Comparison of ABF1 arid RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae

Molecular and Cellular Biology

Volumn 24, Issue 20, 2004, Pages 9152-9164

  Yarragudi, Arunadevi ^a   Miyake, Tsuyoshi ^b   Li, Rong ^b   Morse, Randall H ^a,c  

^a WADSWORTH CENTER   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

^c STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTONOMOUSLY REPLICATING SEQUENCE BINDING FACTOR 1; BINDING PROTEIN; DNA BINDING PROTEIN; RAP PROTEIN; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR AP 1; UNCLASSIFIED DRUG; ABF1 PROTEIN, S CEREVISIAE; ALCOHOL DEHYDROGENASE; HIS4 PROTEIN, S CEREVISIAE; HYDROLASE; IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE; INORGANIC PYROPHOSPHATASE; PROTEIN KINASE; RAP1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; TELOMERE BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN STRUCTURE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA BINDING; GENE ACTIVATION; GENE REPLICATION; GENE REPRESSION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; TELOMERE; TRANSACTIVATION; YEAST; BINDING SITE; CHROMATIN; ENZYME ACTIVATION; GENETICS; METABOLISM; NUCLEOSOME;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

ALCOHOL OXIDOREDUCTASES; AMINOHYDROLASES; BINDING SITES; CHROMATIN; DNA-BINDING PROTEINS; ENZYME ACTIVATION; NUCLEOSOMES; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN KINASES; PYROPHOSPHATASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TELOMERE-BINDING PROTEINS; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 4744375319     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.20.9152-9164.2004     Document Type: Article

References (60)

1. Barbaric, S., M. Munsterkotter, C. Goding, and W. Horz. 1998. Cooperative Pho2-Pho4 interactions at the PHO5 promoter are critical for binding of Pho4 to UASp1 and for efficient transactivation by Pho4 at UASp2. Mol. Cell. Biol. 18:2629-2639.
2. Bodmer-Glavas, M., K. Edler, and A. Barberis. 2001. RNA polymerase II and III transcription factors can stimulate DNA replication by modifying origin chromatin structures. Nucleic Acids Res. 29:4570-4580.
3. Chasman, D. I., N. F. Lue, A. R. Buchman, J. W. LaPointe, Y. Lorch, and R. D. Kornberg. 1990. A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 4:503-514.
4. Devlin, C., K. Tice-Baldwin, D. Shore, and K. T. Arndt. 1991. RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol. Cell. Biol. 11:3642-3651.
5. Diffley, J. F., and B. Stillman. 1989. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science 246:1034-1038.
6. Fourel, G., T. Miyake, P. A. Defossez, R. Li, and E. Gilson. 2002. General regulatory factors (GRFs) as genome partitioners. J. Biol. Chem. 277:41736-41743.
7. Gartenberg, M. R. 2000. The Sir proteins of Saccharomyces cerevisiae: mediators of transcriptional silencing and much more. Curr. Opin. Microbiol. 3:132-137.
8. Goncalves, P. M., G. Griffioen, R. Minnee, M. Bosma, L. S. Kraakman, W. H. Mager, and R. J. Planta. 1995. Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p. Nucleic Acids Res. 23:1475-1480.
9. Goncalves, P. M., K. Maurer, G. van Nieuw Amerongen, K. Bergkamp-Steffens, W. H. Mager, and R. J. Planta. 1996. C-terminal domains of general regulatory factors Abf1p and Rap1p in Saccharomyces cerevisiae display functional similarity. Mol. Microbiol. 19:535-543.
10. Graham, I. R., R. A. Haw, K. G. Spink, K. A. Halden, and A. Chambers. 1999. In vivo analysis of functional regions within yeast Rap1p. Mol. Cell. Biol. 19:7481-7490.
11. Grunstein, M. 1997. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9:383-387.
12. Halfter, H., B. Kavety, J. Vandekerckhove, F. Kiefer, and D. Gallwitz. 1989. Sequence, expression and mutational analysis of BAF1, a transcriptional activator and ARS1-binding protein of the yeast Saccharomyces cerevisiae. EMBO J. 8:4265-4272.
13. Hardy, C. F. J., L. Sussel, and D. Shore. 1992. Dissection of a carboxyl-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing. Mol. Cell. Biol. 12:1209-1217.
14. Higuchi, R., B. Krummel, and R. K. Saiki. 1988. A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res. 16:7351-7367.
15. Hill, J., K. A. Donald, D. E. Griffiths, and G. Donald. 1991. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 19:5791. (Erratum, 19: 6688.)
16. Hu, Y. F., Z. L. Hao, and R. Li. 1999. Chromatin remodeling and activation of chromosomal DNA replication by an acidic transcriptional activation domain from BRCA1. Genes Dev. 13:637-642.
17. Kent, N. A., L. E. Bird, and J. Mellor. 1993. Chromatin analysis in yeast using NP-40 permeabilised sphaeroplasts. Nucleic Acids Res. 21:4653-4654.
18. Kurtz, S., and D. Shore. 1991. RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev. 5:616-628.
19. Lascaris, R. F., E. Groot, P. B. Hoen, W. H. Mager, and R. J. Planta. 2000. Different roles for Abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res. 28:1390-1396.
20. Li, R., D. S. Yu, M. Tanaka, L. Zheng, S. L. Berger, and B. Stillman. 1998. Activation of chromosomal DNA replication in Saccharomyces cerevisiae by acidic transcriptional activation domains. Mol. Cell. Biol. 18:1296-1302.
21. Lieb, J. D., X. Liu, D. Botstein, and P. O. Brown. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:327-334.
22. Marahrens, Y., and B. Stillman. 1992. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255:817-823.
23. Martens, J. A., and C. J. Brandi. 1994. GCN4p activation of the yeast TRP3 gene is enhanced by ABF1p and uses a suboptimal TATA element. J. Biol. Chem. 269:15661-15667.
24. Mencia, M., Z. Moqtaderi, J. V. Geisberg, L. Kuras, and K. Struhl. 2002. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol. Cell 9:823-833.
25. Miller, J. A., and J. Widom. 2003. Collaborative competition mechanism for gene activation in vivo. Mol. Cell. Biol. 23:1623-1632.
26. Miyake, T., C. M. Loch, and R. Li. 2002. Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol. Cell. Biol. 22:505-516.
27. Morse, R. H. 2003. Getting into chromatin: how do transcription factors get past the histones? Biochem. Cell Biol. 81:101-112.
28. Morse, R. H. 1993. Nucleosome disruption by transcription factor binding in yeast. Science 262:1563-1566.
29. Morse, R. H. 2000. RAP, RAP, open up! New wrinkles for RAP1 in yeast. Trends Genet. 16:51-53.
30. Morse, R. H., S. Y. Roth, and R. T. Simpson. 1992. A transcriptionally active tRNA gene interferes with nucleosome positioning in vivo. Mol. Cell. Biol. 12:4015-4025.
31. Pal, S., A. B. Cantor, K. D. Johnson, T. B. Moran, M. E. Boyer, S. H. Orkin, and E. H. Bresnick. 2004. Coregulator-dependent facilitation of chromatin occupancy by GATA-1. Proc. Natl. Acad. Sci. USA 101:980-985.
32. Pilpel, Y., P. Sudarsanam, and G. M. Church. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29: 153-159.
33. Pina, B., J. Fernandez-Larrea, N. Garcia-Reyero, and F. Z. Idrissi. 2003. The different (sur)faces of Rap1p. Mol. Genet. Genomics 268:791-798.
34. Polach, K. J., and J. Widom. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130-149.
35. Pryde, F. E., and E. J. Louis. 1999. Limitations of silencing at native yeast telomeres. EMBO J. 18:2538-2550.
36. Reed, S. H., M. Akiyama, B. Stillman, and E. C. Friedberg. 1999. Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev. 13:3052-3058.
37. 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.
38. Rhode, P. R., S. Elsasser, and J. L. Campbell. 1992. Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:1064-1077.
39. Rhode, P. R., K. S. Sweder, K. F. Oegema, and J. L. Campbell. 1989. The gene encoding ARS-binding factor I is essential for the viability of yeast. Genes Dev. 3:1926-1939.
40. Rolfes, R. J., F. Zhang, and A. G. Hinnebusch. 1997. The transcriptional activators BAS1, BAS2, and ABF1 bind positive regulatory sites as the critical elements for adenine regulation of ADE5,7. J. Biol. Chem. 272: 13343-13354.
41. Ryan, M. P., R. Jones, and R. H. Morse. 1998. SWI-SNF complex participation in transcriptional activation at a step subsequent to activator binding. Mol. Cell. Biol. 18:1774-1782.
42. Ryan, M. P., G. A. Stafford, L. Yu, and R. H. Morse. 2000. Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling. Mol. Cell. Biol. 20:5847-5857.
43. Sabet, N., F. Tong, J. P. Madigan, S. Volo, M. M. Smith, and R. H. Morse. 2003. Global and specific transcriptional repression by the histone H3 amino terminus in yeast. Proc. Natl. Acad. Sci. USA 100:4084-4089.
44. Schroeder, S. C., and P. A. Weil. 1998. Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box binding protein-encoding gene, SPT15. J. Biol. Chem. 273:19884-19891.
45. Shore, D. 1994. RAP1: a protean regulator in yeast. Trends Genet. 10:408-412.
46. Simpson, R. T. 1991. Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog. Nucleic Acid Res. Mol. Biol. 40:143-184.
47. Springer, C., S. Krappmann, M. Kunzler, C. Zmasek, and G. H. Braus. 1997. Regulation of the yeast HIS7 gene by the global transcription factor Abf1p. Mol. Gen. Genet. 256:136-146.
48. Springer, C., M. Kunzler, T. Balmelli, and G. H. Braus. 1996. Amino acid and adenine cross-pathway regulation act through the same 5′-TGACTC- 3′ motif in the yeast HIS7 promoter. J. Biol. Chem. 271:29637-29643.
49. Stafford, G. A., and R. H. Morse. 1997. Chromatin remodeling by transcriptional activation domains in a yeast episome. J. Biol. Chem. 272:11526-11534.
50. Strahl-Bolsinger, S., A. Hecht, K. Luo, and M. Grunstein. 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83-93.
51. Thoma, F. 1992. Nucleosome positioning. Biochim. Biophys. Acta 1130:1-19.
52. Thoma, F., L. W. Bergman, and R. T. Simpson. 1984. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol. Biol. 177:715-733.
53. Valerius, O., C. Brendel, C. Wagner, S. Krappmann, F. Thoma, and G. H. Braus. 2003. Nucleosome position-dependent and -independent activation of HIS7 expression in Saccharomyces cerevisiae by different transcriptional activators. Eukaryot. Cell 2:876-885.
54. Venditti, P., G. Costanzo, R. Negri, and G. Camilloni. 1994. ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim. Biophys. Acta 1219:677-689.
55. Wang, Y., C. L. Liu, J. D. Storey, R. J. Tibshirani, D. Herschlag, and P. O. Brown. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99:5860-5865.
56. Wiltshire, S., S. Raychaudhuri, and S. Eisenberg. 1997. An Abf1p C-terminal region lacking transcriptional activation potential stimulates a yeast origin of replication. Nucleic Acids Res. 25:4250-4256.
57. Winston, F., C. Dollard, and S. L. Ricupero-Hovasse. 1995. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11:53-55.
58. Yu, L., and R. H. Morse. 1999. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:5279-5288.
59. Yu, L., N. Sabet, A. Chambers, and R. H. Morse. 2001. The N-terminal and C-terminal domains of RAP1 are dispensable for chromatin opening and GCN4-mediated HIS4 activation in budding yeast. J. Biol. Chem. 276:33257-33264.
60. Yu, Q., R. Qiu, T. B. Foland, D. Griesen, C. S. Galloway, Y. H. Chiu, J. Sandmeier, J. R. Broach, and X. Bi. 2003. Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression. Nucleic Acids Res. 31:1224-1233.