New Suppressors of THO Mutations Identify Thp3 (Ypr045c)-Csn12 as a Protein Complex Involved in Transcription Elongation

REFERENCES

• Aguilera, A. 2005. Cotranscriptional mRNP assembly: from the DNA to the nuclear pore. Curr. Opin. Cell Biol. 17:242–250.
   PubMed Web of Science ®Google Scholar
• Aguilera, A., and B. Gomez-Gonzalez. 2008. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet. 9:204–217.
   PubMed Web of Science ®Google Scholar
• Amberg, D. C., A. L. Goldstein, and C. N. Cole. 1992. Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Genes Dev. 6:1173–1189.
   PubMedGoogle Scholar
• Buratowski, S. 2005. Connections between mRNA 3′ end processing and transcription termination. Curr. Opin. Cell Biol. 17:257–261.
   PubMed Web of Science ®Google Scholar
• Burns, N., et al. 1994. Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8:1087–1105.
   PubMed Web of Science ®Google Scholar
• Chamovitz, D. A. 2009. Revisiting the COP9 signalosome as a transcriptional regulator. EMBO Rep. 10:352–358.
   PubMedGoogle Scholar
• Chávez, S., et al. 2000. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J. 19:5824–5834.
   PubMed Web of Science ®Google Scholar
• Ciccarelli, F. D., E. Izaurralde, and P. Bork. 2003. The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold. BMC Bioinformatics 4:64.
   PubMed Web of Science ®Google Scholar
• Cole, C. N., and J. J. Scarcelli. 2006. Transport of messenger RNA from the nucleus to the cytoplasm. Curr. Opin. Cell Biol. 18:299–306.
   PubMed Web of Science ®Google Scholar
• Collins, S. R., et al. 2007. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6:439–450.
   PubMed Web of Science ®Google Scholar
• Costanzo, M., et al. 2010. The genetic landscape of a cell. Science 327:425–431.
   PubMed Web of Science ®Google Scholar
• De Antoni, A., and D. Gallwitz. 2000. A novel multi-purpose cassette for repeated integrative epitope tagging of genes in Saccharomyces cerevisiae. Gene 246:179–185.
   PubMed Web of Science ®Google Scholar
• Dohmann, E. M., M. P. Levesque, E. Isono, M. Schmid, and C. Schwechheimer. 2008. Auxin responses in mutants of the Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC9 signalosome. Plant Physiol. 147:1369–1379.
   PubMed Web of Science ®Google Scholar
• Fan, H. Y., and H. L. Klein. 1994. Characterization of mutations that suppress the temperature-sensitive growth of the hpr1 delta mutant of Saccharomyces cerevisiae. Genetics 137:945–956.
   PubMedGoogle Scholar
• Faza, M. B., et al. 2009. Sem1 is a functional component of the nuclear pore complex-associated messenger RNA export machinery. J. Cell Biol. 184:833–846.
   PubMed Web of Science ®Google Scholar
• Feng, S., et al. 2003. The COP9 signalosome interacts physically with SCF COI1 and modulates jasmonate responses. Plant Cell 15:1083–1094.
   PubMed Web of Science ®Google Scholar
• Ferdous, A., F. Gonzalez, L. Sun, T. Kodadek, and S. A. Johnston. 2001. The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II. Mol. Cell 7:981–991.
   PubMed Web of Science ®Google Scholar
• Fiedler, D., et al. 2009. Functional organization of the S. cerevisiae phosphorylation network. Cell 136:952–963.
   PubMed Web of Science ®Google Scholar
• Fischer, T., et al. 2002. The mRNA export machinery requires the novel Sac3p-Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores. EMBO J. 21:5843–5852.
   PubMed Web of Science ®Google Scholar
• Freilich, S., et al. 1999. The COP9 signalosome is essential for development of Drosophila melanogaster. Curr. Biol. 9:1187–1190.
   PubMedGoogle Scholar
• Funakoshi, M., X. Li, I. Velichutina, M. Hochstrasser, and H. Kobayashi. 2004. Sem1, the yeast ortholog of a human BRCA2-binding protein, is a component of the proteasome regulatory particle that enhances proteasome stability. J. Cell Sci. 117:6447–6454.
   PubMed Web of Science ®Google Scholar
• Gallardo, M., and A. Aguilera. 2001. A new hyperrecombination mutation identifies a novel yeast gene, THP1, connecting transcription elongation with mitotic recombination. Genetics 157:79–89.
   PubMedGoogle Scholar
• Gonzalez, F., A. Delahodde, T. Kodadek, and S. A. Johnston. 2002. Recruitment of a 19S proteasome subcomplex to an activated promoter. Science 296:548–550.
   PubMedGoogle Scholar
• González-Aguilera, C., et al. 2008. The THP1-SAC3-SUS1-CDC31 complex works in transcription elongation-mRNA export preventing RNA-mediated genome instability. Mol. Biol. Cell 19:4310–4318.
   PubMed Web of Science ®Google Scholar
• González-Barrera, S., M. Garcia-Rubio, and A. Aguilera. 2002. Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae. Genetics 162:603–614.
   PubMed Web of Science ®Google Scholar
• Grund, S. E., et al. 2008. The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression. J. Cell Biol. 182:897–910.
   PubMed Web of Science ®Google Scholar
• Gustafsson, C. M., et al. 1998. Identification of new mediator subunits in the RNA polymerase II holoenzyme from Saccharomyces cerevisiae. J. Biol. Chem. 273:30851–30854.
   PubMedGoogle Scholar
• Hampsey, M. 1997. A review of phenotypes in Saccharomyces cerevisiae. Yeast 13:1099–1133.
   PubMed Web of Science ®Google Scholar
• Harel-Sharvit, L., et al. 2010. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell 143:552–563.
   PubMed Web of Science ®Google Scholar
• Hecht, A., and M. Grunstein. 1999. Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol. 304:399–414.
   PubMedGoogle Scholar
• Huertas, P., and A. Aguilera. 2003. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell 12:711–721.
   PubMed Web of Science ®Google Scholar
• Huertas, P., M. L. Garcia-Rubio, R. E. Wellinger, R. Luna, and A. Aguilera. 2006. An hpr1 point mutation that impairs transcription and mRNP biogenesis without increasing recombination. Mol. Cell. Biol. 26:7451–7465.
   PubMedGoogle Scholar
• Jensen, T. H., et al. 2004. Modulation of transcription affects mRNP quality. Mol. Cell 16:235–244.
   PubMedGoogle Scholar
• Jimeno, S., M. Garcia-Rubio, R. Luna, and A. Aguilera. 2008. A reduction in RNA polymerase II initiation rate suppresses hyper-recombination and transcription-elongation impairment of THO mutants. Mol. Genet. Genomics 280:327–336.
   PubMedGoogle Scholar
• Jimeno, S., A. G. Rondón, R. Luna, and A. Aguilera. 2002. The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability. EMBO J. 21:3526–3535.
   PubMed Web of Science ®Google Scholar
• Kim, J., M. Guermah, and R. G. Roeder. 2010. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 140:491–503.
   PubMed Web of Science ®Google Scholar
• Krogan, N. J., et al. 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637–643.
   PubMed Web of Science ®Google Scholar
• Lee, D., et al. 2005. The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators. Cell 123:423–436.
   PubMed Web of Science ®Google Scholar
• Lee, J., R. D. Moir, and I. M. Willis. 2009. Regulation of RNA polymerase III transcription involves SCH9-dependent and SCH9-independent branches of the target of rapamycin (TOR) pathway. J. Biol. Chem. 284:12604–12608.
   PubMed Web of Science ®Google Scholar
• Lei, E. P., et al. 2003. Sac3 is an mRNA export factor that localizes to cytoplasmic fibrils of nuclear pore complex. Mol. Biol. Cell 14:836–847.
   PubMed Web of Science ®Google Scholar
• Li, C., and W. H. Wong. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U. S. A. 98:31–36.
   PubMed Web of Science ®Google Scholar
• Luna, R., H. Gaillard, C. González-Aguilera, and A. Aguilera. 2008. Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus. Chromosoma 117:319–331.
   PubMed Web of Science ®Google Scholar
• Madia, F., et al. 2008. Longevity mutation in SCH9 prevents recombination errors and premature genomic instability in a Werner/Bloom model system. J. Cell Biol. 180:67–81.
   PubMed Web of Science ®Google Scholar
• Marín, A., et al. 2003. Relationship between G+C content, ORF-length and mRNA concentration in Saccharomyces cerevisiae. Yeast 20:703–711.
   PubMedGoogle Scholar
• Mason, P. B., and K. Struhl. 2005. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell 17:831–840.
   PubMed Web of Science ®Google Scholar
• Maytal-Kivity, V., E. Pick, R. Piran, K. Hofmann, and M. H. Glickman. 2003. The COP9 signalosome-like complex in S. cerevisiae and links to other PCI complexes. Int. J. Biochem. Cell Biol. 35:706–715.
   PubMed Web of Science ®Google Scholar
• Milgrom, E., R. W. West, Jr., C. Gao, and W. C. Shen. 2005. TFIID and Spt-Ada-Gcn5-acetyltransferase functions probed by genome-wide synthetic genetic array analysis using a Saccharomyces cerevisiae taf9-ts allele. Genetics 171:959–973.
   PubMedGoogle Scholar
• Mundt, K. E., et al. 1999. The COP9/signalosome complex is conserved in fission yeast and has a role in S phase. Curr. Biol. 9:1427–1430.
   PubMed Web of Science ®Google Scholar
• Oron, E., et al. 2007. Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression. Mol. Syst. Biol. 3:108.
   PubMedGoogle Scholar
• Piruat, J. I., and A. Aguilera. 1998. A novel yeast gene, THO2, is involved in RNA pol II transcription and provides new evidence for transcriptional elongation-associated recombination. EMBO J. 17:4859–4872.
   PubMedGoogle Scholar
• Piruat, J. I., and A. Aguilera. 1996. Mutations in the yeast SRB2 general transcription factor suppress hpr1-induced recombination and show defects in DNA repair. Genetics 143:1533–1542.
   PubMedGoogle Scholar
• Piruat, J. I., S. Chávez, and A. Aguilera. 1997. The yeast HRS1 gene is involved in positive and negative regulation of transcription and shows genetic characteristics similar to SIN4 and GAL11. Genetics 147:1585–1594.
   PubMedGoogle Scholar
• Prusty, R., and R. L. Keil. 2004. SCH9, a putative protein kinase from Saccharomyces cerevisiae, affects HOT1-stimulated recombination. Mol. Genet. Genomics 272:264–274.
   PubMedGoogle Scholar
• Rabut, G., and M. Peter. 2008. Function and regulation of protein neddylation. ‘Protein modifications: beyond the usual suspects’ review series. EMBO Rep. 9:969–976.
   PubMed Web of Science ®Google Scholar
• Rigaut, G., et al. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17:1030–1032.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Navarro, S., et al. 2004. Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell 116:75–86.
   PubMed Web of Science ®Google Scholar
• Rondón, A. G., M. Gallardo, M. Garcia-Rubio, and A. Aguilera. 2004. Molecular evidence indicating that the yeast PAF complex is required for transcription elongation. EMBO Rep. 5:47–53.
   PubMed Web of Science ®Google Scholar
• Santos-Rosa, H., and A. Aguilera. 1995. Isolation and genetic analysis of extragenic suppressors of the hyper-deletion phenotype of the Saccharomyces cerevisiae hpr1 delta mutation. Genetics 139:57–66.
   PubMedGoogle Scholar
• Scholes, D. T., M. Banerjee, B. Bowen, and M. J. Curcio. 2001. Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics 159:1449–1465.
   PubMed Web of Science ®Google Scholar
• Steinmetz, E. J., and D. A. Brow. 2003. Ssu72 protein mediates both poly(A)-coupled and poly(A)-independent termination of RNA polymerase II transcription. Mol. Cell. Biol. 23:6339–6349.
   PubMed Web of Science ®Google Scholar
• Strässer, K., et al. 2002. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417:304–308.
   PubMed Web of Science ®Google Scholar
• Urban, J., et al. 2007. Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol. Cell 26:663–674.
   PubMed Web of Science ®Google Scholar
• Wei, N., D. A. Chamovitz, and X. W. Deng. 1994. Arabidopsis COP9 is a component of a novel signaling complex mediating light control of development. Cell 78:117–124.
   PubMed Web of Science ®Google Scholar
• Wei, N., and X. W. Deng. 1992. COP9: a new genetic locus involved in light-regulated development and gene expression in Arabidopsis. Plant Cell 4:1507–1518.
   PubMedGoogle Scholar
• Wei, N., et al. 1998. The COP9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex. Curr. Biol. 8:919–922.
   PubMed Web of Science ®Google Scholar
• Wilmes, G. M., et al. 2008. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol. Cell 32:735–746.
   PubMed Web of Science ®Google Scholar
• Xirodimas, D. P., et al. 2008. Ribosomal proteins are targets for the NEDD8 pathway. EMBO Rep. 9:280–286.
   PubMedGoogle Scholar
• Zhao, Y., et al. 2008. A TFTC/STAGA module mediates histone H2A and H2B deubiquitination, coactivates nuclear receptors, and counteracts heterochromatin silencing. Mol. Cell 29:92–101.
   PubMed Web of Science ®Google Scholar