REFERENCES
- Allmang, C., J. Kufel, G. Chanfreau, P. Mitchell, E. Petfalski, and D. Tollervey. 1999. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18:5399–5410.
- Allmang, C., P. Mitchell, E. Petfalski, and D. Tollervey. 2000. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28:1684–1691.
- Allmang, C., E. Petfalski, A. Podtelenikov, M. Mann, D. Tollervey, and P. Mitchell. 1999. The yeast exosome and human PM-Scl are related complexes of 3′-5′ exonucleases. Genes Dev. 13:2148–2158.
- Anderson, J. S., and R. P. Parker. 1998. The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex. EMBO J. 17:1497–1506.
- Anderson, J. T., S. M. Wilson, K. V. Datar, and M. S. Swanson. 1993. NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability. Mol. Cell. Biol. 13:2730–2741.
- Andrulis, E. D., J. Werner, A. Nazarian, H. Erdjument-Bromage, P. Tempst, and J. T. Lis. 2002. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420:837–841.
- Arts, G. J., S. Kuersten, P. Romby, B. Ehresmann, and I. W. Mattaj. 1998. The role of exportin-t in selective nuclear export of mature tRNAs. EMBO J. 17:7430–7441.
- Botstein, D., S. C. Falco, S. E. Stewart, M. Brennan, S. Scherer, D. T. Stinchcomb, K. Struhl, and R. W. Davis. 1979. Sterile host yeasts (SHY): a eukaryotic system of biological containment for recombinant DNA experiments. Gene 8:17–24.
- Bousquet-Antonelli, C., C. Presutti, and D. Tollervey. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765–775.
- Briggs, M. W., K. T. Burkard, and J. S. Butler. 1998. Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3′ end formation. J. Biol. Chem. 273:13255–13263.
- Burkard, K. T., and J. S. Butler. 2000. A nuclear 3′-5′ exonuclease involved in mRNA degradation interacts with poly(A) polymerase and the hnRNA protein Npl3p. Mol. Cell. Biol. 20:604–616.
- Butler, J. S. 2002. The yin and yang of the exosome. Trends Cell Biol. 12:90–96.
- Colot, H. V., F. Stutz, and M. Rosbash. 1996. The yeast splicing factor MUD13 is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex. Genes Dev. 10:1699–1708.
- Das, B., J. S. Butler, and F. Sherman. 2003. Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae. Mol. Cell. Biol. 23:5502–5515.
- Das, B., S. Das, and F. Sherman. 2006. Mutant LYS2 mRNAs retained and degraded in the nucleus of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103:10871–10876.
- Davis, C. A., and M. Ares, Jr. 2006. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103:3262–3267.
- de la Cruz, J., D. Kressler, D. Tollervey, and P. Linder. 1998. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J. 17:1128–1140.
- Egecioglu, D. E., A. K. Henras, and G. F. Chanfreau. 2006. Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12:26–32.
- 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.
- Gentleman, R. C., V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, and J. Zhang. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80.
- Grosshans, H., G. Simos, and E. Hurt. 2000. Transport of tRNA out of the nucleus—direct channeling to the ribosome? J. Struct. Biol 129:288–294.
- Guthrie, C., and G. R. Fink. 1991. Guide to yeast genetics and molecular biology. Methods Enzymol. 194:389–398.
- Hieronymus, H., M. C. Yu, and P. A. Silver. 2004. Genome-wide mRNA surveillance is coupled to mRNA export. Genes Dev. 18:2652–2662.
- Hilleren, P., T. McCarthy, M. Rosbash, R. Parker, and T. H. Jensen. 2001. Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 413:538–542.
- Jensen, T. H., J. Boulay, J. R. Olesen, J. Colin, M. Weyler, and D. Libri. 2004. Modulation of transcription affects mRNP quality. Mol. Cell 16:235–244.
- Jensen, T. H., J. Boulay, M. Rosbash, and D. Libri. 2001. The DECD box putative ATPase Sub2p is an early mRNA export factor. Curr. Biol. 11:1711–1715.
- 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.
- Kuai, L., B. Das, and F. Sherman. 2005. A nuclear degradation pathway controls the abundance of normal mRNAs in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 102:13962–13967.
- Kuai, L., F. Fang, J. S. Butler, and F. Sherman. 2004. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 101:8581–8586.
- 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.
- Libri, D., K. Dower, J. Boulay, R. Thomsen, M. Rosbash, and T. H. Jensen. 2002. Interactions between mRNA export commitment, 3′-end quality control, and nuclear degradation. Mol. Cell. Biol. 22:8254–8266.
- Midtgaard, S. F., J. Assenholt, A. T. Jonstrup, L. B. Van, T. H. Jensen, and D. E. Brodersen. 2006. Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proc. Natl. Acad. Sci. USA 103:11898–11903.
- Mitchell, P., E. Petfalski, R. Houalla, A. Podtelejnikov, M. Mann, and D. Tollervey. 2003. Rrp47p is an exosome-associated protein required for the 3′ processing of stable RNAs. Mol. Cell. Biol. 23:6982–6992.
- Mitchell, P., and D. Tollervey. 2001. mRNA turnover. Curr. Opin. Cell Biol. 13:320–325.
- Moreau, V., A. Madania, R. P. Martin, and B. Winson. 1996. The Saccharomyces cerevisiae actin-related protein Arp2 is involved in the actin cytoskeleton. J. Cell Biol. 134:117–132.
- Petfalski, E., T. Dandekar, Y. Henry, and D. Tollervey. 1998. Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol. Cell. Biol. 18:1181–1189.
- Phillips, S., and J. S. Butler. 2003. Contribution of domain structure to the RNA 3′ end processing and degradation functions of the nuclear exosome subunit Rrp6p. RNA 9:1098–1107.
- 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.
- Russell, I., and D. Tollervey. 1995. Yeast Nop3p has structural and functional similarities to mammalian pre-mRNA binding proteins. Eur. J. Cell Biol. 66:293–301.
- Samanta, M. P., and S. Liang. 2003. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc. Natl. Acad. Sci. USA 100:12579–12583.
- Torchet, C., C. Bousquet-Antonelli, L. Milligan, E. Thompson, J. Kufel, and D. Tollervey. 2002. Processing of 3′-extended read-through transcripts by the exosome can generate functional mRNAs. Mol. Cell 9:1285–1296.
- 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. Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO J. 19:1357–1365.
- 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. 2:441–452.
- Wyers, F., M. Rougemaille, G. Breard, J.-C. Rousselle, M.-E. Dufour, J. Boulay, F. Devaux, A. Namane, D. Libri, B. Séraphin, and A. Jacquier. 2005. Cryptic Pol II transcript degradation by nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725–737.
- Zenklusen, D., P. Vinciguerra, J. C. Wyss, and F. Stutz. 2002. Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol. Cell. Biol. 22:8241–8253.