Eukaryotic cells contain many different RNA species. Nuclear pre-mRNAs and cytoplasmic mRNAs carry genomic information to the protein synthesis machinery, whereas many stable RNA species have important functional roles. The mature, functional forms of these RNA species are generated by post-transcriptional processing, and evidence has been accumulating that there are functional links between the various processing pathways. This indicates that there are regulatory networks that coordinate different stages of RNA metabolism. This article describes the aims and results, to date, of the European RNOMICS project as an example of an integrated approach to investigate these links.
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Fields, S. & Song, O. A novel genetic system to detect protein–protein interactions. Nature 340, 245–246 (1989).
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).
Fromont-Racine, M., Rain, J. -C. & Legrain, P. Building protein–protein networks by two-hybrid mating strategy. Methods Enzymol. 350, 513–524 (2002).
Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001).
Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002).
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).
Bentley, D. The mRNA assembly line: transcription and processing machines in the same factory. Curr. Opin. Cell Biol. 14, 336–342 (2002).
Calvo, O. & Manley, J. L. Strange bedfellows: polyadenylation factors at the promoter. Genes Dev. 17, 1321–1327 (2003).
Proudfoot, N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16, 272–278 (2004).
Fromont-Racine, M. et al. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17, 95–110 (2000).
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).
He, W. & Parker, R. Functions of Lsm proteins in mRNA degradation and splicing. Curr. Opin. Cell Biol. 12, 346–350 (2000).
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).
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).
Beggs, J. D. RNA processing and the Lsm proteins. Novartis Medal Lecture. Biochem. Soc. Trans. 33, 433–438 (2005).
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).
Vidal, V. P., Verdone, L., Mayes, A. E. & Beggs, J. D. Characterization of U6 snRNA–protein interactions. RNA 5, 1470–1481 (1999).
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).
Verdone, L., Galardi, S., Page, D. & Beggs, J. D. Lsm proteins promote regeneration of pre-mRNA splicing activity. Curr. Biol. 14, 1487–1491 (2004).
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).
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).
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).
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).
Tharun, S. et al. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 404, 515–518 (2000).
Mitchell, P. & Tollervey, D. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′→5′ degradation. Mol. Cell 11, 1405–1413 (2003).
Cao, D. & Parker, R. Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell 113, 533–545 (2003).
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).
Hilleren, P. & Parker, R. Mechanisms of mRNA surveillance in eukaryotes. Annu. Rev. Genet. 33, 229–260 (1999).
Kshirsagar, M. & Parker, R. Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. Genetics 166, 729–739 (2004).
Badis, G., Saveanu, C., Fromont-Racine, M. & Jacquier, A. Targeted mRNA degradation by deadenylation-independent decapping. Mol. Cell 15, 5–15 (2004).
Kadaba, S. et al. Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev. 18, 1227–1240 (2004).
Kuai, L., Fang, F., Butler, J. S. & Sherman, F. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 101, 8581–8586 (2004).
Allmang, C. et al. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18, 5399–5410 (1999).
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).
Krogan, N. J. et al. High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13, 225–239 (2004).
Dreyfus, M. & Regnier, P. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111, 611–613 (2002).
Peng, W. T. et al. A panoramic view of yeast noncoding RNA processing. Cell 113, 919–933 (2003).
Wu, L. F. et al. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genet. 31, 255–265 (2002).
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).
Jorgensen, P. et al. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev. 18, 2491–2505 (2004).
Tschochner, H. & Hurt, E. Pre-ribosomes on the road from the nucleolus to the cytoplasm. Trends Cell Biol. 13, 255–263 (2003).
Saveanu, C. et al. Sequential protein association with nascent 60S ribosomal particles. Mol. Cell. Biol. 23, 4449–4460 (2003).
Granneman, S. & Baserga, S. J. Ribosome biogenesis: of knobs and RNA processing. Exp. Cell Res. 296, 43–50 (2004).
Dez, C. & Tollervey, D. Ribosome synthesis meets the cell cycle. Curr. Opin. Microbiol. 7, 631–637 (2004).
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).
Bassler, J. et al. Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol. Cell 8, 517–529 (2001).
Bentley, D. Coupling RNA polymerase II transcription with pre-mRNA processing. Curr. Opin. Cell Biol. 11, 347–351 (1999).
Hirose, Y. & Manley, J. L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000).
Fatica, A., Dlakic, M. & Tollervey, D. Naf1 p is a box H/ACA snoRNP assembly factor. RNA 8, 1502–1514 (2002).
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).
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).
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).
Dichtl, B. et al. A role for SSU72 in balancing RNA polymerase II transcription elongation and termination. Mol. Cell 10, 1139–1150 (2002).
Dichtl, B. et al. Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination. EMBO J. 21, 4125–4135 (2002).
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).
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).
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).
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).
Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004).
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).
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).
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).
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).
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).
Custodio, N. et al. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 10, 622–633 (2004).
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).
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).
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).
Hieronymus, H. & Silver, P. A. A systems view of mRNP biology. Genes Dev. 18, 2845–2860 (2004).
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).
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).
Yu, M. C. et al. Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes Dev. 18, 2024–2035 (2004).
Shav-Tal, Y., Singer, R. H. & Darzacq, X. Imaging gene expression in single living cells. Nature Rev. Mol. Cell Biol. 5, 855–862 (2004).
Damelin, M. & Silver, P. A. In situ analysis of spatial relationships between proteins of the nuclear pore complex. Biophys. J. 83, 3626–3636 (2002).
Sheff, M. A. & Thorn, K. S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661–670 (2004).
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).
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).
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).
Pan, X. et al. A robust toolkit for functional profiling of the yeast genome. Mol. Cell 16, 487–496 (2004).
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).
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).
Research in the Beggs and Tollervey laboratories is mainly funded by grants from the Wellcome Trust and by an EC grant for the RNOMICS project.
The authors declare no competing financial interests.
Saccharomyces Genome Database
PROTEIN INTERACTION DATABASES
TECHNOLOGIES AND TOOLS
- FLUORESCENCE LIFETIME IMAGING MICROSCOPY (FLIM).
Fluorescence lifetime measurements can yield information on the molecular microenvironment of a fluorescent molecule. Factors such as the binding to macromolecules and the proximity of molecules that can deplete the excited state by FRET can all modify the lifetime of a fluorophore (see Becker & Hickl GmbH Lifetime Imaging Techniques for Optical Microscopy).
- FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING (FRAP).
A microscope technique used to measure the movement (for example, diffusion rates) of fluorescently tagged molecules over time in vivo. Specific regions in a cell are irreversibly photobleached using a laser; fluorescence is restored by diffusion of fluorescently tagged unbleached molecules into the bleached area (see Davidson College, Molecular Biology course notes on FRAP).
- FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET).
The non-radiative transfer of energy from a donor fluorophore to an acceptor fluorophore that is typically <80 Å away. FRET will only occur between fluorophores in which the emission spectrum of the donor has a significant overlap with the excitation of the acceptor. FRET can be used to detect the co-localization of proteins and other molecules with spatial resolution beyond the limits of conventional optical microscopy (see Molecular Probes Invitrogen detection systems).
- SYNTHETIC-LETHAL SCREENS
When two yeast mutations are viable individually, but die when combined, they are described as being synthetic lethal. This genetic interaction indicates a functional relationship, either because they affect alternative pathways for a process, or because the gene products might be components of the same pathway or even of the same complex and the defects caused by the mutations are additive. Screening for mutations that are synthetic lethal with a mutation in a factor of interest might identify functionally related factors.
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Beggs, J., Tollervey, D. Crosstalk between RNA metabolic pathways: an RNOMICS approach. Nat Rev Mol Cell Biol 6, 423–429 (2005). https://doi.org/10.1038/nrm1648
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