7
Views
40
CrossRef citations to date
0
Altmetric
Article

Remodeling Yeast Gene Transcription by Activating the Ty1 Long Terminal Repeat Retrotransposon under Severe Adenine Deficiency

, &
Pages 5543-5554 | Received 12 Mar 2008, Accepted 20 Jun 2008, Published online: 27 Mar 2023

REFERENCES

  • Adams, A., D. E. Gottschling, C. A. Kaiser, and T. Stearns. 1997. Methods in yeast genetics: a Cold Spring Harbor Laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • Barbara, K. E., T. M. Haley, K. A. Willis, and G. M. Santangelo. 2007. The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level. Mol. Genet. Genomics 277:171–188.
  • Baur, M., R. K. Esch, and B. Errede. 1997. Cooperative binding interactions required for function of the Ty1 sterile responsive element. Mol. Cell. Biol. 17:4330–4337.
  • Berretta, J., M. Pinskaya, and A. Morillon. 2008. A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev. 22:615–626.
  • Boeke, J. D., D. Eichinger, D. Castrillon, and G. R. Fink. 1988. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Mol. Cell. Biol. 8:1432–1442.
  • Boeke, J. D., F. LaCroute, and G. R. Fink. 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197:345–346.
  • Boeke, J. D., and S. B. Sandmeyer. 1991. Yeast transposable elements, p. 193-261. In J. R. Broach, J. R. Pringle, and E. W. Jones (ed.), The molecular and cellular biology of the yeast Saccharomyces, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • Boeke, J. D., and J. P. Stoye. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements, p. 343-436. In J. M. Coffin, S. H. Hughes, and H. E. Varmus (ed.), Retroviruses, vol. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • Boeke, J. D., C. A. Styles, and G. R. Fink. 1986. Saccharomyces cerevisiae SPT3 gene is required for transposition and transpositional recombination of chromosomal Ty elements. Mol. Cell. Biol. 6:3575–3581.
  • Bolton, E. C., and J. D. Boeke. 2003. Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Res. 13:254–263.
  • Bradshaw, V. A., and K. McEntee. 1989. DNA damage activates transcription and transposition of yeast Ty retrotransposons. Mol. Gen. Genet. 218:465–474.
  • Burhans, D. T., L. Ramachandran, J. Wang, P. Liang, H. G. Patterton, M. Breitenbach, and W. C. Burhans. 2006. Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome. BMC Evol. Biol. 6:58.
  • Camblong, J., N. Iglesias, C. Fickentscher, G. Dieppois, and F. Stutz. 2007. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131:706–717.
  • Ciriacy, M., K. Freidel, and C. Lohning. 1991. Characterization of trans-acting mutations affecting Ty and Ty-mediated transcription in Saccharomyces cerevisiae. Curr. Genet. 20:441–448.
  • David, L., W. Huber, M. Granovskaia, J. Toedling, C. J. Palm, L. Bofkin, T. Jones, R. W. Davis, and L. M. Steinmetz. 2006. A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. USA 103:5320–5325.
  • 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.
  • Deininger, P. L., and M. A. Batzer. 2002. Mammalian retroelements. Genome Res. 12:1455–1465.
  • Dudley, A. M., L. J. Gansheroff, and F. Winston. 1999. Specific components of the SAGA complex are required for Gcn4- and Gcr1- mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae. Genetics 151:1365–1378.
  • Errede, B. 1993. MCM1 binds to a transcriptional control element in Ty1. Mol. Cell. Biol. 13:57–62.
  • Errede, B., M. Company, and C. A. Hutchison III. 1987. Ty1 sequence with enhancer and mating-type-dependent regulatory activities. Mol. Cell. Biol. 7:258–265.
  • Fulton, A. M., P. D. Rathjen, S. M. Kingsman, and A. J. Kingsman. 1988. Upstream and downstream transcriptional control signals in the yeast retrotransposon, TY. Nucleic Acids Res. 16:5439–5458.
  • Garfinkel, D. J. 2005. Genome evolution mediated by Ty elements in Saccharomyces. Cytogenet. Genome Res. 110:63–69.
  • Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philipsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:546–567.
  • Grandbastien, M. A., C. Audeon, E. Bonnivard, J. M. Casacuberta, B. Chalhoub, A. P. Costa, Q. H. Le, D. Melayah, M. Petit, C. Poncet, S. M. Tam, M. A. Van Sluys, and C. Mhiri. 2005. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110:229–241.
  • Grant, P. A., L. Duggan, J. Cote, S. M. Roberts, J. E. Brownell, R. Candau, R. Ohba, T. Owen-Hughes, C. D. Allis, F. Winston, S. L. Berger, and J. L. Workman. 1997. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11:1640–1650.
  • Gray, W. M., and J. S. Fassler. 1996. Isolation and analysis of the yeast TEA1 gene, which encodes a zinc cluster Ty enhancer-binding protein. Mol. Cell. Biol. 16:347–358.
  • Gray, W. M., and J. S. Fassler. 1993. Role of Saccharomyces cerevisiae Rap1 protein in Ty1 and Ty1-mediated transcription. Gene Expr. 3:237–251.
  • Happel, A. M., M. S. Swanson, and F. Winston. 1991. The SNF2, SNF5 and SNF6 genes are required for Ty transcription in Saccharomyces cerevisiae. Genetics 128:69–77.
  • Hongay, C. F., P. L. Grisafi, T. Galitski, and G. R. Fink. 2006. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127:735–745.
  • Horie, K., E. S. Saito, V. W. Keng, R. Ikeda, H. Ishihara, and J. Takeda. 2007. Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits. Genetics 176:815–827.
  • Houseley, J., and D. Tollervey. 2008. The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast? Biochim. Biophys. Acta 1779:239–246.
  • Irwin, B., M. Aye, P. Baldi, N. Beliakova-Bethell, H. Cheng, Y. Dou, W. Liou, and S. Sandmeyer. 2005. Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res. 15:641–654.
  • Kent, N. A., N. Karabetsou, P. K. Politis, and J. Mellor. 2001. In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev. 15:619–626.
  • Kim, J. M., S. Vanguri, J. D. Boeke, A. Gabriel, and D. F. Voytas. 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464–478.
  • Knight, S. A. B., S. Labbe, L. F. Kwon, D. J. Kosman, and D. J. Thiele. 1996. A widespread transposable element masks expression of a yeast copper transport gene. Genes Dev. 10:1917–1929.
  • Laloux, I., E. Dubois, M. Dewerchin, and E. Jacobs. 1990. TEC1, a gene involved in the activation of Ty1 and Ty1-mediated gene expression in Saccharomyces cerevisiae: cloning and molecular analysis. Mol. Cell. Biol. 10:3541–3550.
  • Laloux, I., E. Jacobs, and E. Dubois. 1994. Involvement of SRE element of Ty1 transposon in TEC1-dependent transcriptional activation. Nucleic Acids Res. 22:999–1005.
  • Landry, J. R., A. Rouhi, P. Medstrand, and D. L. Mager. 2002. The Opitz syndrome gene Mid1 is transcribed from a human endogenous retroviral promoter. Mol. Biol. Evol. 19:1934–1942.
  • Laurent, B. C., I. Treich, and M. Carlson. 1993. The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev. 7:583–591.
  • Lesage, P., and A. L. Todeschini. 2005. Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet. Genome Res. 110:70–90.
  • López, M. C., and H. V. Baker. 2000. Understanding the growth phenotype of the yeast gcr1 mutant in terms of global genomic expression patterns. J. Bacteriol. 182:4970–4978.
  • Madison, J. M., A. M. Dudley, and F. Winston. 1998. Identification and analysis of Mot3, a zinc finger protein that binds to the retrotransposon Ty long terminal repeat (δ) in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:1879–1890.
  • Martens, J. A., P. Y. Wu, and F. Winston. 2005. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev. 19:2695–2704.
  • Maxwell, P. H., and M. J. Curcio. 2007. Host factors that control long terminal repeat retrotransposons in Saccharomyces cerevisiae: implications for regulation of mammalian retroviruses. Eukaryot. Cell 6:1069–1080.
  • McClanahan, T., and K. McEntee. 1984. Specific transcripts are elevated in Saccharomyces cerevisiae in response to DNA damage. Mol. Cell. Biol. 4:2356–2363.
  • Medstrand, P., J. R. Landry, and D. L. Mager. 2001. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J. Biol. Chem. 276:1896–1903.
  • Meyers, B. C., S. V. Tingey, and M. Morgante. 2001. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11:1660–1676.
  • Morillon, A., L. Bénard, M. Springer, and P. Lesage. 2002. Differential effects of chromatin and Gcn4 on the 50-fold range of expression among individual yeast Ty1 retrotransposons. Mol. Cell. Biol. 22:2078–2088.
  • Morillon, A., M. Springer, and P. Lesage. 2000. Activation of the Kss1 invasive-filamentous growth pathway induces Ty1 transcription and retrotransposition in Saccharomyces cerevisiae. Mol. Cell. Biol. 20:5766–5776.
  • Myers, A. M., A. Tzagoloff, D. M. Kinney, and C. J. Lusty. 1986. Yeast shuttle and integrative vectors with multiple cloning sites suitable for construction of lacZ fusions. Gene 45:299–310.
  • Peaston, A. E., A. V. Evsikov, J. H. Graber, W. N. de Vries, A. E. Holbrook, D. Solter, and B. B. Knowles. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7:597–606.
  • Peng, W. T., N. J. Krogan, D. P. Richards, J. F. Greenblatt, and T. R. Hughes. 2004. ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Nucleic Acids Res. 32:1993–1999.
  • Pollard, K. J., and C. L. Peterson. 1997. Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol. Cell. Biol. 17:6212–6222.
  • Rolfe, M., A. Spanos, and G. Banks. 1986. Induction of yeast Ty element transcription by ultraviolet. Nature 319:339–340.
  • Romanish, M. T., W. M. Lock, L. N. van de Lagemaat, C. A. Dunn, and D. L. Mager. 2007. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet. 3:e10.
  • Sacerdot, C., G. Mercier, A. L. Todeschini, M. Dutreix, M. Springer, and P. Lesage. 2005. Impact of ionizing radiation on the life cycle of Saccharomyces cerevisiae Ty1 retrotransposon. Yeast 22:441–455.
  • Scherer, S., C. Mann, and R. W. Davis. 1982. Reversion of a promoter deletion in yeast. Nature 298:815–819.
  • Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18:3091–3092.
  • Sehgal, A., C. Y. Lee, and P. J. Espenshade. 2007. SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast. PLoS Genet. 3:e131.
  • Slotkin, R. K., and R. Martienssen. 2007. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8:272–285.
  • Staleva Staleva, L., and P. Venkov. 2001. Activation of Ty transposition by mutagens. Mutat. Res. 474:93–103.
  • Strand, D. J., and J. F. McDonald. 1985. Copia is transcriptionally responsive to environmental stress. Nucleic Acids Res. 13:4401–4410.
  • Struhl, K. 1986. Constitutive and inducible Saccharomyces cerevisiae promoters: evidence for two distinct molecular mechanisms. Mol. Cell. Biol. 6:3847–3853.
  • Todeschini, A.-L., A. Morillon, M. Springer, and P. Lesage. 2005. Severe adenine starvation activates Ty1 transcription and retrotransposition in Saccharomyces cerevisiae. Mol. Cell. Biol. 25:7459–7472.
  • Turkel, S., X. B. Liao, and P. J. Farabaugh. 1997. Gcr1-dependent transcriptional activation of yeast retrotransposon Ty2-917. Yeast 13:917–930.
  • van de Lagemaat, L. N., J. R. Landry, D. L. Mager, and P. Medstrand. 2003. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet. 19:530–536.
  • Vasiljeva, L., M. Kim, N. Terzi, L. M. Soares, and S. Buratowski. 2008. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol. Cell 29:313–323.
  • Waterston, R. H., K. Lindblad-Toh, E. Birney, J. Rogers, J. F. Abril, P. Agarwal, R. Agarwala, R. Ainscough, M. Alexandersson, P. An, S. E. Antonarakis, J. Attwood, R. Baertsch, J. Bailey, K. Barlow, S. Beck, E. Berry, B. Birren, T. Bloom, P. Bork, M. Botcherby, N. Bray, M. R. Brent, D. G. Brown, S. D. Brown, C. Bult, J. Burton, J. Butler, R. D. Campbell, P. Carninci, S. Cawley, F. Chiaromonte, A. T. Chinwalla, D. M. Church, M. Clamp, C. Clee, F. S. Collins, L. L. Cook, R. R. Copley, A. Coulson, O. Couronne, J. Cuff, V. Curwen, T. Cutts, M. Daly, R. David, J. Davies, K. D. Delehaunty, J. Deri, E. T. Dermitzakis, C. Dewey, N. J. Dickens, M. Diekhans, S. Dodge, I. Dubchak, D. M. Dunn, S. R. Eddy, L. Elnitski, R. D. Emes, P. Eswara, E. Eyras, A. Felsenfeld, G. A. Fewell, P. Flicek, K. Foley, W. N. Frankel, L. A. Fulton, R. S. Fulton, T. S. Furey, D. Gage, R. A. Gibbs, G. Glusman, S. Gnerre, N. Goldman, L. Goodstadt, D. Grafham, T. A. Graves, E. D. Green, S. Gregory, R. Guigo, M. Guyer, R. C. Hardison, D. Haussler, Y. Hayashizaki, L. W. Hillier, A. Hinrichs, W. Hlavina, T. Holzer, F. Hsu, A. Hua, T. Hubbard, A. Hunt, I. Jackson, D. B. Jaffe, L. S. Johnson, M. Jones, T. A. Jones, A. Joy, M. Kamal, E. K. Karlsson, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562.
  • Winston, F. 1992. Analysis of SPT genes: a genetic approach toward analysis of TFIID, histones, and other transcription factors of yeast, p. 1271-1293. In S. L. McKnight and K. R. Yamamoto (ed.), Transcriptional regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • Winston, F., K. J. Durbin, and G. R. Fink. 1984. The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell 39:675–682.
  • 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.
  • Yu, K., and R. T. Elder. 1989. A region internal to the coding sequences is essential for transcription of the yeast Ty1-D15 element. Mol. Cell. Biol. 9:3667–3678.
  • Zhang, Z., and F. S. Dietrich. 2005. Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE. Nucleic Acids Res. 33:2838–2851.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.