References
- Adams, M. D., S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne, P. G. Amanatides, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195 https://doi.org/10.1126/science.287.5461.2185
- Bushnell, D. A. and R. D. Kornberg. 2003. Complete, 12- subunit RNA polymerase II at 4.1-A resolution: Implications for the initiation of transcription. Proc. Natl. Acad. Sci. USA 100: 6969-6973
- Bushnell, D. A., K. D. Westover, R. E. Davis, and R. D. Kornberg. 2004. Structural basis of transcription: An RNA polymerase II-TFIIB cocrystal at 4.5 angstroms. Science 303: 983-988 https://doi.org/10.1126/science.1090838
- Chung, W.-H., J. L. Craighead, W.-H. Chang, C. Ezeokonkwo, A. Bareket-Samish, R. D. Kornberg, and F. J. Asturias. 2003. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Molec. Cell 12: 1003-1013 https://doi.org/10.1016/S1097-2765(03)00387-3
- Collins, S. R., P. Kemmeren, X. C. Zhao, J. F. Greenblatt, F. Spencer, F. C. Holstege, J. S. Weissman, and N. J. Krogan. 2007. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6: 439-450 https://doi.org/10.1074/mcp.M600381-MCP200
- Consortium, T. C. E. S. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018 https://doi.org/10.1126/science.282.5396.2012
- Cramer, P., D. A. Bushnell, J. Fu, A. L. Gnatt, B. Maier-Davis, N. E. Thompson, et al. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288: 640-649 https://doi.org/10.1126/science.288.5466.640
- Cramer, P., D. A. Bushnell, and R. D. Kornberg. 2001. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292: 1863-1876 https://doi.org/10.1126/science.1059493
- Davis, J. A., Y. Takagi, R. D. Kornberg, and F. J. Asturias. 2002. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Molec. Cell 10: 409-415 https://doi.org/10.1016/S1097-2765(02)00598-1
- DeLano, W. L. 2002. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, U.S.A.
- Gavin, A. C., P. Aloy, P. Grandi, R. Krause, M. Boesche, M. Marzioch, et al. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636 https://doi.org/10.1038/nature04532
- Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147 https://doi.org/10.1038/415141a
- 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 https://doi.org/10.1038/nature02046
- Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, et al. 1996. Life with 6000 genes. Science 274: 546, 563-567
- Gupta, P. and K. H. Lee. 2007. Genomics and proteomics in process development: Opportunities and challenges. Trends Biotechnol. 25: 324-330 https://doi.org/10.1016/j.tibtech.2007.04.005
- Initiative, T. A. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815 https://doi.org/10.1038/35048692
- Kim, I. S., H. S. Yun, and I. N. Jin. 2007. Comparative proteomic analyses of the yeast Saccharomyces cerevisiae KNU5377 strain against menadione-induced oxidative stress. J. Microbiol. Biotechnol. 17: 207-217
- Kim, Y.-J., S. Bjorklund, Y. Li, M. H. Sayre, and R. D. Kornberg. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77: 599-608 https://doi.org/10.1016/0092-8674(94)90221-6
- Krogan, N. J., G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, et al. 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643 https://doi.org/10.1038/nature04670
- Kus, B., A. Gajadhar, K. Stanger, R. Cho, W. Sun, N. Rouleau, et al. 2005. A high throughput screen to identify substrates for the ubiquitin ligase Rsp5. J. Biol. Chem. 280: 29470-29478 https://doi.org/10.1074/jbc.M502197200
- Lee, K., H. S. Joo, Y. H. Yang, E. J. Song, and B. G. Kim. 2006. Proteomics for Streptomyces: "Industrial proteomics" for antibiotics. J. Microbiol. Biotechnol. 16: 331-348
- Lee, Y. C., S. Min, B. S. Gim, and Y. J. Kim. 1997. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol. Cell. Biol. 17: 4622-4632 https://doi.org/10.1128/MCB.17.8.4622
- Lindstrom, D. L., S. L. Squazzo, N. Muster, T. A. Burckin, K. C. Wachter, C. A. Emigh, J. A. McCleery, J. R. Yates 3rd, and G. A. Hartzog. 2003. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23: 1368-1378 https://doi.org/10.1128/MCB.23.4.1368-1378.2003
- Meinhart, A., T. Kamenski, S. Hoeppner, S. Baumli, and P. Cramer. 2005. A structural perspective of CTD function. Genes Dev. 19: 1401-1415 https://doi.org/10.1101/gad.1318105
- Mitsuzawa, H., E. Kanda, and A. Ishihama. 2003. Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts. Nucleic Acids Res. 31: 4696-4701 https://doi.org/10.1093/nar/gkg688
- Peiro-Chova, L. and F. Estruch. 2007. Specific defects in different transcription complexes compensate for the requirement of the negative cofactor 2 repressor in Saccharomyces cerevisiae. Genetics 176: 125-138 https://doi.org/10.1534/genetics.106.066829
- Ptacek, J., G. Devgan, G. Michaud, H. Zhu, X. Zhu, J. Fasolo, et al. 2005. Global analysis of protein phosphorylation in yeast. Nature 438: 679-684 https://doi.org/10.1038/nature04187
- Puig, O., F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, and B. Seraphin. 2001. The tandem affinity purification (TAP) method: A general procedure of protein complex purification. Methods 24: 218-229 https://doi.org/10.1006/meth.2001.1183
- Sanders, S. L., J. Jennings, A. Canutescu, A. J. Link, and P. A. Weil. 2002. Proteomics of the eukaryotic transcription machinery: Identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22: 4723-4738 https://doi.org/10.1128/MCB.22.13.4723-4738.2002
- Schaft, D., A. Roguev, K. M. Kotovic, A. Shevchenko, M. Sarov, K. M. Neugebauer, and A. F. Stewart. 2003. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res. 31: 2475-2482 https://doi.org/10.1093/nar/gkg372
- Takagi, Y., G. Calero, H. Komori, J. A. Brown, A. H. Ehrensberger, A. Hudmon, F. Asturias, and R. D. Kornberg. 2006. Head module control of mediator interactions. Mol. Cell. 23: 355-364 https://doi.org/10.1016/j.molcel.2006.06.007
- Venter, J. C., M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural, G. G. Sutton, et al. 2001. The sequence of the human genome. Science 291: 1304-1351 https://doi.org/10.1126/science.1058040
- Yuryev, A., M. Patturajan, Y. Litingtung, R. V. Joshi, C. Gentile, M. Gebara, and J. L. Corden. 1996. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. USA 93: 6975-6980