainard, A.V. and Riggs, D.L. (1996) Regulation of the RNA polymerase I and III transcription systems in response to growth conditions. J. Biol. Chem., 271, 22189-22195.
15. Colbert, T., Lee, S., Schimmack, G. and Hahn, S. (1998) Architecture of protein and DNA contacts within the TFIIIB-DNA complex. Mol. Cell. Biol., 18, 1682-1691.
16. Conesa, C., Swanson, R., Schultz, P., Oudet, P. and Sentenac, A. (1993) On the subunit composition, stoichiometry and phosphorylation of the yeast transcription factor TFIIC/τ. J. Biol. Chem., 268, 18047-18052.
17. Dechampesme, A.M., Koroleva, O., Leger-Silvestre, I., Gas, N. and Camier, S. (1999) Assembly of 5S ribosomal RNA is required at a specific step of the pre-rRNA processing pathway. J. Cell Biol., 145, 1369-1380.
18. Dieci, G., Hermann-Le Denmat, S., Lukhtanov, E., Thuriaux, P., Werner, M. and Sentenac, A. (1995) A universally conserved region of the largest subunit participates in the active site of RNA polymerase III. EMBO J., 14, 3766-3776.
19. Dieci, G., Percudani, R., Giuliodori, S., Bottarelli, L. and Ottonello, S. (2000) TFIIIC-independent in vitro transcription of yeast tRNA genes. J. Mol. Biol., 299, 601-613.
20. Dieci, G., Giuliodori, S., Catellani, M., Percudani, R. and Ottonello, S. (2002) Intragenic promoter adaptation and facilitated RNA polymerase III recycling in the transcription of SCR1, the 7SL RNA gene of Saccharomyces cerevisiae. J. Biol. Chem., 277, 6903-6914.
21. Eschenlauer, J.B., Kaiser, M.W., Gerlach, V.L. and Brow, D.A. (1993) Architecture of a yeast U6 RNA gene promoter. Mol. Cell. Biol., 13, 3015-3026.
22. Ferri, M.L., Peyroche, G., Siaut, M., Lefebvre, O., Carles, C., Conesa, C. and Sentenac, A. (2000) A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70. Mol. Cell. Biol., 20, 488-495.
23. Geiduschek, E.P. and Kassavetis, G.A. (2001) The RNA polymerase III transcription apparatus. J. Mol. Biol., 310, 1-26.
24. Gerlach, V.L., Whitehall, S.K., Geiduschek, E.P. and Brow, D.A. (1995) TFIIIB placement on a yeast U6 RNA gene in vivo is directed primarily by TFIIIC rather than by sequence-specific DNA contacts. Mol. Cell. Biol., 15, 1455-1466.
25. Hani, J. and Feldmann, H. (1998) tRNA genes and retroelement in the yeast genome. Nucleic Acids Res., 26, 689-696.
26. Hecht, A. and Grunstein, M. (1999) Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol., 304, 399-414.
27. Hecht, A., Strahl-Bolsinger, S. and Grunstein, M. (1999) Mapping DNA interaction sites of chromosomal proteins. Crosslinking studies in yeast. Methods Mol. Biol., 119, 469-479.
28. Hermann-Le Denmat, S., Wemer, M., Sentenac, A. and Thuriaux, P. (1994) Suppression of yeast RNA polymerase III mutations by FHL1, a gene coding for a fork head protein involved in rRNA processing. Mol. Cell. Biol., 14, 2905-2913.
29. Huet, J., Conesa, C., Carles, C. and Sentenac, A. (1997) A cryptic DNA binding domain at the C-terminus of TFIIIB70 affects formation, stability and function of preinitiation complexes. J. Biol. Chem., 272, 18341-18349.
30. Huibregtse, J.M. and Engelke, D.R. (1989) Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5′-flanking region. Mol. Cell. Biol., 9, 3244-3252.
31. Iyer, V.R., Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M. and Brown, P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538.
32. Jourdain, S., Acker, J., Ducrot, C., Sentenac, A. and Lefebvre, O. (2003) The tau95 subunit of yeast TFIIIC influences upstream and downstream functions of TFIIIC.DNA complexes. J. Biol. Chem., 278, 10450-10457.
33. Juo, Z.S., Kassavetis, G.A., Wang, J., Geiduschek, E.P. and Sigler, P.B. (2003) Crystal structure of a transcription factor IIIB core interface ternary complex. Nature, 422, 534-539.
34. Kassavetis, G.A., Braun, B.R., Nguyen, L.H. and Geiduschek, E.P. (1990) S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors. Cell, 60, 247-257.
35. Kassavetis, G.A., Joazeiro, C.A.P., Pisano, M., Geiduschek, E.P., Colbert, T., Hahn, S. and Blanco, J.A. (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.
36. Kassavetis, G.A., Barbeleben, C., Kumar, A., Ramirez, E. and Geiduschek, E.P. (1997) Domains of the Brf component of RNA polymerase III transcription factor III (TFIIIB): functions in assembly of TFIIIB-DNA complexes and recruitment of RNA polymerase to the promoter. Mol. Cell. Biol., 17, 5299-5306.
37. Kassavetis, G.A., Kumar, A., Letts, G.A. and Geiduschek, E.P. (1998) A post-recruitment function for the RNA polymerase III transcription-initiation factor IIIB. Proc. Natl Acad. Sci. USA, 95, 9196-9201.
38. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
39. Kumar, A., Kassavetis, G.A., Geiduschek, E.P., Hambalko, M. and Brent, C.J. (1997) Functional dissection of the B″ component of RNA polymerase III transcription factor IIIB: a scaffolding protein with multiple roles in assembly and initiation of transcription. Mol. Cell. Biol., 17, 1868-1880.
40. Lee, J.-Y., Evans, C.F. and Engelke, D.R. (1991a) Expression of RNase P RNA in Saccharomyces cerevisiae is controlled by an unusual RNA polymerase III promoter. Proc. Natl Acad. Sci. USA, 88, 6986-6990.
41. Lee, J.Y., Rohlman, C.E., Molony, L.A. and Engelke, D.R. (1991b) Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P. Mol. Cell. Biol., 11, 721-730.
42. Lefebvre, O., Rüth, J. and Sentenac, A. (1994) A mutation in the largest subunit of yeast THIIIC affects tRNA and 5S RNA synthesis. J. Biol. Chem., 269, 23374-23381.
43. Lieb, J.D., Liu, X., Botstein, D. and Brown, P.O. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet., 28, 327-334.
44. Longtine, M.S., McKenzie, A., III, Demarini, D.J., Shah, N.G., Wach, A., Brachat, A., Philipsen, P. and Pringle, J.R. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast, 14, 953-961.
45. Lowe, T.M. and Eddy, S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1171.
46. Margottin, F., Dujardin, G., Gérard, M., Egly, J.-M., Huet, J. and Sentenac, A. (1991) Participation of the TATA factor in transcription of the yeast U6 gene by RNA polymerase C. Science, 251, 424-426.
47. Marsolier, M.-C., Tanaka, S., Livingstone-Zatchej, M., Grunstein, M., Thoma, F. and Sentenac, A. (1995) Reciprocal interferences between nucleosomal organization and transcriptional activation of the yeast SNR6 gene. Genes Dev., 9, 410-422.
48. Marzouki, N., Camier, S., Ruet, A., Moenne, A. and Sentenac, A. (1986) Selective proteolysis defines two DNA binding domains in yeast transcription factor tau. Nature, 323, 176-178.
49. Olivas, W.M., Muhlrad, D. and Parker, R. (1997) Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucleic Acids Res., 25, 4619-4625.
50. Percudani, R., Pavesi, A. and Ottonello, S. (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol., 268, 322-330.
51. Persinger, J., Sengupta, S.M. and Bartholomew, B. (1999) Spatial organization of the core region of yeast TFIIIB-DNA complexes. Mol. Cell. Biol., 19, 5218-5234.
52. Prioleau, M.-N., Huet, J., Sentenac, A. and Méchali, M. (1994) Competition between chromatin and transcription complex assembly regulates gene expression during early development. Cell, 77, 439-449.
53. Ren, B. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
54. Sandmeyer, S. (1998) Targeting transposition: at home in the genome. Genome Res., 8, 416-418.
55. Schramm, L. and Hemandez, N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev., 16, 2593-2620.
56. Sentenac, A. (1985) Eukaryotic RNA polymerases. CRC Crit. Rev., 18, 31-91.
57. 70 and TFIIIC. J. Biol. Chem., 270, 28463-28470.
58. Shah, S.M., Kumar, A., Geiduschek, E.P. and Kassavetis, G.A. (1999) Alignment of the B″ subunit of RNA polymerase III transcription factor IIIB in its promoter complex. J. Biol. Chem., 274, 28736-28744.
59. Sikorski, R.S. and Hieter, P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122, 19-27.
60. Werner, M., Chaussivert, N., Willis, I.M. and Sentenac, A. (1993) Interacfion between a complex of RNA polymerase III subunits and the 70-kDa component of transcription factor IIIB. J. Biol. Chem., 268, 20721-20724.
61. White, R.J. (1998) RNA Polymerase III Transcription. Springer-Verlag, Berlin, Germany.
62. Whitehall, S.K., Kassavetis, G.A. and Getduschek, E.P. (1995) The symmetry of the yeast U6 RNA gene's TATA box and the orientafion of the TATA-binding protein in yeast TFIIIB. Genes Dev., 9, 2974-2985.
63. Willis, I.M. (1993) RNA polymerase III: genes, factors and transcriptional specificity. Eur. J. Biochem., 212, 1-11.