Abstract
Expression of crs1 pre-mRNA, encoding a meiotic cyclin, is blocked in actively growing fission yeast cells by a multifaceted mechanism. The most striking feature is that in vegetative cells, crs1 transcripts are continuously synthesized but are targeted for degradation rather than splicing and polyadenylation. Turnover of crs1 RNA requires the exosome, as do previously described nuclear surveillance and silencing mechanisms, but does not involve a noncanonical poly(A) polymerase. Instead, crs1 transcripts are targeted for destruction by a factor previously implicated in turnover of meiotic RNAs in growing cells. Like exosome mutants, mmi1 mutants splice and polyadenylate vegetative crs1 transcripts. Two regulatory elements are located at the 3′ end of the crs1 gene, consistent with the increased accumulation of spliced RNA in polyadenylation factor mutants. This highly integrated regulatory strategy may ensure a rapid response to adverse conditions, thereby guaranteeing survival.
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References
Harigaya, Y. & Yamamoto, M. Molecular mechanisms underlying the mitosis-meiosis decision. Chromosome Res. 15, 523–537 (2007).
Averbeck, N., Sunder, S., Sample, N., Wise, J.A. & Leatherwood, J. Negative control contributes to an extensive program of meiotic splicing in fission yeast. Mol. Cell 18, 491–498 (2005).
Juneau, K., Palm, C., Miranda, M. & Davis, R.W. High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc. Natl. Acad. Sci. USA 104, 1522–1527 (2007).
Spingola, M. & Ares, M., Jr. A yeast intronic splicing enhancer and Nam8p are required for Mer1p-activated splicing. Mol. Cell 6, 329–338 (2000).
Kishida, M., Nagai, T., Nakaseko, Y. & Shimoda, C. Meiosis-dependent mRNA splicing of the fission yeast Schizosaccharomyces pombe mes1+ gene. Curr. Genet. 25, 497–503 (1994).
Malapeira, J. et al. A meiosis-specific cyclin regulated by splicing is required for proper progression through meiosis. Mol. Cell. Biol. 25, 6330–6337 (2005).
Shimoseki, M. & Shimoda, C. The 5′ terminal region of the Schizosaccharomyces pombe mes1 mRNA is crucial for its meiosis-specific splicing. Mol. Genet. Genomics 265, 673–682 (2001).
Moldon, A. et al. Promoter-driven splicing regulation in fission yeast. Nature 455, 997–1000 (2008).
Cramer, P., Pesce, C.G., Baralle, F.E. & Kornblihtt, A.R. Functional association between promoter structure and transcript alternative splicing. Proc. Natl. Acad. Sci. USA 94, 11456–11460 (1997).
Tasic, B. et al. Promoter choice determines splice site selection in protocadherin α and γ pre-mRNA splicing. Mol. Cell 10, 21–33 (2002).
Niwa, M., Rose, S.D. & Berget, S.M. In vitro polyadenylation is stimulated by the presence of an upstream intron. Genes Dev. 4, 1552–1559 (1990).
Hansen, K., Birse, C.E. & Proudfoot, N.J. Nascent transcription from the nmt1 and nmt2 genes of Schizosaccharomyces pombe overlaps neighbouring genes. EMBO J. 17, 3066–3077 (1998).
Iino, Y. & Yamamoto, M. Negative control for the initiation of meiosis in Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 82, 2447–2451 (1985).
Mata, J., Lyne, R., Burns, G. & Bahler, J. The transcriptional program of meiosis and sporulation in fission yeast. Nat. Genet. 32, 143–147 (2002).
Mata, J., Wilbrey, A. & Bahler, J. Transcriptional regulatory network for sexual differentiation in fission yeast. Genome Biol. 8, R217 (2007).
Wilhelm, B.T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239–1243 (2008).
Takagaki, Y. & Manley, J.L. Complex protein interactions within the human polyadenylation machinery identify a novel component. Mol. Cell. Biol. 20, 1515–1525 (2000).
Watanabe, T. et al. Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. Nucleic Acids Res. 29, 2327–2337 (2001).
Gilmartin, G.M. Eukaryotic mRNA 3′ processing: a common means to different ends. Genes Dev. 19, 2517–2521 (2005).
Liu, D. et al. Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis. Nucleic Acids Res. 35, 234–246 (2007).
Wilusz, J., Pettine, S.M. & Shenk, T. Functional analysis of point mutations in the AAUAAA motif of the SV40 late polyadenylation signal. Nucleic Acids Res. 17, 3899–3908 (1989).
Bousquet-Antonelli, C., Presutti, C. & Tollervey, D. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102, 765–775 (2000).
Wilusz, C.J. & Wilusz, J. Bringing the role of mRNA decay in the control of gene expression into focus. Trends Genet. 20, 491–497 (2004).
Wang, S.W., Stevenson, A.L., Kearsey, S.E., Watt, S. & Bahler, J. Global role for polyadenylation-assisted nuclear RNA degradation in posttranscriptional gene silencing. Mol. Cell. Biol. 28, 656–665 (2008).
Houseley, J., LaCava, J. & Tollervey, D. RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol. 7, 529–539 (2006).
LaCava, J. et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121, 713–724 (2005).
Win, T.Z. et al. Requirement of fission yeast Cid14 in polyadenylation of rRNAs. Mol. Cell. Biol. 26, 1710–1721 (2006).
Kinoshita, N., Goebl, M. & Yanagida, M. The fission yeast dis3+ gene encodes a 110-kDa essential protein implicated in mitotic control. Mol. Cell. Biol. 11, 5839–5847 (1991).
Dziembowski, A., Lorentzen, E., Conti, E. & Seraphin, B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat. Struct. Mol. Biol. 14, 15–22 (2007).
Buhler, M., Haas, W., Gygi, S.P. & Moazed, D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129, 707–721 (2007).
Harigaya, Y. et al. Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature 442, 45–50 (2006).
Ohnacker, M., Barabino, S.M., Preker, P.J. & Keller, W. The WD-repeat protein pfs2p bridges two essential factors within the yeast pre-mRNA 3′-end-processing complex. EMBO J. 19, 37–47 (2000).
Wang, S.W., Asakawa, K., Win, T.Z., Toda, T. & Norbury, C.J. Inactivation of the pre-mRNA cleavage and polyadenylation factor Pfs2 in fission yeast causes lethal cell cycle defects. Mol. Cell. Biol. 25, 2288–2296 (2005).
Hilleren, P., McCarthy, T., Rosbash, M., Parker, R. & Jensen, T.H. Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 413, 538–542 (2001).
Proudfoot, N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16, 272–278 (2004).
Shobuike, T., Tatebayashi, K., Tani, T., Sugano, S. & Ikeda, H. The dhp1+ gene, encoding a putative nuclear 5′ → 3′ exoribonuclease, is required for proper chromosome segregation in fission yeast. Nucleic Acids Res. 29, 1326–1333 (2001).
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).
Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004).
Luo, W., Johnson, A.W. & Bentley, D.L. The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev. 20, 954–965 (2006).
Basi, G., Schmid, E. & Maundrell, K. TATA box mutations in the Schizosaccharomyces pombe nmt1 promoter affect transcription efficiency but not the transcription start point or thiamine repressibility. Gene 123, 131–136 (1993).
Maundrell, K. nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J. Biol. Chem. 265, 10857–10864 (1990).
Fong, N. & Bentley, D.L. Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II: different functions for different segments of the CTD. Genes Dev. 15, 1783–1795 (2001).
Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002).
Aranda, A. & Proudfoot, N.J. Definition of transcriptional pause elements in fission yeast. Mol. Cell. Biol. 19, 1251–1261 (1999).
Birse, C.E., Lee, B.A., Hansen, K. & Proudfoot, N.J. Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J. 16, 3633–3643 (1997).
Chakraborty, S., Sarmah, B., Chakraborty, N. & Datta, A. Premature termination of RNA polymerase II mediated transcription of a seed protein gene in Schizosaccharomyces pombe. Nucleic Acids Res. 30, 2940–2949 (2002).
Cooke, C., Hans, H. & Alwine, J.C. Utilization of splicing elements and polyadenylation signal elements in the coupling of polyadenylation and last-intron removal. Mol. Cell. Biol. 19, 4971–4979 (1999).
Niwa, M. & Berget, S.M. Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns. Genes Dev. 5, 2086–2095 (1991).
Stoilov, P., Rafalska, I. & Stamm, S. YTH: a new domain in nuclear proteins. Trends Biochem. Sci. 27, 495–497 (2002).
Kornblihtt, A.R. Promoter usage and alternative splicing. Curr. Opin. Cell Biol. 17, 262–268 (2005).
Ansari, A. & Hampsey, M. A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping. Genes Dev. 19, 2969–2978 (2005).
O'Sullivan, J.M. et al. Gene loops juxtapose promoters and terminators in yeast. Nat. Genet. 36, 1014–1018 (2004).
Andrulis, E.D. et al. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420, 837–841 (2002).
Gullerova, M., Barta, A. & Lorkovic, Z.J. Rct1, a nuclear RNA recognition motif-containing cyclophilin, regulates phosphorylation of the RNA polymerase II C-terminal domain. Mol. Cell. Biol. 27, 3601–3611 (2007).
Quesada, V., Macknight, R., Dean, C. & Simpson, G.G. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J. 22, 3142–3152 (2003).
Henderson, I.R., Liu, F., Drea, S., Simpson, G.G. & Dean, C. An allelic series reveals essential roles for FY in plant development in addition to flowering-time control. Development 132, 3597–3607 (2005).
Beaudoing, E. & Gautheret, D. Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res. 11, 1520–1526 (2001).
Jang, Y.K. et al. Differential expression of the rhp51+ gene, a recA and RAD51 homolog from the fission yeast Schizosaccharomyces pombe. Gene 169, 125–130 (1996).
Munoz, M.J., Daga, R.R., Garzon, A., Thode, G. & Jimenez, J. Poly(A) site choice during mRNA 3′-end formation in the Schizosaccharomyces pombe wos2 gene. Mol. Genet. Genomics 267, 792–796 (2002).
Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795–823 (1991).
Acknowledgements
The authors would like to thank M. Yamamoto (University of Tokyo), C. Norbury (Oxford University) and R. Maraia (US National Institutes of Health (NIH)) for strains (Supplementary Table 3). We are grateful to our colleagues K. Baker, J. Gott, H. Lou, T. Nilsen, C. Patterson, H. Salz and S. Sanders for helpful discussions and critical reading of the manuscript. This work was funded by NIH grants R01-GM073217, awarded jointly to J.A.W. and J.L., R01-GM064682, awarded to D.S.M., and R01-GM38070, awarded to J.A.W.
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D.S.M. performed the TRO experiments, designed the real-time PCR assay and participated in development of the model as well as writing of the manuscript; N.C. constructed and analyzed the chimeric and mutant alleles of crs1 to define the regulatory element, performed the RNA analyses on trans-acting factor mutants and qPCR, and expertly proofread the manuscript; S.S. analyzed processing of crs1 RNA over a meiotic time course and conducted initial experiments to map the crs1 regulatory element; N.A. mapped the crs1 RNA termini by RACE and constructed the crs1 deletion strain. H.-M.C. and J.L. discovered the splicing defect in the pfs2-11 mutant; J.A.W. wrote the manuscript and contributed to the design and interpretation of all experiments.
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McPheeters, D., Cremona, N., Sunder, S. et al. A complex gene regulatory mechanism that operates at the nexus of multiple RNA processing decisions. Nat Struct Mol Biol 16, 255–264 (2009). https://doi.org/10.1038/nsmb.1556
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DOI: https://doi.org/10.1038/nsmb.1556
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