1887

Chapter 26 : Ty1 and Ty5 of Saccharomyces cerevisiae

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Ty1 and Ty5 of Saccharomyces cerevisiae, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap26-1.gif /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap26-2.gif

Abstract:

Ty1 and Ty5 of are long terminal repeat (LTR) retrotransposons, members of a large and ubiquitous class of mobile genetic elements. Like the retroviruses, LTR retrotransposons replicate by reverse transcribing RNA into DNA and then integrating the DNA transposition intermediate into the genome of their host. This chapter begins with a description of Ty1 and Ty5, including their origins and genetic organization. Subsequent sections deal with four discrete steps in the LTR retrotransposon life cycle, namely, (i) transcription and transcriptional regulation; (ii) protein expression, processing, and virus-like particle assembly; (iii) reverse transcription; and (iv) integration. The study of activating mutations has unveiled a complex array of both positively and negatively acting factors responsible for Ty1’s transcriptional regulation. The discussion of reverse transcription in the remainder of the chapter focuses on the native Ty1 enzyme. Negative post transcriptional regulation of Ty1 was suggested by the paradoxical observation that Ty1 mRNA is very abundant, yet mature Ty1 proteins are scarce and transposition infrequent. In the postgenomics era, is the proving ground for new technologies that are beginning to offer unprecedented insights into the complex regulatory and metabolic networks that underlie cellular biology. The development of the research tools and the accumulated knowledge that results from their use will undoubtedly greatly facilitate Ty1 and Ty5 research in the coming years.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26

Key Concept Ranking

Mobile Genetic Elements
1.2909262
DNA Synthesis
0.87788755
Genetic Recombination
0.796711
Transcription Start Site
0.59927994
RNA Polymerase II
0.5298165
1.2909262
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

The LTR retrotransposon life cycle begins with the transcription of an insertion in the nuclear genome. The resulting mRNA is transported out of the nucleus, where it is translated to produce the two primary gene products, homologs of retroviral proteins Gag and Pol. These proteins are then proteolytically processed by an element-encoded protease. The Gag proteins assemble in the cytoplasm into a VLP. Within the VLPs are packaged the Pol gene products, namely, PR, RT, and IN. Also packaged within the particle is template mRNA and a cellular tRNA that is used to prime reverse transcription. It is within the particle that reverse transcription of the template mRNA is carried out to generate the linear cDNA. This cDNA is then transported into the nucleus as part of a preintegration complex that includes the element-encoded IN. IN inserts the cDNA into the host genome, creating a duplication of 5 bp of host DNA, and thereby completing the life cycle. The primary difference between the LTR retrotransposons and retroviruses is that the VLP does not leave the host through membrane budding and fusion, which is carried out by the retroviral gene product.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Genomic organization of Ty1 and Ty5. DNA sequences are indicated by the upper open boxes. LTR sequences are shown as solid triangles. The short thin lines denote the location of the PBS and polypurine tracts (PPT), which prime minus- and plus-strand DNA synthesis, respectively. Open reading frames are indicated by the open boxes below each element. Amino acid sequence domains conserved in retroviral proteins include PR, IN, RT, and RH. RNA-binding (RB) domain denotes the finger motif characteristic of nucleocapsid proteins. Ty1 and Ty5 are drawn to scale.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

A single-step selection strategy for reverse transcription. Additional details are provided in the text. The squiggly line indicates mRNA. AI, artificial intron; SD, splice donor; SA, splice acceptor.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Sequences that mediate Ty transcription. The arrowheads indicate the transcription start site, and the lollipop marks the site of transcription termination for Ty1. These sites define the U5, R, and U3 regions of the LTR. Other Ty1 sequences important for transcription include the TATA box and TS1 and TS2, the latter of which are required for 3′-end formation. The locations within the elements of -acting sequences involved in transcriptional regulation are noted: FRE, domain II, and PRE. Above the elements are listed the proteins or protein complexes that act on these sites or in their vicinity. The figures are drawn proportionally.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

The pheromone response and filamentous growth signaling pathways. Both pathways share several common components. Fus3p is the mating MAPK and Kss1p is the filamentous growth MAPK. The pathways culminate in the activation of Ste12p, which induces transcription of target genes. Ste12p binds to PRE in the regulatory regions of genes involved in the mating response. In the case of the filamentous growth pathway, Ste12p binds in conjunction with Tec1p to FREs. In the absence of Fus3p, Kss1p can cross-activate transcription of genes with FREs, including Ty1 elements (indicated by the dashed arrow).

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

+1 translational frameshifting as carried out by Ty1. The mRNA sequence is shown at the top of the figure. Below are the paired aminoacylated tRNAs. Circles represent the amino acid residues.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

Scheme for Ty1 and Ty5 protein processing. Question marks indicate predicted Ty5 proteins that have not been identified experimentally. The figure is adapted from references and .

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8
Figure 8

Ty1 VLPs. (A) An electron micrograph of an cell overexpressing Ty1. (B) Cryoelectron microscopy three-dimensional reconstructions of Ty1 1-381 virions with icosahedral T numbers of 3 and 4 (reprinted from the [ ] with permission provided by H. Saibil and the publisher).

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9
Figure 9

The mechanism of reverse transcription. Details of each step are provided in the text. The template mRNA is depicted as a squiggly line. Solid lines indicate DNA; solid lines with arrowheads indicate DNA strands in the process of being extended by reverse transcriptase.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10
Figure 10

Conserved features of RT. The open boxes represent the amino acid sequences of RT and RH for HIV, Ty1, and Ty5. The seven conserved amino acid sequence domains of RT are numbered and shaded in gray (60). The conserved sequence domains correspond to structural features in the enzyme that form a handlike structure: F, finger domain; P, palm; T, thumb. Note that the N terminus of Ty5 RT has not been determined. The black boxes in RH indicate conserved regions that can be aligned to the E. coli RH sequence. Conserved catalytic residues are indicated, and the amino acid positions are provided for HIV and Ty1

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 11
Figure 11

The minus-strand primer for reverse transcription. At the top is shown the location of sequences near the Ty1 5′-LTR that are complementary to the initiator methionine tRNA. Asterisks specify residues within the initiator tRNA that are complementary to box 0, 1, and 2.1/2/2 in the Ty1 message. Note that box 0 allows for G:U pairing with the initiator tRNA. Filled circles represent sequences complementary to the Ty1 and Ty5 PBSs.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 12
Figure 12

Plus-strand DNA synthesis. The lowercase letters at the left of the figure refer to steps in reverse transcription depicted in Fig. 9 . Lowercase letters followed by a number indicate steps in Fig. 9 that have been expanded to include additional detail. The figures are adapted from reference . (A) Model for inheritance of primer tRNA sequences. The open circle represents a mutation in the primer tRNA. The closed circle represents the first modified base, the site at which reverse transcription stops. If the mutation is copied into the plus-strand strong-stop DNA (step g), then following plus-strand transfer (step h), a heteroduplex is formed. Following mismatch repair, which is unbiased in yeast, genetic information should flow from the tRNA into the preintegrative cDNA. (B) The plus-strand primer recycling model. Details for each step are provided in the text.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 13
Figure 13

The integration reaction. The conserved LTR end sequences are shown. Details of the reaction are provided in the text. TSD, target site duplication. The figure was adapted from reference .

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 14
Figure 14

Conserved features of IN. The open boxes represent the amino acid sequences of IN for HIV, Ty1, and Ty5. Conserved amino acid residues are indicated that define the zinc-binding motif and the catalytic domain (shaded gray). The large C termini of both Ty1 and Ty5 are rich in serine and proline. NLS, the Ty1 nuclear localization signal; TD, the Ty5 targeting domain.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 15
Figure 15

Model for Ty1 and Ty5 target specificity. The Ty1 preintegration complex recognizes sites of RNAP III transcription, such as tRNA genes. Ty1 integrates preferentially into an approximately 750-base window upstream of the transcription start site. Ty5 integrates preferentially into an approximately 3-kb window flanking the silencers or the subtelomeric X repeat. Both sites are bound by the Sir complex, which includes Sir3p and Sir4p. A targeting domain (TD) is located within the C terminus of Ty5 IN that interacts with Sir4p. This interaction is thought to tether the preintegration complex to target sites.

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817954.chap26
1. Adams, S. E.,, K. M. Dawson,, K. Gull,, S. M. Kingsman,, and A. J. Kingsman. 1987. The expression of hybrid HIV:Ty virus-like particles in yeast. Nature 329:6870.
2. Adams, S. E.,, J. Mellor,, K. Gull,, R. B. Sim,, M. F. Tuite,, S. M. Kingsman,, and A. J. Kingsman. 1987. The functions and relationships of Ty-VLP proteins in yeast reflect those of mammalian retroviral proteins. Cell 49:111119.
3. Al-Khayat, H. A.,, D. Bhella,, J. M. Kenney,, J. F. Roth,, A. J. Kingsman,, E. Martin-Rendon,, and H. R. Saibil. 1999. Yeast Ty retrotransposons assemble into virus-like particles whose T-numbers depend on the C-terminal length of the capsid protein. J. Mol. Biol. 292:6573.
4. Balasundaram, D.,, J. D. Dinman,, C. W. Tabor,, and H. Tabor. 1994. SPE1 and SPE2: two essential genes in the biosynthesis of polyamines that modulate +1 ribosomal frameshifting in Saccharomyces cerevisiae. J. Bacteriol. 176:71267128.
5. Balasundaram, D.,, J. D. Dinman,, R. B. Wickner,, C. W. Tabor,, and H. Tabor. 1994. Spermidine deficiency increases +1 ribosomal frameshifting efficiency and inhibits Ty1 retrotransposition in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 91:172176.
6. Baur, M.,, R. K. Esch,, and B. Errede. 1997. Cooperative binding interactions required for function of the Ty1 sterile responsive element. Mol. Cell. Biol. 17:43304337.
7. Belcourt, M. F.,, and P. J. Farabaugh. 1990. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell 62:339352.
8. Berwin, B.,, and E. Barklis. 1993. Retrovirus-mediated insertion of expressed and non-expressed genes at identical chromosomal locations. Nucleic Acids Res. 21:23992407.
9. Boeke, J. D. 1989. Transposable elements in Saccharomyces cerevisiae, p. 335374. In D. E. Berg and M. M. Howe (ed.), Mobile DNA. American Society for Microbiology, Washington, D.C..
10. Boeke, J. D.,, and S. E. Devine. 1998. Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93:10871089.
11. Boeke, J. D.,, T. Eickbush,, S. B. Sandmeyer,, and D. F. Voytas,. 2000. Metaviridae, p. 359367. In M. H. V. van Regenmortel,, C. M. Fauquet,, D. H. L. Bishop,, E. B. Carsten,, M. K. Estes,, S. M. Lemon,, J. Maniloff,, M. A. Mayo,, D. J. McGeoch,, C. R. Pringle,, and R. B. Wickner (ed.), Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, N.Y..
12. Boeke, J. D.,, T. Eickbush,, S. B. Sandmeyer,, and D. F. Voytas,. 2000. Pseudoviridae, p. 349-–357. In M. H. V. van Regenmortel,, C. M. Fauquet,, D. H. L. Bishop,, E. B. Carsten,, M. K. Estes,, S. M. Lemon,, J. Maniloff,, M. A. Mayo,, D. J. McGeoch,, C. R. Pringle,, and R. B. Wickner (ed.), Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, N.Y.
13. Boeke, J. D.,, D. J. Garfinkel,, C. A. Styles,, and G. R. Fink. 1985. Ty elements transpose through an RNA intermediate. Cell 40:491500.
14. Boeke, J. D.,, and S. B. Sandmeyer,. 1991. Yeast transposable elements, p. 193261. In J. Broach,, E. Jones,, and J. Pringle (ed.), The Molecular and Cellular Biology of the Yeast Saccharomyces, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
15. Boeke, J. D.,, H. Xu,, and G. R. Fink. 1988. A general method for the chromosomal amplification of genes in yeast. Science 239:280282.
16. Bolognesi, D. P.,, R. C. Montelaro,, H. Frank,, and W. Schafer. 1978. Assembly of type C oncornaviruses: a model. Science 199:183186.
17. Brachmann, C. B.,, and J. D. Boeke. 1997. Mapping the multimerization domains of the Gag protein of yeast retrotransposon Ty1. J. Virol. 71:812817.
18. Braiterman, L. T.,, and J. D. Boeke. 1994. In vitro integration of retrotransposon Ty1: a direct physical assay. Mol. Cell. Biol. 14:57195730.
19. Braiterman, L. T.,, and J. D. Boeke. 1994. Ty1 in vitro integration: effects of mutations in cis and in trans. Mol. Cell. Biol. 14:57315740.
20. Braiterman, L. T.,, G. M. Monokian,, D. J. Eichinger,, S. L. Merbs,, A. Gabriel,, and J. D. Boeke. 1994. In-frame linker insertion mutagenesis of yeast transposon Ty1: phenotypic analysis. Gene 139:1926.
21. Brierley, C.,, and A. J. Flavell. 1990. The retrotransposon copia controls the relative levels of its gene products posttranscriptionally by differential expression from its two major mRNAs. Nucleic Acids Res. 18:29472951.
22. Brookman, J. L.,, A. J. Stott,, P. J. Cheeseman,, C. S. Adamson,, D. Holmes,, J. Cole,, and N. R. Burns. 1995. Analysis of TYA protein regions necessary for formation of the Ty1 virus-like particle structure. Virology 212:6976.
23. Brookman, J. L.,, A. J. Stott,, P. J. Cheeseman,, N. R. Burns,, S. E. Adams,, A. J. Kingsman,, and K. Gull. 1995. An immunological analysis of Ty1 virus-like particle structure. Virology 207:5967.
24. Brown, P. O., 1997. Integration, p. 161204. In J. M. Coffin,, S. H. Hughes,, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
25. Bryk, M.,, M. Banerjee,, M. Murphy,, K. E. Knudsen,, D. J. Garfinkel,, and M. J. Curcio. 1997. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11:255269.
26. Burck, C. L.,, Y. O. Chernoff,, R. Liu,, P. J. Farabaugh,, and S.W. Liebman. 1999. Translational suppressors and antisuppressors alter the efficiency of the Ty1 programmed translational frameshift. RNA 5:14511457.
27. Burns, N. R.,, H. R. Saibil,, N. S. White,, J. F. Pardon,, P. A. Timmins,, S. M. Richardson,, B. M. Richards,, S. E. Adams,, S.M. Kingsman,, and A. J. Kingsman. 1992. Symmetry, flexibility and permeability in the structure of yeast retrotransposon virus-like particles. EMBO J. 11:11551164.
28. Cameron, J. R.,, E. Y. Loh,, and R. W. Davis. 1979. Evidence for transposition of dispersed repetitive DNA families in yeast. Cell 16:739751.
29. Chalker, D. L.,, and S. B. Sandmeyer. 1990. Transfer RNA genes are genomic targets for de novo transposition of the yeast retrotransposon Ty3. Genetics 126:837850.
30. Chapman, K. B.,, and J. D. Boeke. 1991. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 65:483492.
31. Chapman, K. B.,, A. S. Bystrom,, and J. D. Boeke. 1992. Initiator methionine tRNA is essential for Ty1 transposition in yeast. Proc. Natl. Acad. Sci. USA 89:32363240.
32. Clare, J.,, and P. Farabaugh. 1985. Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression. Proc. Natl. Acad. Sci. USA 82:28292833.
33. Clare, J. J.,, M. Belcourt,, and P. J. Farabaugh. 1988. Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon. Proc. Natl. Acad. Sci. USA 85:68166820.
34. Coffin, J., 1993. Reverse transcription and evolution, p. 445479. In A. M. Skalka, and S. P. Goff (ed.), Reverse Transcriptase. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
35. Conte, D., Jr.,, E. Barber,, M. Banerjee,, D. J. Garfinkel,, and M. J. Curcio. 1998. Posttranslational regulation of Ty1 retrotransposition by mitogen-activated protein kinase Fus3. Mol. Cell. Biol. 18:25022513.
36. Conte, D., Jr.,, and M. J. Curcio. 2000. Fus3 controls Ty1 transpositional dormancy through the invasive growth MAPK pathway. Mol. Microbiol. 35:415427.
37. Curcio, M. J.,, and D. J. Garfinkel. 1994. Heterogeneous functional Ty1 elements are abundant in the Saccharomyces cerevisiae genome. Genetics 136:12451259.
38. Curcio, M. J.,, and D. J. Garfinkel. 1999. New lines of host defense: inhibition of Ty1 retrotransposition by Fus3p and NER/TFIIH. Trends Genet. 15:4345.
39. Curcio, M. J.,, and D. J. Garfinkel. 1992. Posttranslational control of Ty1 retrotransposition occurs at the level of protein processing. Mol. Cell. Biol. 12:28132825.
40. Curcio, M. J.,, and D. J. Garfinkel. 1991. Regulation of retrotransposition in Saccharomyces cerevisiae. Mol. Microbiol. 5:18231829.
41. Curcio, M. J.,, and D. J. Garfinkel. 1991. Single-step selection for Ty1 element retrotransposition. Proc. Natl. Acad. Sci. USA 88:936940.
42. Curcio, M. J.,, A. M. Hedge,, J. D. Boeke,, and D. J. Garfinkel. 1990. TyRNA levels determine the spectrum of retrotransposition events that activate gene expression in Saccharomyces cerevisiae. Mol. Gen. Genet. 220:213221.
43. Curcio, M. J.,, N. J. Sanders,, and D. J. Garfinkel. 1988. Transpositional competence and transcription of endogenous Ty elements in Saccharomyces cerevisiae: implications for regulation of transposition. Mol. Cell. Biol. 8:35713581.
44. Dalgaard, J. Z.,, M. Banerjee,, and M. J. Curcio. 1996. A novel Ty1-mediated fragmentation method for native and artificial yeast chromosomes reveals that the mouse steel gene is a hotspot for Ty1 integration. Genetics 143:673683.
45. Daniel, R.,, R. A. Katz,, and A. M. Skalka. 1999. A role for DNA-PK in retroviral DNA integration. Science 284:644647.
46. Derr, L. K. 1998. The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae. Genetics 148:937945.
47. Derr, L. K.,, and J. N. Strathern. 1993. A role for reverse transcripts in gene conversion. Nature 361:170173.
48. Derr, L. K.,, J. N. Strathern,, and D. J. Garfinkel. 1991. RNA-mediated recombination in S. cerevisiae. Cell 67:355364.
49. Devine, S. E.,, and J. D. Boeke. 1994. Efficient integration of artificial transposons into plasmid targets in vitro: a useful tool for DNA mapping, sequencing and genetic analysis. Nucleic Acids Res. 22:37653772.
50. Devine, S. E.,, and J. D. Boeke. 1996. Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNApolymerase III. Genes Dev. 10:620633.
51. Dinman, J. D.,, T. Icho,, and R. B. Wickner. 1991. A −1 ribosomal frameshift in a double-strandedRNAvirus of yeast forms a Gag-Pol fusion protein. Proc. Natl. Acad. Sci. USA 88:174178.
52. Dinman, J. D.,, and T. G. Kinzy. 1997. Translational misreading: mutations in translation elongation factor 1alpha differentially affect programmed ribosomal frameshifting and drug sensitivity. RNA 3:870881.
53. Dombroski, B. A.,, Q. Feng,, S. L. Mathias,, D. M. Sassaman,, A. F. Scott,, H. H. Kazazian, Jr.,, and J. D. Boeke. 1994. An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 14:44854492.
54. Donze, D.,, C. R. Adams,, J. Rine,, and R. T. Kamakaka. 1999. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13:698708.
55. Downs, J. A.,, and S. P. Jackson. 1999. Involvement of DNA end-binding protein Ku in Ty element retrotransposition. Mol. Cell. Biol. 19:62606268.
56. Dubois, E.,, E. Jacobs,, and J. C. Jauniaux. 1982. Expression of the ROAM mutations in Saccharomyces cerevisiae: involvement of trans-acting regulatory elements and relation with the Ty1 transcription. EMBO J. 1:11331139.
57. Eibel, H.,, and P. Philippsen. 1984. Preferential integration of yeast transposable element Ty into a promoter region. Nature 307:386388.
58. Eichinger, D. J.,, and J. D. Boeke. 1988. The DNA intermediate in yeast Ty1 element transposition copurifies with virus-like particles: cell-free Ty1 transposition. Cell 54:955966.
59. Eichinger, D. J.,, and J. D. Boeke. 1990. A specific terminal structure is required for Ty1 transposition. Genes Dev. 4:324330.
60. Eickbush, T. H., 1994. Origin and evolutionary relationships of retroelements, p. 121157. In S. S. Morse (ed.), The Evolutionary Biology of Viruses. Raven Press, Ltd., New York, N.Y..
61. Elder, R. T.,, E. Y. Loh,, and R. W. Davis. 1983. RNA from the yeast transposable element Ty1 has both ends in the direct repeats, a structure similar to retrovirus RNA. Proc. Natl. Acad. Sci. USA 80:24322436.
62. Elder, R. T.,, T. P. St. John, D. T. Stinchcomb, R. W. Davis, and S. Scherer. 1981. Studies on the transposable element Ty1 of yeast. I. RNA homologous to Ty1. II. Recombination and expression of Ty1 and adjacent sequences. Cold Spring Harb. Symp. Quant. Biol. 45:581591.
63. Errede, B. 1993. MCM1 binds to a transcriptional control element in Ty1. Mol. Cell. Biol. 13:5762.
64. Errede, B.,, T. S. Cardillo,, F. Sherman,, E. Dubois,, J. Deschamps,, and J. M. Wiame. 1980. Mating signals control expression of mutations resulting from insertion of a transposable repetitive element adjacent to diverse yeast genes. Cell 22:427436.
65. Errede, B.,, M. Company,, J. D. Ferchak,, C. A. D. Hutchison,, and W. S. Yarnell. 1985. Activation regions in a yeast transposon have homology to mating type control sequences and to mammalian enhancers. Proc. Natl. Acad. Sci. USA 82:54235427.
66. Errede, B.,, M. Company,, and C. A. D. Hutchison. 1987. Ty1 sequence with enhancer and mating-type-dependent regulatory activities. Mol. Cell. Biol. 7:258265.
67. Farabaugh, P. J. 1996. Programmed translational frameshifting. Annu. Rev. Genet. 30:507528.
68. Farabaugh, P. J.,, and A. Vimaladithan. 1998. Effect of frameshift-inducing mutants of elongation factor 1alpha on programmed +1 frameshifting in yeast. RNA 4:3846.
69. Farabaugh, P. J.,, H. Zhao,, and A. Vimaladithan. 1993. A novel programmed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell 74:93103.
70. Fassbender, S.,, K. H. Bruhl,, M. Ciriacy,, and U. Kuck. 1994. Reverse transcriptase activity of an intron encoded polypeptide. EMBO J. 13:20752083.
71. Fassler, J. S.,, and F. Winston. 1989. The Saccharomyces cerevisiae SPT13/GAL11 gene has both positive and negative regulatory roles in transcription. Mol. Cell. Biol. 9:56025609.
72. Feng, Y. X.,, S. P. Moore,, D. J. Garfinkel,, and A. Rein. 2000. The genomic RNA in Ty1 virus-like particles is dimeric. J. Virol. 74:1081910821.
73. Fischer, G.,, S. A. James,, I. N. Roberts,, S. G. Oliver,, and E. J. Louis. 2000. Chromosomal evolution in Saccharomyces. Nature 405:451454.
74. Freiberg, G.,, A. D. Mesecar,, H. Huang,, J. Y. Hong,, and S. W. Liebman. 2000. Characterization of novel rad6/ubc2 ubiquitin-conjugating enzyme mutants in yeast. Curr. Genet. 37:221233.
75. Friant, S.,, T. Heyman,, A. S. Bystrom,, M. Wilhelm,, and F. X. Wilhelm. 1998. Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo. Mol. Cell. Biol. 18:799806.
76. Friant, S.,, T. Heyman,, O. Poch,, M. Wilhelm,, and F. X. Wilhelm. 1997. Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex. Yeast 13:639645.
77. Friant, S.,, T. Heyman,, M. L. Wilhelm,, and F. X. Wilhelm. 1996. Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon. Nucleic Acids Res. 24:441449.
78. 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. 16:54395458.
79. Gabriel, A.,, and J. D. Boeke. 1991. Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata. Proc. Natl. Acad. Sci. USA 88:97949798.
80. Gabriel, A.,, and E. H. Mules. 1999. Fidelity of retrotransposon replication. Ann. N.Y. Acad. Sci. 870:108118.
81. Gabriel, A.,, M. Willems,, E. H. Mules,, and J. D. Boeke. 1996. Replication infidelity during a single cycle of Ty1 retrotransposition. Proc. Natl. Acad. Sci. USA 93:77677771.
82. Gai, X.,, and D. F. Voytas. 1998. A single amino acid change in the yeast retrotransposon Ty5 abolishes targeting to silent chromatin. Mol. Cell 1:10511055.
83. Gaisne, M.,, A. M. Becam,, J. Verdiere,, and C. J. Herbert. 1999. A ‘natural’ mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr. Genet. 36:195200.
84. Garfinkel, D. J. 1997. Genetic loose change: how retroelements and reverse transcriptase heal broken chromosomes. Trends Microbiol. 5:173175.
85. Garfinkel, D. J.,, J. D. Boeke,, and G. R. Fink. 1985. Ty element transposition: reverse transcriptase and virus-like particles. Cell 42:507517.
86. Garfinkel, D. J.,, A. M. Hedge,, S. D. Youngren,, and T. D. Copeland. 1991. Proteolytic processing of pol-TYB proteins from the yeast retrotransposon Ty1. J. Virol. 65:45734581.
87. Garfinkel, D. J.,, M. F. Mastrangelo,, N. J. Sanders,, B. K. Shafer,, and J. N. Strathern. 1988. Transposon tagging using Ty elements in yeast. Genetics 120:95108.
88. Garfinkel, D. J.,, and J. N. Strathern. 1991. Ty mutagenesis in Saccharomyces cerevisiae. Methods Enzymol. 194:342361.
89. 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. 16:347358.
90. Gray, W. M.,, and J. S. Fassler. 1993. Role of Saccharomyces cerevisiae Rap1 protein in Ty1 and Ty1-mediated transcription. Gene Expr. 3:237251.
91. Hani, J.,, and H. Feldmann. 1998. tRNA genes and retroelements in the yeast genome. Nucleic Acids Res. 26:689696.
92. Heidmann, T.,, O. Heidmann,, and J. F. Nicolas. 1988. An indicator gene to demonstrate intracellular transposition of defective retroviruses. Proc. Natl. Acad. Sci. USA 85:22192223.
93. Henikoff, S. 1998. Conspiracy of silence among repeated transgenes. Bioessays 20:532535.
94. Herskowitz, I.,, J. Rine,, and J. Strathern,. 1992. Mating-type determination and mating-type interconversion in Saccharomyces cerevisiae, p. 583656. In J. Broach,, E. Jones,, and J. Pringle (ed.), The Molecular and Cellular Biology of the Yeast Saccharomyces, vol. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
95. Heyman, T.,, B. Agoutin,, S. Friant,, F. X. Wilhelm,, and M. L. Wilhelm. 1995. Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3′ LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition. J. Mol. Biol. 253:291303.
96. Hirschman, J. E.,, K. J. Durbin,, and F. Winston. 1988. Genetic evidence for promoter competition in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:46084615.
97. Huang, H.,, J. Y. Hong,, C. L. Burck,, and S. W. Liebman. 1999. Host genes that affect the target-site distribution of the yeast retrotransposon Ty1. Genetics 151:13931407.
98. Huang, H.,, A. Kahana,, D. E. Gottschling,, L. Prakash,, and S. W. Liebman. 1997. The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:66936699.
99. Hull, M. W.,, J. Erickson,, M. Johnston,, and D. R. Engelke. 1994. tRNA genes as transcriptional repressor elements. Mol. Cell. Biol. 14:12661277.
100. Imai, S.,, C. M. Armstrong,, M. Kaeberlein,, and L. Guarente. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795800.
101. Irwin, P. A.,, and D. F. Voytas. 2001. Expression and processing of proteins encoded by the Saccharomyces retrotransposon Ty5. J. Virol. 75:17901797.
102. Jacks, T. 1990. Translational suppression in gene expression in retroviruses and retrotransposons. Curr. Top. Microbiol. Immunol. 157:93124.
103. Ji, H.,, D. P. Moore,, M. A. Blomberg,, L. T. Braiterman,, D. F. Voytas,, G. Natsoulis,, and J. D. Boeke. 1993. Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73:10071018.
104. Jordan, I. K.,, and J. F. McDonald. 1999. Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome. Mol. Biol. Evol. 16:419422.
105. Jordan, I. K.,, and J. F. McDonald. 1999. The role of interelement selection in Saccharomyces cerevisiae Ty element evolution. J. Mol. Evol. 49:352357.
106. Kalpana, G. V.,, S. Marmon,, W. Wang,, G. R. Crabtree,, and S. P. Goff. 1994. Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5. Science 266:20022006.
107. Kang, X. L.,, F. Yadao,, R. D. Gietz,, and B. A. Kunz. 1992. Elimination of the yeast RAD6 ubiquitin conjugase enhances base-pair transitions and G.C—T.A transversions as well as transposition of the Ty element: implications for the control of spontaneous mutation. Genetics 130:285294.
108. Karst, S. M.,, M. L. Rutz,, and T. M. Menees. 2000. The yeast retrotransposons Ty1 and Ty3 require the RNA lariat debranching enzyme, Dbr1p, for efficient accumulation of reverse transcripts. Biochem. Biophys. Res. Commun. 268:112127.
109. Katz, R. A.,, and A. M. Skalka. 1994. The retroviral enzymes. Annu. Rev. Biochem. 63:133173.
110. Kaufman, P. D.,, J. L. Cohen,, and M. A. Osley. 1998. Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor I. Mol. Cell. Biol. 18:47934806.
111. Kawakami, K.,, S. Pande,, B. Faiola,, D. P. Moore,, J. D. Boeke,, P. J. Farabaugh,, J. N. Strathern,, Y. Nakamura,, and D. J. Garfinkel. 1993. A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics 135:309320.
112. Kawakami, K.,, B. K. Shafer,, D. J. Garfinkel,, J. N. Strathern,, and Y. Nakamura. 1992. Ty element-induced temperaturesensitive mutations of Saccharomyces cerevisiae. Genetics 131:821832.
113. Ke, N.,, X. Gao,, J. B. Keeney,, J. D. Boeke,, and D. F. Voytas. 1999. The yeast retrotransposon Ty5 uses the anticodon stem-loop of the initiator methionine tRNA as a primer for reverse transcription. RNA 5:929938.
114. Ke, N.,, P. A. Irwin,, and D. F. Voytas. 1997. The pheromone response pathway activates transcription of Ty5 retrotransposons located within silent chromatin of Saccharomyces cerevisiae. EMBO J. 16:62726280.
115. Ke, N.,, and D. F. Voytas. 1999. cDNA of the yeast retrotransposon Ty5 preferentially recombines with substrates in silent chromatin. Mol. Cell. Biol. 19:484494.
116. Ke, N.,, and D. F. Voytas. 1997. High frequency cDNA recombination of the Saccharomyces retrotransposon Ty5: the LTR mediates formation of tandem elements. Genetics 147:545556.
117. Keeney, J. B.,, K. B. Chapman,, V. Lauermann,, D. F. Voytas,, S. U. Astrom,, U. von Pawel-Rammingen,, A. Bystrom,, and J. D. Boeke. 1995. Multiple molecular determinants for retrotransposition in a primer tRNA. Mol. Cell. Biol. 15:217226.
118. Kenna, M. A.,, C. B. Brachmann,, S. E. Devine,, and J. D. Boeke. 1998. Invading the yeast nucleus: a nuclear localization signal at the C terminus of Ty1 integrase is required for transposition in vivo. Mol. Cell. Biol. 18:11151124.
119. Kennedy, B. K.,, N. R. Austriaco, Jr.,, J. Zhang,, and L. Guarente. 1995. Mutation in the silencing gene SIR4 can delay aging in S. cerevisiae. Cell 80:485496.
120. Kennedy, B. K.,, M. Gotta,, D. A. Sinclair,, K. Mills,, D. S. McNabb,, M. Murthy,, S. M. Pak,, T. Laroche,, S. M. Gasser,, and L. Guarente. 1997. Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae. Cell 89:381391.
121. Kikuchi, Y.,, Y. Ando,, and T. Shiba. 1986. Unusual priming mechanism of RNA-directed DNA synthesis in copia retrovirus-like particles of Drosophila. Nature 323:824826.
122. Kikuchi, Y.,, and N. Sasaki. 1992. Hyperprocessing of tRNA by the catalyticRNAof RNase P. Cleavage of a natural tRNA within the mature tRNA sequence and evidence for an altered conformation of the substrate tRNA. J. Biol. Chem. 267:1197211976.
123. Kikuchi, Y.,, N. Sasaki,, and Y. Ando-Yamagami. 1990. Cleavage of tRNA within the mature tRNA sequence by the catalytic RNA of RNase P: implication for the formation of the primer tRNA fragment for reverse transcription in copia retrovirus-like particles. Proc. Natl. Acad. Sci. USA 87:81058109.
124. 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. 8:464478.
125. Knight, S. A.,, 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. 10:19171929.
126. 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. 10:35413550.
127. Laloux, I.,, E. Jacobs,, and E. Dubois. 1994. Involvement of SRE element of Ty1 transposon in TEC1-dependent transcriptional activation. Nucleic Acids Res. 22:9991005.
128. Landry, J.,, A. Sutton,, S. T. Tafrov,, R. C. Heller,, J. Stebbins,, L. Pillus,, and R. Sternglanz. 2000. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl. Acad. Sci. USA 97:58075811.
129. Lauermann, V.,, and J. D. Boeke. 1997. Plus-strand strong-stop DNA transfer in yeast Ty retrotransposons. EMBO J. 16:66036612.
130. Lauermann, V.,, and J. D. Boeke. 1994. The primer tRNA sequence is not inherited during Ty1 retrotransposition. Proc. Natl. Acad. Sci. USA 91:98479851.
131. Lauermann, V.,, K. Nam,, J. Trambley,, and J. D. Boeke. 1995. Plus-strand strong-stop DNA synthesis in retrotransposon Ty1. J. Virol. 69:78457850.
131.a. Lawler, J. F., Jr.,, G. V. Merkulov,, and J. D. Boeke. 2001. Frameshift signal transplantation and the unambiguous analysis of mutations in the yeast retrotransposon Ty1 Gag-Pol overlap region. J. Virol. 75:67696775.
132. Lee, B. S.,, L. Bi,, D. J. Garfinkel,, and A. M. Bailis. 2000. Nucleotide excision repair/TFIIH helicases RAD3 and SSL2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms. Mol. Cell. Biol. 20:24362445.
133. Lee, B. S.,, C. P. Lichtenstein,, B. Faiola,, L. A. Rinckel,, W. Wysock,, M. J. Curcio,, and D. J. Garfinkel. 1998. Posttranslational inhibition of Ty1 retrotransposition by nucleotide excision repair/transcription factor TFIIH subunits Ss12p and Rad3p. Genetics 148:17431761.
134. Leis, J.,, D. Baltimore,, J. M. Bishop,, J. Coffin,, E. Fleissner,, S. P. Goff,, S. Oroszlan,, H. Robinson,, A. M. Skalka,, H. M. Temin,, and V. Vogt. 1988. Standardized and simplified nomenclature for proteins common to all retroviruses. J. Virol. 62:18081809.
135. Levin, H. L.,, D. C. Weaver,, and J. D. Boeke. 1993. Novel gene expression mechanism in a fission yeast retroelement: Tf1 proteins are derived from a single primary translation product. EMBO J. 12:48854895.
136. Liao, X. B.,, J. J. Clare,, and P. J. Farabaugh. 1987. The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element. Proc. Natl. Acad. Sci. USA 84:85208524.
137. Liebman, S. W.,, and G. Newnam. 1993. A ubiquitin-conjugating enzyme, RAD6, affects the distribution of Ty1 retrotransposon integration positions. Genetics 133:499508.
138. Loo, S.,, and J. Rine. 1995. Silencing and heritable domains of gene expression. Annu. Rev. Cell. Dev. Biol. 11:519548.
139. Luschnig, C.,, M. Hess,, O. Pusch,, J. Brookman,, and A. Bachmair. 1995. The gag homologue of retrotransposon Ty1 assembles into spherical particles in Escherichia coli. Eur. J. Biochem. 228:739744.
140. Lustig, A. J. 1998. Mechanisms of silencing in Saccharomyces cerevisiae. Curr. Opin. Genet. Dev. 8:233239.
141. Ma, W. P.,, and R. J. Crouch. 1996. Escherichia coli RNase HI inhibits murine leukaemia virus reverse transcription in vitro and yeast retrotransposon Ty1 transposition in vivo. Genes Cells 1:581593.
142. Madhani, H. D.,, and G. R. Fink. 1997. Combinatorial control required for the specificity of yeast MAPK signaling. Science 275:13141317.
143. Madhani, H. D.,, and G. R. Fink. 1998. The control of filamentous differentiation and virulence in fungi. Trends Cell. Biol. 8:348353.
144. Malim, M. H.,, S. E. Adams,, K. Gull,, A. J. Kingsman,, and S. M. Kingsman. 1987. The production of hybrid Ty:IFN virus-like particles in yeast. Nucleic Acids Res. 15:75717580.
145. Martin-Rendon, E.,, D. W. Hurd,, G. Marfany,, S. M. Kingsman,, and A. J. Kingsman. 1996. Identification of proteolytic cleavage sites within the Gag analogue protein of Ty1 virus-like particles. Mol. Microbiol. 22:10351043.
146. Martin-Rendon, E.,, G. Marfany,, S. Wilson,, D. J. Ferguson,, S.M. Kingsman,, and A. J. Kingsman. 1996. Structural determinants within the subunit protein of Ty1 virus-like particles. Mol. Microbiol. 22:667679.
147. Mastrangelo, M. F.,, K. G. Weinstock,, B. K. Shafer,, A. M. Hedge,, D. J. Garfinkel,, and J. N. Strathern. 1992. Disruption of a silencer domain by a retrotransposon. Genetics 131:519529.
148. Mathias, S. L.,, A. F. Scott,, H. H. Kazazian, Jr.,, J. D. Boeke,, and A. Gabriel. 1991. Reverse transcriptase encoded by a human transposable element. Science 254:18081810.
149. McClintock, B. 1984. The significance of responses of the genome to challenge. Science 226:792801.
150. Melamed, C.,, Y. Nevo,, and M. Kupiec. 1992. Involvement of cDNA in homologous recombination between Ty elements in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:16131620.
151. Mellor, J.,, A. M. Fulton,, M. J. Dobson,, N. A. Roberts,, W. Wilson,, A. J. Kingsman,, and S. M. Kingsman. 1985. The Ty transposon of Saccharomyces cerevisiae determines the synthesis of at least three proteins. Nucleic Acids Res. 13:62496263.
152. Mellor, J.,, M. H. Malim,, K. Gull,, M. F. Tuite,, S. McCready,, T. Dibbayawan,, S.M. Kingsman,, and A. J. Kingsman. 1985. Reverse transcriptase activity and Ty RNA are associated with virus-like particles in yeast. Nature 318:583586.
153. Merkulov, G. V.,, J. F. Lawler, Jr., Y. Eby, and J. D. Boeke. 2001. Ty1 proteolytic cleavage sites are required for retrotransposition: all sites are not created equal. J. Virol. 75:638644.
154. Merkulov, G. V.,, K. M. Swiderek,, C. B. Brachmann,, and J. D. Boeke. 1996. A critical proteolytic cleavage site near the C-terminus of the yeast retrotransposon Ty1 Gag protein. J. Virol. 70:55485556.
155. Monokian, G. M.,, L. T. Braiterman,, and J. D. Boeke. 1994. In-frame linker insertion mutagenesis of yeast transposon Ty1: mutations, transposition and dominance. Gene 139:918.
156. Moore, J. K.,, and J. E. Haber. 1996. Capture of retrotransposon DNA at the sites of chromosomal double- strand breaks. Nature 383:644646.
157. Moore, S. P.,, and D. J. Garfinkel. 2000. Correct integration of model substrates by Ty1 integrase. J. Virol. 74:1152211530.
158. Moore, S. P.,, and D. J. Garfinkel. 1994. Expression and partial purification of enzymatically active recombinant Ty1 integrase in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 91:18431847.
159. Moore, S. P.,, M. Powers,, and D. J. Garfinkel. 1995. Substrate specificity of Ty1 integrase. J. Virol. 69:46834692.
160. Moore, S. P.,, L. A. Rinckel,, and D. J. Garfinkel. 1998. A Ty1 integrase nuclear localization signal required for retrotransposition. Mol. Cell. Biol. 18:11051114.
161. 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. 20:57665776.
162. Morse, R. H. 2000. RAP, RAP, open up! New wrinkles for RAP1 in yeast. Trends Genet. 16:5153.
163. Mules, E. H.,, O. Uzun,, and A. Gabriel. 1998. In vivo Ty1 reverse transcription can generate replication intermediates with untidy ends. J. Virol. 72:64906503.
164. Mules, E. H.,, O. Uzun,, and A. Gabriel. 1998. Replication errors during in vivo Ty1 transposition are linked to heterogeneous RNase H cleavage sites. Mol. Cell. Biol. 18:10941104.
165. Muller, F.,, K. H. Bruhl,, K. Freidel,, K. V. Kowallik,, and M. Ciriacy. 1987. Processing of TY1 proteins and formation of Ty1 virus-like particles in Saccharomyces cerevisiae. Mol. Gen. Genet. 207:421429.
166. Muller, F.,, W. Laufer,, U. Pott,, and M. Ciriacy. 1991. Characterization of products of TY1-mediated reverse transcription in Saccharomyces cerevisiae. Mol. Gen. Genet. 226:145153.
167. Nam, K.,, R. H. Hudson,, K. B. Chapman,, K. Ganeshan,, M. J. Damha,, and J. D. Boeke. 1994. Yeast lariat debranching enzyme. Substrate and sequence specificity. J. Biol. Chem. 269:2061320621.
168. Natsoulis, G.,, and J. D. Boeke. 1991. New antiviral strategy using capsid-nuclease fusion proteins. Nature 352:632635.
169. Natsoulis, G.,, W. Thomas,, M. C. Roghmann,, F. Winston,, and J. D. Boeke. 1989. Ty1 transposition in Saccharomyces cerevisiae is nonrandom. Genetics 123:269279.
170. Naumov, G. I.,, E. S. Naumova,, R. A. Lantto,, E. J. Louis,, and M. Korhola. 1992. Genetic homology between Saccharomyces cerevisiae and its sibling species S. paradoxus and S. bayanus: electrophoretic karyotypes. Yeast 8:599612.
171. Nevo-Caspi, Y.,, and M. Kupiec. 1997. cDNA-mediated Ty recombination can take place in the absence of plus-strand cDNA synthesis, but not in the absence of the integrase protein. Curr. Genet. 32:3240.
172. Nevo-Caspi, Y.,, and M. Kupiec. 1996. Induction of Ty recombination in yeast by cDNA and transcription: role of the RAD1 and RAD52 genes. Genetics 144:947955.
173. Nevo-Caspi, Y.,, and M. Kupiec. 1994. Transcriptional induction of Ty recombination in yeast. Proc. Natl. Acad. Sci. USA 91:1271112715.
174. Nissley, D. V.,, P. L. Boyer,, D. J. Garfinkel,, S. H. Hughes,, and J. N. Strathern. 1998. Hybrid Ty1/HIV-1 elements used to detect inhibitors and monitor the activity of HIV-1 reverse transcriptase. Proc. Natl. Acad. Sci. USA 95:1390513910.
175. Nissley, D. V.,, D. J. Garfinkel,, and J. N. Strathern. 1996. HIV reverse transcription in yeast. Nature 380:30.
176. Nonet, M.,, C. Scafe,, J. Sexton,, and R. Young. 1987. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol. 7:16021611.
177. Palmer, K. J.,, W. Tichelaar,, N. Myers,, N. R. Burns,, S. J. Butcher,, A. J. Kingsman,, S. D. Fuller,, and H. R. Saibil. 1997. Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles. J. Virol. 71:68636868.
178. Petes, T. D.,, R. E. Malone,, and L. S. Symington,. 1991. Recombination in yeast, p. 407521. In J. Broach,, E. Jones,, and J. Pringle (ed.), The Molecular and Cellular Biology of the Yeast Saccharomyces, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
179. Picologlou, S.,, N. Brown,, and S. W. Liebman. 1990. Mutations in RAD6, a yeast gene encoding a ubiquitin-conjugating enzyme, stimulate retrotransposition. Mol. Cell. Biol. 10:10171022.
180. Pochart, P.,, B. Agoutin,, C. Fix,, G. Keith,, and T. Heyman. 1993. A very poorly expressed tRNA(Ser) is highly concentrated together with replication primer initiator tRNA(Met) in the yeast Ty1 virus-like particles. Nucleic Acids Res. 21:15171521.
181. Pochart, P.,, B. Agoutin,, S. Rousset,, R. Chanet,, V. Doroszkiewicz,, and T. Heyman. 1993. Biochemical and electron microscope analyses of the DNA reverse transcripts present in the virus-like particles of the yeast transposon Ty1. Identification of a second origin of Ty1 DNA plus strand synthesis. Nucleic Acids Res. 21:35133520.
182. Prakash, L. 1994. The RAD6 gene and protein of Saccharomyces cerevisiae. Ann. N. Y. Acad. Sci. 726:267273.
183. Preston, B. D.,, and J. P. Dougherty. 1996. Mechanisms of retroviral mutation. Trends Microbiol. 4:1621.
184. Pruss, D.,, F. D. Bushman,, and A. P. Wolffe. 1994. Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc. Natl. Acad. Sci. USA 91:59135917.
185. Qian, Z.,, H. Huang,, J. Y. Hong,, C. L. Burck,, S. D. Johnston,, J. Berman,, A. Carol,, and S. W. Liebman. 1998. Yeast Ty1 retrotransposition is stimulated by a synergistic interaction between mutations in chromatin assembly factor I and histone regulatory proteins. Mol. Cell. Biol. 18:47834792.
186. Rattray, A. J.,, B. K. Shafer,, and D. J. Garfinkel. 2000. The Saccharomyces cerevisiae DNA recombination and repair functions of the RAD52 epistasis group inhibit Ty1 transposition. Genetics 154:543556.
187. Rhim, H.,, J. Park,, and C. D. Morrow. 1991. Deletions in the tRNA(Lys) primer-binding site of human immunodeficiency virus type 1 identify essential regions for reverse transcription. J. Virol. 65:45554564.
188. Ribeiro-dos-Santos, G.,, A. C. Schenberg,, D. C. Gardner,, and S. G. Oliver. 1997. Enhancement of Ty transposition at the ADH4 and ADH2 loci in meiotic yeast cells. Mol. Gen. Genet. 254:555561.
189. Rinckel, L. A.,, and D. J. Garfinkel. 1996. Influences of histone stoichiometry on the target site preference of retrotransposons Ty1 and Ty2 in Saccharomyces cerevisiae. Genetics 142:761776.
190. Roeder, G. S.,, A. B. Rose,, and R. E. Pearlman. 1985. Transposable element sequences involved in the enhancement of yeast gene expression. Proc. Natl. Acad. Sci. USA 82: 54285432.
191. Sharon, G.,, T. J. Burkett,, and D. J. Garfinkel. 1994. Efficient homologous recombination of Ty1 element cDNA when integration is blocked. Mol. Cell. Biol. 14:65406551.
192. Simchen, G.,, F. Winston,, C. A. Styles,, and G. R. Fink. 1984. Ty-mediated gene expression of the LYS2 and HIS4 genes of Saccharomyces cerevisiae is controlled by the same SPT genes. Proc. Natl. Acad. Sci. USA 81:24312434.
193. Smith, J.,, E. Caputo,, and J. Boeke. 1999. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol. Cell. Biol. 19:31843197.
194. Smith, J. S.,, and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11: 241254.
195. Smith, J. S.,, C. B. Brachmann,, I. Celic,, M. A. Kenna,, S. Muhammad,, V. J. Starai,, J. L. Avalos,, J. C. Escalante-Semerena,, C. Grubmeyer,, C. Wolberger,, and J. D. Boeke. 2000. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 97:66586663.
196. Smith, J. S.,, C. B. Brachmann,, L. Pillus,, and J. D. Boeke. 1998. Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p. Genetics 149:12051219.
197. Smith, V.,, K. N. Chou,, D. Lashkari,, D. Botstein,, and P. O. Brown. 1996. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 274:20692074.
198. Sprague, G. F., Jr.,, and J. W. Thorner,. 1992. Pheromone response and signal transduction of Saccharomyces cerevisiae, p. 657744. In J. Broach,, E. Jones,, and J. Pringle (ed.), The Molecular and Cellular Biology of the Yeast Saccharomyces, vol. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
199. Stone, E. M.,, and L. Pillus. 1998. Silent chromatin in yeast: an orchestrated medley featuring Sir3p. Bioessays 20:3040.
200. Svejstrup, J. Q.,, P. Vichi,, and J. M. Egly. 1996. The multiple roles of transcription/repair factor TFIIH. Trends Biochem. Sci. 21:346350.
201. Tavis, J. E.,, and D. Ganem. 1993. Expression of functional hepatitis B virus polymerase in yeast reveals it to be the sole viral protein required for correct initiation of reverse transcription. Proc. Natl. Acad. Sci. USA 90:41074111.
202. Telesnitsky, A.,, and S. P. Goff,. 1997. Reverse transcriptase and the generation of retroviral DNA, p. 121160. In J. M. Coffin,, S. H. Hughes,, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
203. Teng, S. C.,, B. Kim,, and A. Gabriel. 1996. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383:641644.
204. Tumer, N. E.,, B. A. Parikh,, P. Li,, and J. D. Dinman. 1998. The pokeweed antiviral protein specifically inhibits Ty1-directed +1 ribosomal frameshifting and retrotransposition in Saccharomyces cerevisiae. J. Virol. 72:10361042.
205. Vega-Palas, M. A.,, S. Venditti,, and E. Di Mauro. 1997. Telomeric transcriptional silencing in a natural context. Nat. Genet. 15:232233.
206. Vogt, V. M., 1997. Retroviral virions and genomes, p. 2770. In J. M. Coffin,, S. H. Hughes,, and H. E. Varmus (ed.), Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
207. Voytas, D. F.,, and J. D. Boeke. 1992. Yeast retrotransposon revealed. Nature 358:717.
208. Voytas, D. F.,, and J. D. Boeke. 1993. Yeast retrotransposons and tRNAs. Trends Genet. 9:421427.
209. Wang, W.,, J. Cote,, Y. Xue,, S. Zhou,, P. A. Khavari,, S. R. Biggar,, C. Muchardt,, G. V. Kalpana,, S. P. Goff,, M. Yaniv,, J. L. Workman,, and G. R. Crabtree. 1996. Purification and biochemical heterogeneity of the mammalian SWI-SNFcomplex. EMBO J. 15:53705382.
210. Weinstock, K. G.,, M. F. Mastrangelo,, T. J. Burkett,, D. J. Garfinkel,, and J. N. Strathern. 1990. Multimeric arrays of the yeast retrotransposon Ty. Mol. Cell. Biol. 10:28822892.
211. Weissenbach, J.,, G. Dirheimer,, R. Falcoff,, J. Sanceau,, and E. Falcoff. 1977. Yeast tRNALeu (anticodon U—A—G) translates all six leucine codons in extracts from interferon treated cells. FEBS Lett. 82:7176.
212. Wilhelm, M.,, M. Boutabout,, T. Heyman,, and F. X. Wilhelm. 1999. Reverse transcription of the yeast Ty1 retrotransposon: the mode of first strand transfer is either intermolecular or intramolecular. J. Mol. Biol. 288:505510.
213. Wilhelm, M.,, M. Boutabout,, and F. X. Wilhelm. 2000. Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNaseHdomain exhibits polymerase and RNase H activities. Biochem. J. 2:337342.
214. Wilhelm, M.,, T. Heyman,, S. Friant,, and F. X. Wilhelm. 1997. Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts. Nucleic Acids Res. 25:21612166.
215. Wilhelm, M.,, F. X. Wilhelm,, G. Keith,, B. Agoutin,, and T. Heyman. 1994. Yeast Ty1 retrotransposon: the minus-strand primer binding site and a cis-acting domain of the Ty1 RNA are both important for packaging of primer tRNA inside virus-like particles. Nucleic Acids Res. 22:45604565.
216. Wilke, C. M.,, S. H. Heidler,, N. Brown,, and S. W. Liebman. 1989. Analysis of yeast retrotransposon Ty insertions at the CAN1 locus. Genetics 123:655665.
217. Wilson, W.,, M. H. Malim,, J. Mellor,, A. J. Kingsman,, and S. M. Kingsman. 1986. Expression strategies of the yeast retrotransposon Ty: a short sequence directs ribosomal frameshifting. Nucleic Acids Res. 14:70017016.
218. 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 39:675682.
219. Winston, F.,, and P. Sudarsanam. 1998. The SAGA of Spt proteins and transcriptional analysis in yeast: past, present, and future. Cold Spring Harb. Symp. Quant. Biol. 63:553561.
219.a. Xie, W.,, X. Gai,, Y. Zhu,, D. C. Zappulla,, R. Sternglanz,, and D. F. Voytas. 2001. Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol. Cell. Biol. 21:66066614.
220. Xu, H.,, and J. D. Boeke. 1987. High-frequency deletion between homologous sequences during retrotransposition of Ty elements in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 84:85538557.
221. Xu, H.,, and J. D. Boeke. 1990. Host genes that influence transposition in yeast: the abundance of a rare tRNA regulates Ty1 transposition frequency. Proc. Natl. Acad. Sci. USA 87:83608364.
222. Xu, H.,, and J. D. Boeke. 1991. Inhibition of Ty1 transposition by mating pheromones in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:27362743.
223. Xu, H.,, and J. D. Boeke. 1990. Localization of sequences required in cis for yeast Ty1 element transposition near the long terminal repeats: analysis of mini-Ty1 elements. Mol. Cell. Biol. 10:26952702.
224. Yoshioka, K.,, H. Honma,, M. Zushi,, S. Kondo,, S. Togashi,, T. Miyake,, and T. Shiba. 1990. Virus-like particle formation of Drosophila copia through autocatalytic processing. EMBO J. 9:535541.
225. Youngren, S. D.,, J. D. Boeke,, N. J. Sanders,, and D. J. Garfinkel. 1988. Functional organization of the retrotransposon Ty from Saccharomyces cerevisiae: Ty protease is required for transposition. Mol. Cell. Biol. 8:14211431.
226. Yu, G.,, and J. S. Fassler. 1993. SPT13 (GAL11) of Saccharomyces cerevisiae negatively regulates activity of the MCM1 transcription factor in Ty1 elements. Mol. Cell. Biol. 13:6371.
227. Yu, K.,, and R. T. Elder. 1989. Some of the signals for 3′-end formation in transcription of the Saccharomyces cerevisiae Ty-D15 element are immediately downstream of the initiation site. Mol. Cell. Biol. 9:24312444.
228. Zennou, V.,, C. Petit,, D. Guetard,, U. Nerhbass,, L. Montagnier,, and P. Charneau. 2000. HIV-1 genome nuclear import is mediated by a central DNA flap. Cell 101:173185.
229. Zhu, Y.,, S. Zou,, D. Wright,, and D. Voytas. 1999. Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p. Genes Dev. 13:27382749.
230. Zou, S.,, N. Ke,, J. M. Kim,, and D. F. Voytas. 1996. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 10:634645.
231. Zou, S.,, J. M. Kim,, and D. F. Voytas. 1996. The Saccharomyces retrotransposon Ty5 influences the organization of chromosome ends. Nucleic Acids Res. 24:48254831.
232. Zou, S.,, and D. F. Voytas. 1997. Silent chromatin determines target preference of the Saccharomyces retrotransposon Ty5. Proc. Natl. Acad. Sci. USA 94:74127416.
233. Zou, S.,, D. A. Wright,, and D. F. Voytas. 1995. The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR. Proc. Natl. Acad. Sci. USA 92:920924.

Tables

Generic image for table
Table 1

Ty1-encoded protein nomenclature

Citation: Voytas D, Boeke J. 2002. Ty1 and Ty5 of Saccharomyces cerevisiae, p 631-662. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch26