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Article

cis- and trans-Acting Determinants of Transcription Termination by Yeast RNA Polymerase II

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Pages 2688-2696 | Received 01 Dec 2005, Accepted 13 Jan 2006, Published online: 27 Mar 2023

REFERENCES

  • Abou Elela, S., and M. Ares, Jr. 1998. Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyadenylated but functional U2 snRNA. EMBO J. 17:3738–3746.
  • Armache, K. J., H. Kettenberger, and P. Cramer. 2003. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA 100:6964–6968.
  • Birse, C. E., L. Minvielle-Sebastia, B. A. Lee, W. Keller, and N. J. Proudfoot. 1998. Coupling termination of transcription to messenger RNA maturation in yeast. Science 280:298–301.
  • Buratowski, S. 2005. Connections between mRNA 3′ end processing and transcription termination. Curr. Opin. Cell Biol. 17:257–261.
  • Bushnell, D. A., and R. D. Kornberg. 2003. Complete, 12-subunit RNA polymerase II at 4.1- Å resolution: implications for the initiation of transcription. Proc. Natl. Acad. Sci. USA 100:6969–6973.
  • Butler, J. S. 2002. The yin and yang of the exosome. Trends Cell Biol. 12:90–96.
  • Carroll, K. L., D. A. Pradhan, J. A. Granek, N. D. Clarke, and J. L. Corden. 2004. Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol. Cell. Biol. 24:6241–6252.
  • Chapon, C., T. R. Cech, and A. J. Zaug. 1997. Polyadenylation of telomerase RNA in budding yeast. RNA 3:1337–1351.
  • Cheng, H., X. He, and C. Moore. 2004. The essential WD repeat protein Swd2 has dual functions in RNA polymerase II transcription termination and lysine 4 methylation of histone H3. Mol. Cell. Biol. 24:2932–2943.
  • Conrad, N. K., S. M. Wilson, E. J. Steinmetz, M. Patturajan, D. A. Brow, M. S. Swanson, and J. L. Corden. 2000. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154:557–571.
  • Cramer, P., D. A. Bushnell, J. Fu, A. L. Gnatt, B. Maier-Davis, N. E. Thompson, R. R. Burgess, A. M. Edwards, P. R. David, and R. D. Kornberg. 2000. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288:640–649.
  • 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.
  • Davis, J. A., Y. Takagi, R. D. Kornberg, and F. A. Asturias. 2002. Structure of the yeast RNA polymerase II holoenzyme: mediator conformation and polymerase interaction. Mol. Cell 10:409–415.
  • Dheur, S., L. T. A. Vo, F. Voisinet-Hakil, M. Minet, J. M. Schmitter, F. Lacroute, F. Wyers, and L. Minvielle-Sebastia. 2003. Pti1p and Ref2p found in association with the mRNA 3′ end formation complex direct snoRNA maturation. EMBO J. 22:2831–2840.
  • Dichtl, B., R. Aasland, and W. Keller. 2004. Functions for S. cerevisiae Swd2p in 3′ end formation of specific mRNAs and snoRNAs and global histone 3 lysine 4 methylation. RNA 10:965–977.
  • Dichtl, B., D. Blank, M. Ohnacker, A. Friedlein, D. Roeder, H. Langen, and W. Keller. 2002. A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. Mol. Cell 10:1139–1150.
  • Fatica, A., M. Morlando, and I. Bozzoni. 2000. Yeast snoRNA accumulation relies on a cleavage-dependent/polyadenylation-independent 3′-processing apparatus. EMBO J. 19:6218–6229.
  • Filipowicz, W., and V. Pogacic. 2002. Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol. 14:319–327.
  • Ganem, C., F. Devaux, C. Torchet, C. Jacq, S. Quevillon-Cheruel, G. Labesse, C. Facca, and G. Faye. 2003. Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast. EMBO J. 22:1588–1598.
  • Graber, J. H., G. D. McAllister, and T. F. Smith. 2002. Probabilistic prediction of Saccharomyces cerevisiae mRNA 3′-processing sites. Nucleic Acids Res. 30:1851–1858.
  • Grandemange, S., S. Schaller, S. Yamano, S. Du Manoir, G. V. Shpakovski, M. G. Mattei, C. Kedinger, and M. Vigneron. 2001. A human RNA polymerase II subunit is encoded by a recently generated multigene family. BMC Mol. Biol. 2:14.
  • Guo, Z., and F. Sherman. 1996. 3′-end-forming signals of yeast mRNA. Trends Biochem. Sci. 21:477–481.
  • Hahn, S. 2004. Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11:394–403.
  • Hernandez, N. 2001. Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J. Biol. Chem. 276:26733–26736.
  • Kadaba, S., A. Krueger, T. Trice, A. M. Krecic, A. G. Hinnebusch, and J. Anderson. 2004. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev. 18:1227–1240.
  • Kainz, M., and R. L. Gourse. 1998. The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination. J. Mol. Biol. 284:1379–1390.
  • Kettenberger, H., K. J. Armache, and P. Cramer. 2004. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16:955–965.
  • Kim, M., S. H. Ahn, N. J. Krogan, J. F. Greenblatt, and S. Buratowski. 2004. Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J. 23:354–364.
  • Krishnamurthy, S., X. He, M. Reyes-Reyes, C. Moore, and M. Hampsey. 2004. Ssu72 is an RNA polymerase II CTD phosphatase. Mol. Cell 14:387–394.
  • LaCava, J., J. Houseley, C. Saveanu, E. Petfalski, E. Thompson, A. Jacquier, and D. Tollervey. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121:713–724.
  • Lesser, C. F., and C. Guthrie. 1993. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics 133:851–863.
  • Medlin, J. E., P. Uguen, A. Taylor, D. L. Bentley, and S. Murphy. 2003. The C-terminal domain of pol II and a DRB-sensitive kinase are required for 3′ processing of U2 snRNA. EMBO J. 22:925–934.
  • Morlando, M., P. Greco, B. Dichtl, A. Fatica, W. Keller, and I. Bozzoni. 2002. Functional analysis of yeast snoRNA and snRNA 3′-end formation mediated by uncoupling of cleavage and polyadenylation. Mol. Cell. Biol. 22:1379–1389.
  • Nedea, E., X. He, M. Kim, J. Pootoolal, G. Zhong, V. Canadien, T. Hughes, S. Buratowski, C. L. Moore, and J. Greenblatt. 2003. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3′-ends. J. Biol. Chem. 278:33000–33010.
  • Proudfoot, N. 2004. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16:272–278.
  • Shearwin, K. E., B. P. Callen, and J. B. Egan. 2005. Transcriptional interference—a crash course. Trends Genet. 21:339–345.
  • Steinmetz, E. J., and D. A. Brow. 1998. Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc. Natl. Acad. Sci. USA 95:6699–6704.
  • Steinmetz, E. J., and D. A. Brow. 1996. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol. Cell. Biol. 16:6993–7003.
  • 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.
  • Steinmetz, E. J., N. K. Conrad, D. A. Brow, and J. L. Corden. 2001. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413:327–331.
  • Tan, Q., K. L. Linask, R. H. Ebright, and N. A. Woychik. 2000. Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes Dev. 14:339–348.
  • Ursic, D., K. Chinchilla, J. S. Finkel, and M. R. Culbertson. 2004. Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing. Nucleic Acids Res. 32:2441–2452.
  • Vanacova, S., J. Wolf, G. Martin, D. Blank, S. Dettwiler, A. Friedlein, H. Langen, G. Keith, and W. Keller. 2005. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3:e189.
  • van Hoof, A., P. Lennertz, and R. Parker. 2000. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 20:441–452.
  • Wise, J. A. 1991. Preparation and analysis of low molecular weight RNAs and small ribonucleoproteins. Methods Enzymol. 194:405–415.
  • Woychik, N. A., K. McKune, W. S. Lane, and R. A. Young. 1993. Yeast RNA polymerase II subunit RPB11 is related to a subunit shared by RNA polymerase I and III. Gene Expr. 3:77–82.
  • Wyers, F., M. Rougemaille, G. Badis, J. C. Rousselle, M. E. Dufour, J. Boulay, B. Regnault, F. Devaux, A. Namane, B. Seraphin, D. Libri, and A. Jacquier. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725–737.
  • 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.
  • Zhao, J., L. Hyman, and C. Moore. 1999. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63:405–445.

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