Retrotransposable elements in the Dictyostelium discoideum genome

Cellular and Molecular Life Sciences

Volumn 54, Issue 5, 1998, Pages 383-393

  Winckler, T ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

Dictyostelium; Evolution; Repetitive DNA; Retrotransposon; Review; tRNA gene

Indexed keywords

REPETITIVE DNA; TRANSFER RNA;

DICTYOSTELIUM DISCOIDEUM; GENOME; NONHUMAN; RETROPOSON; REVIEW;

ANIMALS; DICTYOSTELIUM; DNA, FUNGAL; DNA, PROTOZOAN; REPETITIVE SEQUENCES, NUCLEIC ACID; RETROELEMENTS; RNA, TRANSFER;

EID: 0031835901     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s000180050168     Document Type: Review

References (73)

1. Doolittle R. and Sapienza C. (1980) Selfish genes, the phenotypic paradigm and genome evolution. Nature 284: 601-603
2. Orgel L. and Crick F. (1980) Selfish DNA: the ultimate parasite. Nature 284: 604-607
3. McDonald J. (1993) Evolution and consequences of transposable elements. Curr. Opin. Genet. Dev. 3: 855-864
4. Kidwell M. and Lisch D. (1997) Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94: 7704-7711
5. Devine S., Chissoe S., Eby Y., Wilson R. and Boeke J. (1997) A transposon-based strategy for sequencing repetitive DNA in eukaryotic genomes. Genome Res. 7: 551-563
6. Hodgson C. (1996). Retro-vectors for Human Gene Therapy, R. G. Landes Company, Austin, Texas
7. Varmus H. and Brown P. (1989). Retroviruses. In: Mobile DNA, pp. 53-108, Howe M. M. and Berg D. E. (eds), American Society for Microbiology, Washington, DC
8. Katz R. and Skalka A. (1994) The retroviral enzymes. Ann. Rev. Biochem. 63: 133-173
9. Sandmeyer S. (1992) Yeast retrotransposons. Curr. Opin. Genet. Dev. 2: 705-711
10. Smit A. F. A. (1996) The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748
11. Boeke J. D. (1997) LINEs and Alus - the polyA connection. Nat. Genet. 16: 6-7
12. Boeke J. and Corces V. (1989) Transcription and reverse transcription of retrotransposons. Ann. Rev. Microbiol. 43: 403-434
13. Boeke J. and Chapman K. (1991) Retrotransposition mechanisms. Curr. Opin. Cell Biol. 3: 502-507
14. Pryciak P. and Varmus H. (1992) Nucleosomes, DNA-binding proteins and DNA sequence modulate retroviral integration target site selection. Cell 69: 769-780
15. Eickbush T. (1992) Transposing without ends: the non-LTR retrotransposable elements. New Biol. 4: 430-440
16. Xiong Y. and Eickbush T. (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-3362
17. Michel F. and Ferat J. (1995) Structure and activities of group II introns. Ann. Rev. Biochem. 64: 435-461
18. Moran J., Zimmerly S., Eskes R., Kennell J., Lambowitz A., Butow R. et al. (1995) Mobile group II introns of yeast mitochondrial DNA are novel site-specific retroelements. Mol. Cell. Biol. 15: 2828-2838
19. Mizrokhi L., Georgieva S. and Ilyin Y. (1988) jockey, a mobile Drosophila element similar to mammalian LINEs, is transcribed from the internal promoter by RNA polymerase II. Cell 54: 685-691
20. Swergold G. (1990) Identification, charaterization, and cell specificity of a human LINE-1 promoter. Mol. Cel. Biol. 10: 6718-6729
21. Minchiotti G. and Di Nocera P. (1991) Convergent transcription initiates from oppositely oriented promoters within the 5′ end regions of Drosophila melanogaster F elements. Mol. Cell. Biol. 11: 5171-5180
22. McLean C., Bucheton A. and Finnegan D. (1993) The 5′ untranslated region of the I factor, a long interspersed nuclear element-like retrotransposon of Drosophila melanogaster, contains an internal promoter and sequences that regulate expression. Mol. Cell. Biol. 13: 1042-1050
23. Luan D., Korman M., Jakubczak J. and Eickbush T. (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595-605
24. Martín F., Marañón C., Olivares M., Alonso C. and López C. (1995) Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the Ape family of DNA repair enzymes. J. Mol. Biol. 247: 49-59
25. Feng Q. M., Moran J. V., Kazazian H. H. and Boeke J. D. (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905-916
26. Zimmerly S., Guo H., Perlman P. and Lambowitz A. (1995) Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82: 545-554
27. Zimmerly S., Guo H., Eskes R., Yang L., Perlman P. and Lambowitz A. (1995) A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83: 529-538
28. Loomis W. F. and Smith D. W. (1995) Consensus phylogeny of Dictyostelium. Experientia 51: 1110-1115
29. Marx K. A., Hess S. T. and Blake R. D. (1993) Characteristics of the large (dA)(dT) homopolymer tracts in D. discoideum gene flanking and intron sequences. J. Biomol. Struct. Dyn. 11: 57-66
30. Kuspa A., Dingermann T. and Nellen W. (1995) Analysis of gene function in Dictyostelium. Experientia 51: 1116-1123
31. Reymond C. D., Schaap P., Veron M. and Williams J. G. (1995) Dual role of cAMP during Dictyostelium development. Experientia 51: 1166-1174
32. Van Haastert P. J. M. (1995) Transduction of the chemotactic cAMP signal across the plasma membrane of Dictyostelium cells. Experientia 51: 1144-1154
33. Chen M. Y., Insall R. H. and Devreotes P. N. (1996) Signaling through chemoattractant receptors in Dictyostelium. Trends Genet. 12: 52-57
34. Gross J. D. (1994) Developmental decisions in Dictyostelium discoideum. Microbiol. Rev. 58: 330-351
35. Firtel R. A. (1995) Integration of signaling information in controlling cell fate decisions in Dictyostelium. Genes Devel. 9: 1427-1444
36. Loomis W. F. (1996) Genetic networks that regulate development in Dictyostelium cells. Microbiol. Rev. 60: 135
37. Schaap P., Tang Y. H. and Othmer H. G. (1996) A model for pattern formation in Dictyostelium discoideum. Differentiation 60: 1-16
38. Zuker C. and Lodish H. F. (1981) Repetitive DNA sequences cotranscribed with developmentally regulated Dictyostelium mRNAs. Proc. Natl. Acad. Sci. USA 78: 5386-5390
39. Zuker C., Cappello J., Chisholm R. L. and Lodish H. F. (1983) A repetitive Dictyostelium gene family that is induced during differentition and by heat shock. Cell 34: 997-1005
40. Rosen E., Sivertsen A. and Firtel R. A. (1983) An unusual transposon encoding heat shock inducible and developmentally regulated transcripts in Dictyostelium. Cell 35: 243-251
41. Cappello J., Handelsman K. and Lodish H. F. (1985) Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence. Cell 43: 105-115
42. Zuker C., Cappello J., Lodish H. F., George P. and Chung S. (1984) Dictyostelium transposable element DIRS-1 has 350-base-pair inverted terminal repeats that contain a heat shock promoter. Proc. Natl. Acad. Sci. USA 81: 2660-2664
43. Cappello J., Zuker C. and Lodish H. F. (1984) Repetitive Dictyostelium heat-shock promoter functions in Saccharomyces cerevisiae. Mol. Cell. Biol. 4: 591-598
44. Cohen S. M., Cappello J., Zuker C. and Lodish H. F. (1984) Transcription of DIRS-1, an unusual Dictyostelium transposable element. In: Molecular Biology of Development, pp. 491-508, Davidson E. H. and Firtel R. A. (eds), A. R. Liss, New York
45. Cappello J., Cohen S. M. and Lodish H. F. (1984) Dictyostelium transposable element DIRS-1 preferentially inserts into DIRS-1 sequences. Mol. Cell. Biol. 4: 2207-2213
46. 45a Leng P., Klatte D. H., Schumann G., Boeke J. and Steck T. L. (1998) Identification of skipper, a novel retrotransposon in Dictyostelium. Nucleic Acids Res., in press
47. Kim S. (1976) Three-dimensional structure of transfer RNA. In: Progress in Nucleic Acids Research and Molecular Biology, pp. 181-216, Cohn W. (ed.), Academic Press, New York
48. Geiduschek E. and Tocchini-Valentini G. (1988) Transcription by polymerase III. Ann. Rev. Biochem. 57: 873-914
49. Willis I. (1993) RNA polymerase III: genes, factors and transcriptional specificity. Eur. J. Biochem. 212: 1-11
50. Marschalek R. and Dingermann T. (1991) Structure, organization and function of transfer RNA genes from the cellular slime mold Dictyostelium discoideum. Adv. Gene Technol. 2: 103-143
51. Bukenberger M., Dingermann T., Meissner W., Seifart K. H. and Winckler T. (1994) Isolation of transcription factor IIIC from Dictyostelium discoideum. Eur. J. Biochem. 220: 839-846
52. Pazin M., Bhargava P., Geiduschek E. and Kadonaga J. (1997) Nucleosome mobility and the maintenance of nucleosome positioning. Science 276: 809-812
53. Marschalek R., Brechner T., Amon-Böhm E. and Dingermann T. (1989) Transfer RNA genes: landmarks for integration of mobile genetic elements in Dictyostelium discoideum. Science 244: 1493-1496
54. Hofmann J., Schumann G., Borschet G., Gosseringer R., Bach M., Bertling W. M. et al. (1991) Transfer RNA genes from Dictyostelium discoideum are frequently associated with repetitive elements and contain consensus boxes in their 5′-flanking and 3′-flanking regions. J. Mol. Biol. 222: 537-552
55. Marschalek R., Hofmann J., Schumann G. and Dingermann T. (1992) Two distinct subforms of the retrotransposable DRE element in NC4 strains of Dictyostelium discoideum. Nucleic Acids Res. 20: 6247-6252
56. Marschalek R., Hofmann J., Schumann G., Gösseringer R. and Dingermann T. (1992) Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes. Mol. Cell. Biol. 12: 229-239
57. Marschalek R., Hofmann J., Schumann G., Bach M. and Dingermann T. (1993) Different organization of the transfer RNA-gene-associated repetitive element, DRE, in NC4-derived strains and in other wild-type Dictyostelium discoideum strains. Eur. J. Biochem. 217: 627-631
58. Schumann G., Zündorf I., Hofmann J., Marschalek R. and Dingermann T. (1994) Internally located and oppositely oriented polymerase II promoters direct convergent transcription of a LINE-like retroelement, the Dictyostelium Repetitive Element, from Dictyostelium discoideum. Mol. Cell. Biol. 14: 3074-3084
59. McMillan J. and Singer M. (1993) Translation of the human LINE-1 element, L1Hs. Proc. Natl. Acad. Sci. USA 90: 11533-11537
60. Hildebrandt M. and Nellen W. (1992) Differential antisense transcription from the Dictyostelium EB4 gene locus implications on antisense-mediated regulation of messenger RNA stability. Cell 69: 197-204
61. Geier A., Horn J., Dingermann T. and Winckler T. (1996) Nuclear protein factor binds specifically to the 3′-regulatory module of the long-interspersed-nuclear-element-like Dictyostelium repetitive element. Eur. J. Biochem. 241: 70-76
62. Hori R. and Firtel R. A. (1994) Identification and characterization of multiple A/T-rich cis-acting elements that control expression from Dictyostelium actin promoters: the Dictyostelium actin upstream activating sequence confers growth phase expression and has enhancer-like properties. Nucleic Acids Res. 22: 5099-5111
63. Poole S. J. and Firtel R. A. (1984) Genomic instability and mobile genetic elements in regions surrounding two discoidin I genes of Dictyostelium discoideum. Mol. Cell. Biol. 4: 671-680
64. Marschalek R., Borschet G. and Dingermann T. (1990) Genomic organization of the transposable element Tdd-3 from Dictyostelium discoideum. Nucleic Acids Res. 18: 5751-5757
65. Firtel R. (1989). Mobile genetic elements in the cellular slime mold Dictyostelium discoideum. In: Mobile DNA, pp. 557-566, Howe M. M. and Berg D. E. (eds). American Society for Microbiology, Washington, DC
66. Winckler T., Tschepke C., de Hostos E., Jendretzke A. and Dingermann T. (1997) Tdd-3, a transfer RNA gene-associated poly(A) retrotransposon from Dictyostelium discoideum. Mol. Gen. Genet., in press
67. Brodeur G., Sandmeyer S. and Olson M. (1983) Consistent association between sigma elements and tRNA genes in yeast. Proc. Natl. Acad. Sci. USA 80: 3292-3296
68. Perreau V., Santos M. and Tuite M. (1997) beta, a novel repetitive DNA element associated with tRNA genes in the pathogenic yeast Candida albicans. Mol. Microbiol. 25: 229-236
69. Roeder G. and Fink G. (1980) DNA rearrangements associated with a transposable element in yeast. Cell 21: 239-249
70. Voytas D. and Boeke J. (1993) Yeast retrotransposons and tRNAs. Trends in Genet. 9: 421-427
71. Voytas D. (1996) Retroelements in genome organization. Science 274: 737-738
72. Kirchner J., Conolly C. and Sandmeyer S. (1995) Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267: 1488-1491
73. Connolly C. and Sandmeyer S. (1997) RNA polymerase III interferes with Ty3 integration. FEBS Lett. 405: 305-311