Unusual features of the urodele genome: Do they have a role in evolution and development?

International Journal of Developmental Biology

Volumn 40, Issue 4, 1996, Pages 637-643

  Vignali, Robert ^a,b   Nardi, Irma ^b  

^a Laboratori di Biologia Cellulare e dello Sviluppo   (Italy)

^b UNIVERSITY OF PISA   (Italy)

Author keywords

Development; Evolution; Genome; Repeated DNA; Urodeles

Indexed keywords

DNA; REPETITIVE DNA;

CHROMOSOME; EVOLUTION; GENOME; KARYOTYPE; LIZARD; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; REVIEW;

ANIMALS; DNA; EVOLUTION, MOLECULAR; REPETITIVE SEQUENCES, NUCLEIC ACID; RETROELEMENTS; URODELA;

EID: 0029816007     PISSN: 02146282     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (98)

1. ANDRONICO, F., DE LUCCHINI, S., GRAZIANI, F., NARDI, I., BATISTONI, R. and BARSACCHI-PILONE, G (1985). Molecular organization of ribosomal RNA genes clustered at variable chromosomal sites in Trituras vulgaris meridionalis (Amphibia, Urodela). J. Mol. Biol 186. 219-229
2. ARNHEIM, N (1983). Concerted evolution of multigene families. In Evolution of Genes and Proteins (Eds. R. Koehn and M. Nei) Sinauer, Sunderland, pp 38-61.
3. ARNHEIM, N , KRYSTAL, M , SCHMICKEL, R., WILSON, G , RYDER, O. and ZIMMER, E. (1980) Molecular evidence for genetic exchanges among ribosomal genes on nonhomologous chromosomes in man and apes Proc. Natl. Acad. Sci. USA 77: 7323-7327.
4. BALDWIN, L and MACGREGOR, H.C. (1985). Centromeric satellite DNA in the newt Triturus cristatus karelinii and related species: its distribution and transcription on lampbrush chromosomes. Chromosoma 92. 100-107.
5. BANVILLE, D. and BOIE, Y. (1989). Retroviral long terminal repeat is the promoter of the gene encoding the tumor-associated calcium-binding protein oncomodulin in the rat. J Mol Biol 207: 481-490.
6. BARSACCHI, G. (1991). Satellite DNA in the newts (Amphibia, Urodela). In Symposium on the Evolution of Terrestrial Vertebrates (Eds. G. Ghiara, F. Angelini, E. Olmo and L. Varano) Selected Symposia and Monographs U.Z.I., Vol. 4. Mucchi, Modena, 1991, pp 171-198
7. BARSACCHI-PILONE, G., BATISTONI, R., ANDRONICO, F., VITELLI, L. and NARDI, I. (1986). Heterochromatic DNA in Triturus (Amphibia, Urodela). I. A satellite DNA component of the pericentric C-bands Chromosoma 93. 435-446
8. BATISTONI, R , NARDI, I., REBECCHI, L., NARDONE, M. and DEMARTIS, A. (1991). A centromeric satellite DNA in the European Plethodontid salamanders (Amphibia, Urodela). Genome 34: 1007-1012.
9. BATISTONI, R , PESOLE, G., MARRACCI, S and NARDI, I (1995). A tandemly repeated DNA family originated trom SINE-related elements in the European Plethodontid salamanders (Amphibia, Urodela). J. Mol. Evol. 40. 608-615.
10. BATISTONI, R , VIGNALI, R., NEGRONI, A., CREMISI, F. and BARSACCHIPILONE, G. (1986). A highly repetitive DNA family is dispersed in small clusters throughout the Triturus genome. Cell Biol. Int. Rep 10: 486
11. BENNETT, M.D (1932). Nucleotypic basis of the spatial ordering of chromosomes in eukaryotes and the implications of the order for genome evolution and phenotypic variation. In Genome Evolution (Eds. G.A. Dover and R.B. Flavell). Academic Press, London, pp. 239-261.
12. BRITTEN, R.J and DAVIDSON, E.H. (1971). Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q. Rev. Biol. 46: 111-138.
13. BRITTEN, R.J and KOHNE, D E. (1968). Repeated sequences in DNA. Science 161: 529-540.
14. BROWN, D.D. and DAWID, I.B. (1968). Specific gene amplification in oocytes. Science 160. 272-280.
15. CALLAN, H.G. (1982). Lampbrush chromosomes. Proc. R. Soc. Lond. Ser. B 214: 417-448.
16. CALLAN, H.G. (1991). Centromere fusions and telomere fusions during meiosis in Amphibia. In Amphibian Cytogenetics and Evolution (Eds. D.M. Green and S K. Sessions) Academic Press, San Diego, pp. 217-231.
17. CAVALIER-SMITH, T. (Ed) (1985). Cell volume and the evolution of eukaryote genome size. In The Evolution of Genome Size. John Wiley & Sons, Chichester, pp. 105-184.
18. CHARLESWORTH, B., SNIEGOWSKI, P. and STEPHAN, W. (1994). The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220.
19. CHO, K., MINSK, B. and WAGNER, J.A. (1990) NICER elements: a family of nerve growth factor-inducible cAMP-extinguishable retrovirus-like elements. Proc. Natl. Acad. Sci. USA 87: 3778-3782.
20. CREMISI, F., SCARABINO, D., CARLUCCIO, M A., SALVADORI, P. and BARSACCHI, G. (1992). A newt ribozyme: a catalyse activity in search of a function. Proc. Natl. Acad. Sci. USA 89: 1651-1555.
21. CREMISI, F , VIGNALI, R . BATISTONI, R and BARSACCHI, G. (1988). Heterochromatic DNA in Triturus (Amphibia, Urodela) II. A centromeric satellite DNA. Chromosoma 97. 204-211.
22. DE LUCCHINI, S., ANDRONICO, F., ANDREAZZOLI, M , GIULIANI, M., SAVINO, R. and NARDI, I. (1988) Extra-ribosomal spacer sequences in Triturus. J Mol Biol. 204: 805-813.
23. DE LUCCHINI, S , NARDI, I., BARSACCHI, G., BATISTONI, R. and ANDRONICO, F. (1993). Molecular cytogenetics of the ribosomal (18S + 28S and 5S) DNA loci in primitive and advanced urodele amphibians Genome 35 762-773
24. DEGROOTE, F., PONT, G., MICARD, D. and PICARD, G. (1989) Extrachromosomal circular DNAs in Drosophila melanogaster: comparison between embryos and Kc0% cells Chromosoma 98: 201-206.
25. DIAZ, M.O. BARSACCHI-PILONE G , MAHON, K A and GALL, J.G. (1981) Transcripts from both strands of a satellite DNA occur on lampbrush chromosome loops of the newt Notophthalmus Cell 24: 649-659.
26. DOLLÉ, P., DIERICH, A., LeMEUR, M , SCHIMMANG, T , SCHUHBAUR, B., CHAMBON, P and DUBOULE, D. (1993). Disruption of the Hoxd-13 gene induces localized heterochrony leading to mice with neotenic limbs. Cell 75: 431-441.
27. DOOLITTLE, W F (1982). Selfish DNA after fourteen months. In Genome Evolution (Eds G A. Dover and R.B. Flavell) Academic Press London, pp. 3-28.
28. DOOLITTLE, W.F. and SAPIENZA, C (1980). Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.
29. DORER, D.R. and HENIKOFF, S. (1994). Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77: 993-1002.
30. DOVER, G A (1980). Ignorant DNA? Nature 285: 618-620.
31. DOVER, G.A. (1982). Molecular drive: a cohesive mode of species evolution. Nature 299: 111-117.
32. DOVER, G.A (1986). Molecular drive in multigene families: how biological novelties arise, spread and are assimilated. Trends Genet. 2: 159-165.
33. DOVER, G A (1987) DNA turnover and the molecular clock. J. Mol. Evol. 26. 47-58.
34. DOVER, G.A. (1993). Evolution of genetic redundancy for advanced players. Curr. Opin. Genet. Dev. 3. 902-910.
35. DOVER, G.A., BROWN, S.D.M , COEN, E.S., DALLAS, J , STRACHAN, T. and TRICK, M. (1982). The dynamics of genome evolution and species differentiation. In Genome Evolution (Eds. G.A. Dover and R.B. Flavell). Academic Press, London, pp. 343-374.
36. ENDOH, H. and OKADA, N (1986). Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc. Natl. Acad. Sci. USA 83: 251-255.
37. EPSTEIN, L.M. and COATS, S.R (1991). Tissue-specific permutations of self-cleaving newt satellite-2 transcripts. Gene 107: 213-218.
38. EPSTEIN, L.M and GALL, J.G. (1987a). Self-cleaving transcripts of satellite DNA from the newt. Cell 48: 535-543.
39. EPSTEIN, L.M. and GALL, J.G. (1987b) Transcripts of newt satellite DNA self-cleave in vitro. Cold Spring Harbor Symp. Quant Biol. 52: 261-265.
40. EPSTEIN, L.M., MAHON, K.A and GALL, J.G. (1986). Transcription of a satellite DNA in the newt J. Cell Biol 103. 1137-1144.
41. FINNEGAN, D.J. (1992). Transposable elements. Curr. Opin. Genet Dev. 2: 861-867.
42. GALL, J.G. (1981) Chromosome structure and the C-value paradox. J. Cell Biol. 91: 3s-14s.
43. GOIN, O B., GOIN, C J and BACHMANN, K (1968). DNA and amphibian life history. Copeia 1968: 532-540
44. GREENE, J.M., OTANI, H., GOOD, P.J. and DAWID, I B. (1993). A novel family of retrotransposon-like elements in Xenopus laevis with a transcript inducible by two growth factors Nucleic Acids Res 21: 2375-2381.
45. HANKELN, T., ROHWEDDER, A , WEICH, B and SCHMIDT, E.R. (1994). Transposition of minisatellite-like DNA in Chironomus midges. Genome 37: 542-549.
46. HORNER, H A. and MACGREGOR, H.C. (1983). C value and cell volume: their significance in the evolution and development of amphibians. J. Cell Sci. 63: 135-146
47. JEFFREYS, A.J., WILSON, V. and THEIN, S.L. (1985). Hypervariable 'minisatellite' regions in human DNA Nature 314: 67-73
48. KRYSTAL, M., D'EUSTACHIO, P., RUDDLE F.H. and ARNHEIM, N (1981). Human nucleolus organizers on nonhomologous chromosomes can share the same ribosomal gene variants Proc. Natl. Acad. Sci. USA 78: 5744-5748.
49. KUHL, D.P.A. and C T CASKEY (1993) Trinucleotide repeats and genome variation. Curr Opin. Genet. Dev 3: 404-407
50. LEVINSON, G and GUTMAN, G A (1987). Slipped-strand mispairing: a major mechanism for DNA sequence evolution Mol. Biol Evol. 4: 203-221
51. MACGREGOR, H.C. (1982). Big chromosomes and speciation amongst Amphibia in Genome Evolution (Eds G.A Dover and R.B. Flavell) Academic Press, London, pp 325-341
52. MACGREGOR, H.C , VARLEY, J.M. and MORGAN, G.T. (1981). The transcription of satellite and ribosomal DNA sequences on lampbrush chromosomes of crested newts In International Cell Biology 1980-81 (Ed. H.G. Schweiger) Springer, Berlin, Heidelberg, New York, pp 33-46.
53. MACKAY, T. (1986). Transposable element-induced fitness mutations in Drosophila melanogaster Genet. Res 48: 77-87.
54. MANCINO, G , RAGGHIANTI, M. and BUCCI-INNOCENTI, S. (1977).Cytotaxonomy and cytogenetics in European newt species. In The Reproductive Biology of Amphibians (Eds D.H. Taylor and S.I Guttman). Plenum Press, New York, pp. 411-447
55. MARRACCI, S , BATISTONI, R , PESOLE, G., CITTI, L. and NARDI, I. (1996). Gypsy/ Ty-3-like elements in the genome of the terrestrial salamander Hydromantes (Amphibia, Urodela). J. Mol. Evol. (In press).
56. MARTIN, C.C. and GORDON, R. (1995). Differentiation trees, a junk DNA molecular clock, and the evolution of neoteny in salamanders. J. Evol. Biol. 8: 339-354
57. MARTIN, S.L. (1991). LINEs. Curr. Opin. Genet. Dev. 1: 505-508.
58. McDONALD, J.F. (1993). Evolution and consequences of transposable elements. Curr. Opin. Genet. Dev. 3: 855-864.
59. MIKLOS, G.L.G. (1985). Localized highly repetitive DNA sequences in vertebrate and invertebrate genomes. In Molecular Evolutionary Genetics (Ed. R.J MacIntyre). Plenum Press, New York, pp. 241-321.
60. MIZUNO, S. and MACGREGOR, H.C. (1974). Chromosomes, DNA sequences, and evolution in salamanders of the genus Plethodon. Chromosoma 48: 239-296.
61. MORESCALCHI, A. (1975). Chromosome evolution in the caudate Amphibia. In Evolutionary Biology, Vol. 8 (Eds. T.H. Dobzhansky, M.K. Hecht and W C. Steere). Plenum Press, New York, pp. 339-387.
62. MORESCALCHI, A. (1992). Structural and molecular approaches to the phylogeny of Amphibia. Boll. Zool. 59: 23-31.
63. MOZER, B.A. and BENZER, S. (1994). Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain. Development 120: 1049-1058.
64. Glu in the newt. J. Mol. Biol. 222: 391-404.
65. NARDI, I. (1991). Cytogenetics of the European Plethodontid salamanders, genus Hydromantes. In Amphibian Cytogenetics and Evolution (Eds. D.M. Green and S.K. Sessions). Academic Press, San Diego, pp. 131-156.
66. NARDI, I., BARSACCHI-PILONE, G., BATISTONI, R. and ANDRONICO, F. (1977). Chromosome location of the ribosomal RNA genes in Triturus vulgaris meridionalis (Amphibia, Urodela). II. Intraspecific variability in number and position of the chromosome loci for 18S + 28S ribosomal RNA. Chromosoma 64: 67-84.
67. NOWAK, R. (1994). Mining treasures from "junk-DNA". Science 263: 608-610.
68. OELDORF, E., NISHIOKA, M. and BACHMANN, K. (1978). Nuclear DNA amounts and developmental rate in holarctic anura. Z. Zool. Syst. Evol. Forsch. 16. 216-224.
69. OHNO, S (1972). So much 'junk' DNA in our genome. In Evolution of Genetic Systems (Ed. H.H. Smith). Brookhaven Symposium in Biology, Vol. 23. Gordon and Breach, New York, pp. 366-370.
70. OKADA, N. (1991). SINEs. Curr. Opin. Genet Dev. 1: 498-504.
71. OLMO, E. (1991) Genome variations in the transition from amphibians to reptiles. J. Mol. Evol. 33: 68-75.
72. OLMO, E. and MORESCALCHI, A. (1975). Evolution of the genome and cell sizes in salamanders. Experientia 31: 804-806.
73. OLMO, E. and MORESCALCHI, A (1978). Genome and cell size in frogs: a comparison with salamanders. Experientia 34: 44-46.
74. ORGEL, L.E and CRICK, F.H.C. (1980). Selfish DNA: the ultimate parasite. Nature 284: 604-606.
75. PAGEL, M. and JOHNSTONE, R.A. (1992). Variation across species in the size of the nuclear genome supports the junk-DNA explanation for C-value paradox Proc. R. Soc. Lond B 249: 119-124.
76. PASERO, P., SJAKSTE, N., BLETTRY, C., GOT, C. and MARILLEY, M. (1993). Long-range organization and sequence-directed curvature of Xenopus laevis satellite 1 DNA. Nucleic Acids Res. 21: 4703-4710.
77. PASYUKOVA, E G., BELYAEVA, E. Sp., KOGAN, G.L., KAIDANOV, L.Z. and GVOZDEV, V.A. (1986). Concerted transpositions of mobile genetic elements coupled with fitness changes in Drosophila melanogaster. Mol Biol. Evol. 3: 299-312.
78. PONT, G , DEGROOTE, F and PICARD, G (1987). Some extrachromosomal circular DNAs from Drosophila embryos are homologous to tandemly repeated genes. J Mol. Biol 195: 447-451.
79. RENAULT, S., DEGROOTE, F. and PICARD, G. (1993). identification of short tandemly repeated sequences in extrachromosomal circular DNAs from Drosophila melanogaster embryos. Genome 36: 244-254.
80. SCHIFF, R., ITIN, A. and KESHET, E. (1991). Transcription activation of mouse retrotransposons in vivo: specific expression in steroidogenic cells in response to trophic hormones. Genes Dev. 5: 521-532.
81. SCHMID, M., STEINLEIN, C., NANDA, I. and EPPLEN, J.T. (1990). Chromosome banding in Amphibia. In Cytogenetics of Amphibians and Reptiles (Ed. E. Olmo) ALS, Birkhauser Verlag, Basel, pp. 21-45.
82. SESSIONS, S.K. and LARSON, A. (1987). Developmental correlates of genome size in Plethodontid salamanders and their implications for genome evolution Evolution 41: 1239-1251.
83. SMITH, G.P. (1973). Unequal crossover and the evolution of multigene families. Cold Spring Harbor Symp. Quant. Biol. 38: 507-513.
84. SMITH, G.P. (1976). Evolution of repeated DNA sequences by unequal crossovers. Science 191: 528-535.
85. SMITH, G.R. (1983). Chi hotspots of generalized recombination. Cell 34: 709-710.
86. SMITH, G.R. (1991) Conjugational recombination in E coli: myths and mechanisms. Cell 64: 19-27.
87. STAVENHAGEN, J.B and ROBINS, D.M. (1988). An ancient provirus has imposed androgen regulation on the adjacent Mouse Sex-Limited Protein gene. Cell 55: 247-255.
88. STRAUSS, N.A. (1971). Comparative DNA renaturation kinetics in amphibians. Proc. Natl. Acad. Sci. USA 68: 799-802.
89. THOMAS, C A. (1971).The genetic organization of chromosomes. Annu. Rev. Genet. 5: 237-256.
90. VARLEY, J.M., MACGREGOR, H.C. and BARNETT, L. (1990). Characterisation of a short highly repeated and centromerically localised DNA sequence in crested and marbled newts of the genus Triturus. Chromosoma 100. 15-31
91. VARLEY, J.M., MACGREGOR, H.C. and ERBA, H P. (1980a) Satellite DNA is transcribed on lampbrush chromosomes. Nature 283. 686-688.
92. VARLEY, J.M., MACGREGOR, H.C , NARDI, I., ANDREWS, C and ERBA, H P (1980b). Cytological evidence of transcription of highly repeated DNA sequences during the lampbrush stage in Triturus cristatus carnifex. Chromosoma 80: 289-307.
93. VIGNALI, R., RIJLI, F.M , BATISTONI, R., FRATTA, D., CREMISI, F. and BARSACCHI, G. (1991). Two dispersed highly repeated DNA families of Triturus vulgaris meridionalis (Amphibia, Urodela) are widely conserved among Salamandridae. Chromosoma 100: 87-96.
94. VOGT, P. (1992). Code domains in tandem repetitive DNA sequence structures. Chromosoma 101. 585-589.
95. VOYTAS, D.F. and BOEKE, J D. (1993). Yeast retrotransposons and tRNAs. Trends Genet. 9: 421-427.
96. WAHLS, W.P., WALLACE, L.J. and MOORE, P.D. (1990) Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells Cell 60: 95-103.
97. WHITEHOUSE, H.L.K (1982). Genetic Recombination. Understanding the Mechanisms. John Wiley, New York.
98. WU, Z. (1987). Satellite DNA from the Chinese fat newt, Pachytriton brevipes, and related species. Sci. Rep Amphibian Biol. Hiroshima Univ. 9: 239-259.