Escherichia coli Dam-methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4

Molecular Biology

Volumn 45, Issue 4, 2011, Pages 591-599

  Spasskaya, D S ^a   Karpov, D S ^a   Karpov, V L ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

binding site; Dam methylase; Escherichia coli; Rpn4; Saccharomyces cerevisiae

Indexed keywords

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 79961140948     PISSN: 00268933     EISSN: 16083245     Source Type: Journal    
DOI: 10.1134/S0026893311030186     Document Type: Article

References (30)

1. Mannhaupt G., Schnall R., Karpov V., Vetter I., Feldmann H. 1999. Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett. 450, 27-34.
2. Kapranov A. B., Kuryatova M. V., Preobrazhenskaya O. V., Tutyaeva V. V., Stucka R., Feldmann H., Karpov V. L. 2001. Isolation and identification of PACE-binding protein Rpn4, a new transcriptional activator regulating 26S-proteasomal and other genes. Mol. Biol. (Moscow). 35, 356-364.
3. Xie Y., Varshavsky A. 2001. RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit. Proc. Natl. Acad. Sci. U. S. A. 98, 3056-3061.
4. Gasch A. P., Moses A. M., Chiang D. Y., Fraser H. B., Berardini M., Eisen M. B. 2004. Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol. 2, e398.
5. Karpov D. S., Preobrazhenskaya O. V., Karpov V. L. 2009. Expression regulation of the proteasomal genes in eukaryotes. Mol. Biol. (Moscow). 43, 223-232.
6. Jelinsky S. A., Estep P., Church G. M., Samson L. D. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell. Biol. 20, 8157-8167.
7. Owsianik G., Balzil L., Ghislain M. 2002. Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae. Mol. Microbiol. 43, 1295-1308.
8. Hahn J. S., Neef D. W., Thiele D. J. 2006. A stress regulatory network for co-ordinated activation of proteasome expression mediated by yeast heat shock transcription factor. Mol. Microbiol. 60, 240-251.
9. Teixeira M. C., Dias P. J., Simoes T., Sa-Correia I. 2008. Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrr1. Biochem. Biophys. Res. Commun. 367, 249-255.
10. Harbison C. T., Gordon D. B., Lee T. I., Rinaldi N. J., Macisaac K. D., Danford T. W., Hannett N. M., Tagne J. B., Reynolds D. B., Yoo J., Jennings E. G., Zeitlinger J., Pokholok D. K., Kellis M., Rolfe P. A., Tak U. S., Agawa K. T., Lander E. S., Gifford D. K., Fraenkel E., Young R. A. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature. 431, 99-104.
11. Zhu C., Byers K. J., McCord R. P., Shi Z., Berger M. F., Newburger D. E., Saulrieta K., Smith Z., Shah M. V., Radhakrishnan M., Philippakis A. A., Hu Y., De Masi F., Pacek M., Rolfs A., Murthy T., Labaer J., Bulyk M. L. 2009. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 19, 556-566.
12. Ju D., Wang X., Ha S. W., Fu J., Xie Y. 2010. Inhibition of proteasomal degradation of rpn4 impairs nonhomologous end-joining repair of DNA double-strand breaks. PLoS One. 5, e9877.
13. van Steensel B., Henikoff S. 2000. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nature Biotechnol. 18, 424-428.
14. Orian A., van Steensel B., Delrow J., Bussemaker H. J., Li L., Sawado T., Williams E., Loo L. W., Cowley S. M., Yost C., Pierce S., Edgar B. A., Parkhurst S. M., Eisenman R. N. 2003. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev. 17, 1101-1114.
15. Bianchi-Frias D., Orian A., Delrow J. J., Vazquez J., Rosales-Nieves A. E., Parkhurst S. M. 2004. Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS Biol. 2, E178.
16. Song S., Cooperman J., Letting D. L., Blobel G. A., Choi J. K. 2004. Identification of cyclin D3 as a direct target of E2A using DamID. Mol. Cell Biol. 24, 8790-8802.
17. Holland S., Ioannou D., Haines S., Brown W. R. 2005. Comparison of Dam tagging and chromatin immunoprecipitation as tools for the identification of the binding sites for S. pombe CENP-C. Chromosome Res. 13, 73-83.
18. Lebrun E., Fourel G., Defossez P. A., Gilson E. 2003. A methyltransferase targeting assay reveals silencertelomere interactions in budding yeast. Mol. Cell Biol. 23, 1498-1508.
19. Venkatasubrahmanyam S., Hwang W. W., Meneghini M. D., Tong A. H., Madhani H. D. 2007. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A. Z. Proc. Natl. Acad. Sci. U. S. A. 104, 16609-16614.
20. Gietz D., St Jean A., Woods R. A., Schiestl R. H. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20, 1425.
21. Ju D., Wang L., Mao X., Xie Y. 2004. Homeostatic regulation of the proteasome via an Rpn4-dependent feedback circuit. Biochem. Biophys. Res. Commun. 321, 51-57.
22. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Smith J. A., Seidman J. G., Struhl K. 1998. Current Protocols in Molecular Biology. NY: Wiley.
23. Christianson T. W., Sikorski R. S., Dante M., Shero J. H., Hieter P. 1992. Multifunctional yeast high-copy-number shuttle vectors. Gene. 110, 119-122.
24. Gietz R. D., Sugino A. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 74, 527-534.
25. Greil F., Moorman C., van Steensel B. 2006. DamID: Mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol. 410, 342-359.
26. Hoekstra M. F., Malone R. E. 1986. Excision repair functions in Saccharomyces cerevisiae recognize and repair methylation of adenine by the Escherichia coli dam gene. Mol. Cell Biol. 6, 3555-3558.
27. London M. K., Keck B. I., Ramos P. C., Dohmen R. J. 2004. Regulatory mechanisms controlling biogenesis of ubiquitin and the proteasome. FEBS Lett. 567, 259-264.
28. Karpov D. S., Osipov S. A., Preobrazhenskaya O. V., Karpov V. L. 2008. Rpn4p is a positive and negative transcriptional regulator of the ubiquitin-proteasome system. Mol. Biol. (Moscow). 42, 456-463.
29. Kladde M. P., Simpson R. T. 1994. Positioned nucleosomes inhibit Dam methylation in vivo. Proc. Natl. Acad. Sci. U. S. A. 91, 1361-1365.
30. Singh J., Klar A. J. 1992. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: A novel in vivo probe for chromatin structure of yeast. Genes Dev. 6, 186-196.