- Fields, S. & Song, O. A novel genetic system to detect protein–protein interactions. Nature 340, 245–246 (1989).
CAS PubMed Google Scholar
- Fromont-Racine, M., Rain, J. -C. & Legrain, P. Towards a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16, 277–282 (1997).
CAS PubMed Google Scholar
- Fromont-Racine, M., Rain, J. -C. & Legrain, P. Building protein–protein networks by two-hybrid mating strategy. Methods Enzymol. 350, 513–524 (2002).
CAS PubMed Google Scholar
- Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001).
CAS PubMed PubMed Central Google Scholar
- Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).
CAS PubMed Google Scholar
- Gould, K. L., Ren, L., Feoktistova, A. S., Jennings, J. L. & Link, A. J. Tandem affinity purification and identification of protein complex components. Methods 33, 239–244 (2004).
CAS PubMed Google Scholar
- Bentley, D. The mRNA assembly line: transcription and processing machines in the same factory. Curr. Opin. Cell Biol. 14, 336–342 (2002).
CAS PubMed Google Scholar
- Calvo, O. & Manley, J. L. Strange bedfellows: polyadenylation factors at the promoter. Genes Dev. 17, 1321–1327 (2003).
CAS PubMed Google Scholar
- Proudfoot, N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16, 272–278 (2004).
CAS PubMed Google Scholar
- Fromont-Racine, M. et al. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17, 95–110 (2000).
CAS PubMed PubMed Central Google Scholar
- Bouveret, E., Rigaut, G., Shevchenko, A., Wilm, M. & Séraphin, B. An Sm-like protein complex that participates in mRNA degradation. EMBO J. 19, 1661–1671 (2000).
CAS PubMed PubMed Central Google Scholar
- He, W. & Parker, R. Functions of Lsm proteins in mRNA degradation and splicing. Curr. Opin. Cell Biol. 12, 346–350 (2000).
CAS PubMed Google Scholar
- Pannone, B. K. & Wolin, S. L. Sm-like proteins wRING the neck of mRNA. Curr. Biol. 10, R478–R481 (2000).
- Kambach, C., Walke, S. & Nagai, K. Structure and assembly of the spliceosomal small nuclear ribonucleoprotein particles. Curr. Opin. Struct. Biol. 9, 222–230 (1999).
CAS PubMed Google Scholar
- Fernandez, C. F., Pannone, B. K., Chen, X., Fuchs, G. & Wolin, S. L. An Lsm2–Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5. Mol. Biol. Cell 15, 2842–2852 (2004).
CAS PubMed PubMed Central Google Scholar
- Beggs, J. D. RNA processing and the Lsm proteins. Novartis Medal Lecture. Biochem. Soc. Trans. 33, 433–438 (2005).
CAS PubMed Google Scholar
- Mayes, A. E., Verdone, L., Legrain, P. & Beggs, J. D. Characterization of Sm-like proteins in yeast and their association with U6 snRNA. EMBO J. 18, 4321–4331 (1999).
CAS PubMed PubMed Central Google Scholar
- Vidal, V. P., Verdone, L., Mayes, A. E. & Beggs, J. D. Characterization of U6 snRNA–protein interactions. RNA 5, 1470–1481 (1999).
CAS PubMed PubMed Central Google Scholar
- Achsel, T. et al. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3′-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J. 18, 5789–5802 (1999).
CAS PubMed PubMed Central Google Scholar
- Verdone, L., Galardi, S., Page, D. & Beggs, J. D. Lsm proteins promote regeneration of pre-mRNA splicing activity. Curr. Biol. 14, 1487–1491 (2004).
CAS PubMed Google Scholar
- Kufel, J., Allmang, C., Verdone, L., Beggs, J. D. & Tollervey, D. Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol. Cell. Biol. 22, 5248–5256 (2002).
CAS PubMed PubMed Central Google Scholar
- Kufel, J., Allmang, C., Verdone, L., Beggs, J. & Tollervey, D. A complex pathway for 3′ processing of the yeast U3 snoRNA. Nucleic Acids Res. 31, 6788–6797 (2003).
CAS PubMed PubMed Central Google Scholar
- Kufel, J., Allmang, C., Petfalski, E., Beggs, J. & Tollervey, D. Lsm proteins are required for normal processing and stability of ribosomal RNAs. J. Biol. Chem. 278, 2147–2156 (2003).
CAS PubMed Google Scholar
- Kufel, J., Bousquet-Antonelli, C., Beggs, J. D. & Tollervey, D. Nuclear pre-mRNA decapping and 5′ degradation in yeast require the Lsm2–8p complex. Mol. Cell. Biol. 24, 9646–9657 (2004).
CAS PubMed PubMed Central Google Scholar
- Tharun, S. et al. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 404, 515–518 (2000).
CAS PubMed Google Scholar
- Mitchell, P. & Tollervey, D. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′→5′ degradation. Mol. Cell 11, 1405–1413 (2003).
CAS PubMed Google Scholar
- Cao, D. & Parker, R. Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell 113, 533–545 (2003).
CAS PubMed Google Scholar
- Takahashi, S., Araki, Y., Sakuno, T. & Katada, T. Interaction between Ski7p and Upf1p is required for nonsense-mediated 3′–5′ mRNA decay in yeast. EMBO J. 22, 3951–3959 (2003).
CAS PubMed PubMed Central Google Scholar
- Hilleren, P. & Parker, R. Mechanisms of mRNA surveillance in eukaryotes. Annu. Rev. Genet. 33, 229–260 (1999).
CAS PubMed Google Scholar
- Kshirsagar, M. & Parker, R. Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. Genetics 166, 729–739 (2004).
CAS PubMed PubMed Central Google Scholar
- Badis, G., Saveanu, C., Fromont-Racine, M. & Jacquier, A. Targeted mRNA degradation by deadenylation-independent decapping. Mol. Cell 15, 5–15 (2004).
CAS PubMed Google Scholar
- Kadaba, S. et al. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev. 18, 1227–1240 (2004).
CAS PubMed PubMed Central Google Scholar
- Kuai, L., Fang, F., Butler, J. S. & Sherman, F. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 101, 8581–8586 (2004).
CAS PubMed PubMed Central Google Scholar
- Allmang, C. et al. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18, 5399–5410 (1999).
CAS PubMed PubMed Central Google Scholar
- Van, H. A., Lennertz, P. & Parker, R. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 20, 441–452 (2000).
Google Scholar
- Krogan, N. J. et al. High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13, 225–239 (2004).
CAS PubMed Google Scholar
- Dreyfus, M. & Regnier, P. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111, 611–613 (2002).
CAS PubMed Google Scholar
- Peng, W. T. et al. A panoramic view of yeast noncoding RNA processing. Cell 113, 919–933 (2003).
CAS PubMed Google Scholar
- Wu, L. F. et al. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genet. 31, 255–265 (2002).
CAS PubMed Google Scholar
- Wade, C., Shea, K. A., Jensen, R. V. & McAlear, M. A. EBP2 is a member of the yeast RRB regulon, a transcriptionally coregulated set of genes that are required for ribosome and rRNA biosynthesis. Mol. Cell. Biol. 21, 8638–8650 (2001).
CAS PubMed PubMed Central Google Scholar
- Jorgensen, P. et al. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev. 18, 2491–2505 (2004).
CAS PubMed PubMed Central Google Scholar
- Tschochner, H. & Hurt, E. Pre-ribosomes on the road from the nucleolus to the cytoplasm. Trends Cell Biol. 13, 255–263 (2003).
CAS PubMed Google Scholar
- Saveanu, C. et al. Sequential protein association with nascent 60S ribosomal particles. Mol. Cell. Biol. 23, 4449–4460 (2003).
CAS PubMed PubMed Central Google Scholar
- Granneman, S. & Baserga, S. J. Ribosome biogenesis: of knobs and RNA processing. Exp. Cell Res. 296, 43–50 (2004).
CAS PubMed Google Scholar
- Dez, C. & Tollervey, D. Ribosome synthesis meets the cell cycle. Curr. Opin. Microbiol. 7, 631–637 (2004).
CAS PubMed Google Scholar
- Saveanu, C. et al. Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps. EMBO J. 20, 6475–6484 (2001).
CAS PubMed PubMed Central Google Scholar
- Bassler, J. et al. Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol. Cell 8, 517–529 (2001).
CAS PubMed Google Scholar
- Bentley, D. Coupling RNA polymerase II transcription with pre-mRNA processing. Curr. Opin. Cell Biol. 11, 347–351 (1999).
CAS PubMed Google Scholar
- Hirose, Y. & Manley, J. L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000).
CAS PubMed Google Scholar
- Fatica, A., Dlakic, M. & Tollervey, D. Naf1 p is a box H/ACA snoRNP assembly factor. RNA 8, 1502–1514 (2002).
CAS PubMed PubMed Central Google Scholar
- Dez, C., Noaillac-Depeyre, J., Caizergues-Ferrer, M. & Henry, Y. Naf1p, an essential nucleoplasmic factor specifically required for accumulation of box H/ACA small nucleolar RNPs. Mol. Cell. Biol. 22, 7053–7065 (2002).
CAS PubMed PubMed Central Google Scholar
- Yang, P. K., Rotondo, G., Legrain, P. & Chanfreau, G. The Shq1p–Naf1p complex is required for box H/ACA small nucleolar ribonucleoprotein particle biogenesis. J. Biol. Chem. 277, 45235–45242 (2002).
CAS PubMed Google Scholar
- Barilla, D., Lee, B. A. & Proudfoot, N. J. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 98, 445–450 (2001).
CAS PubMed PubMed Central Google Scholar
- Dichtl, B. et al. A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. Mol. Cell 10, 1139–1150 (2002).
CAS PubMed Google Scholar
- Dichtl, B. et al. Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination. EMBO J. 21, 4125–4135 (2002).
CAS PubMed PubMed Central Google Scholar
- Licatalosi, D. D. et al. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell 9, 1101–1111 (2002).
CAS PubMed Google Scholar
- Skaar, D. A. & Greenleaf, A. L. The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3′ cleavage/polyadenylation through the processing component Pti1p. Mol. Cell 10, 1429–1439 (2002).
CAS PubMed Google Scholar
- Zorio, D. A. R. & Bentley, D. L. The link between mRNA processing and transcription: communication works both ways. Exp. Cell Res. 296, 91–97 (2004).
CAS PubMed Google Scholar
- Sadowski, M., Dichtl, B., Hubner, W. & Keller, W. Independent functions of yeast Pcf11p in pre-mRNA 3′ end processing and in transcription termination. EMBO J. 22, 2167–2177 (2003).
CAS PubMed PubMed Central Google Scholar
- Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004).
CAS PubMed Google Scholar
- West, S., Gromak, N. & Proudfoot, N. J. Human 5′→3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432, 522–525 (2004).
CAS PubMed Google Scholar
- Kyburz, A., Sadowski, M., Dichtl, B. & Keller, W. The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3′-end formation. Nucleic Acids Res. 31, 3936–3945 (2003).
CAS PubMed PubMed Central Google Scholar
- Ganem, C. et al. Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast. EMBO J. 22, 1588–1598 (2003).
CAS PubMed PubMed Central Google Scholar
- Krishnamurthy, S., He, X., Reyes-Reyes, M., Moore, C. & Hampsey, M. Ssu72 is an RNA polymerase II CTD phosphatase. Mol. Cell 14, 387–394 (2004).
CAS PubMed Google Scholar
- Gallagher, J. E. et al. RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. Genes Dev. 18, 2506–2517 (2004).
CAS PubMed PubMed Central Google Scholar
- Custodio, N. et al. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 10, 622–633 (2004).
CAS PubMed PubMed Central Google Scholar
- Lelivelt, M. J. & Culbertson, M. R. Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. Mol. Cell. Biol. 19, 6710–6719 (1999).
CAS PubMed PubMed Central Google Scholar
- He, F. et al. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol. Cell 12, 1439–1452 (2003).
CAS PubMed Google Scholar
- Grigull, J., Mnaimneh, S., Pootoolal, J., Robinson, M. D. & Hughes, T. R. Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol. Cell. Biol. 24, 5534–5547 (2004).
CAS PubMed PubMed Central Google Scholar
- Hieronymus, H. & Silver, P. A. A systems view of mRNP biology. Genes Dev. 18, 2845–2860 (2004).
CAS PubMed Google Scholar
- Garcia-Martinez, J., Aranda, A. & Perez-Ortin, J. E. Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol. Cell 15, 303–313 (2004).
CAS PubMed Google Scholar
- Kotovic, K. M., Lockshon, D., Boric, L. & Neugebauer, K. M. Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast. Mol. Cell. Biol. 23, 5768–5779 (2003).
CAS PubMed PubMed Central Google Scholar
- Yu, M. C. et al. Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes Dev. 18, 2024–2035 (2004).
CAS PubMed PubMed Central Google Scholar
- Shav-Tal, Y., Singer, R. H. & Darzacq, X. Imaging gene expression in single living cells. Nature Rev. Mol. Cell Biol. 5, 855–862 (2004).
CAS Google Scholar
- Damelin, M. & Silver, P. A. In situ analysis of spatial relationships between proteins of the nuclear pore complex. Biophys. J. 83, 3626–3636 (2002).
CAS PubMed PubMed Central Google Scholar
- Sheff, M. A. & Thorn, K. S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661–670 (2004).
CAS PubMed Google Scholar
- Dix, I., Russell, C. S., Ben-Yehuda, S., Kupiec, M. & Beggs, J. D. The identification and characterization of a novel splicing protein, Isy1p, of Saccharomyces cerevisiae. RNA 5, 360–368 (1999).
CAS PubMed PubMed Central Google Scholar
- Ben-Yehuda, S. et al. Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics 156, 1503–1517 (2000).
CAS PubMed PubMed Central Google Scholar
- Albers, M., Diment, A., Muraru, M., Russell, C. S. & Beggs, J. D. Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors. RNA 9, 138–150 (2003).
CAS PubMed PubMed Central Google Scholar
- Pan, X. et al. A robust toolkit for functional profiling of the yeast genome. Mol. Cell 16, 487–496 (2004).
CAS PubMed Google Scholar
- Clark, T. A., Sugnet, C. W. & Ares, M. Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907–910 (2002).
CAS PubMed Google Scholar
- Braga, J., Desterro, J. M. & Carmo-Fonseca, M. Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes. Mol. Biol. Cell 15, 4749–4760 (2004).
CAS PubMed PubMed Central Google Scholar