Recent evidence for the Exon Theory of Genes

Genetica

Volumn 118, Issue 2-3, 2003, Pages 251-266

  Roy, Scott William ^a  

^a NONE   (United States)

Author keywords

Evolution; Introns early; Introns late

Indexed keywords

EVOLUTION, MOLECULAR; EXONS; INTRONS; MODELS, GENETIC;

EUKARYOTA;

EID: 0037629718     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1024190617462     Document Type: Review

References (52)

1. Blake, C.C.F., 1978. Do genes-in-pieces imply proteins-in-pieces? Nature 273: 267.
2. Blake, C., 1983. Introns - present from the beginning? Nature 306: 535-537.
3. Boedtker, H. & S. Aho, 1984. Collagen gene structure - the paradox may be resolved. Biochem. Soc. Symp. 49: 67-85.
4. Brenner, S.E., C. Chothia & T.L. Hubbard, 1998. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. PNAS 95(11): 6073-6078.
5. Cavalier-Smith, T., 1985. Selfish DNA and the origin of introns. Nature 315: 283-284.
6. Cho, G. & R.F. Doolittle, 1997. Intron distribution in ancient paralogs supports random insertion and not random loss. J. Mol. Evol. 44: 573-584.
7. De Souza, S.J., M. Long & W. Gilbert, 1996. Introns and gene evolution. Genes to Cells 1: 493-505.
8. De Souza, S.J., M. Long, L. Shoenbach, S.W. Roy & W. Gilbert, 1996. Introns correlate with module boundaries in ancient proteins. PNAS 93: 14632-14636.
9. De Souza, S.J., M. Long, R.J. Klein, S. Roy, S. Lin & W. Gilbert, 1998. Towards a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. PNAS 95: 5094-5099.
10. Dibb, N.J. & A.J. Newman, 1989. Evidence that introns arose at proto-splice sites. EMBO 8(7): 2015-2021.
11. Doolittle, W.F., 1978. Genes-in-pieces: were they ever together? Nature 272: 581-582.
12. Duret, L., 2001. Why do genes have introns? Recombination might add a new piece to the puzzle. Trends Genet. 17(4): 172-175.
13. Eiferman, F.A., P.R. Young, R.W. Scott & S.M. Tilghman, 1981. Protein intragenic amplification and divergence in the mouse alpha-fetoprotein gene. Nature 294: 713-718.
14. Fedorov, A., G. Suboch, M. Bujakov & L. Fedorova, 1992. Analysis of nonuniformity in intron phase distribution. Nucl. Acids Res. 20(10): 2553-2557.
15. Fedorov, A., X. Cao, S. Saxonov, S.J. De Souza, S.W. Roy & W. Gilbert, 2001. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. PNAS 98(23): 13177-13182.
16. Gilbert, W., 1978. Why genes in pieces? Nature 271: 501.
17. Gilbert, W., 1979. Introns and exons: playgrounds of evolution. ICN-UCLA Symp. Mol. Cell. Biol. 14: 1.
18. Gilbert, W., 1987. The exon theory of genes. Cold Spring Harb. Symp. Quant. Biol. 901-905.
19. Gilbert, W. & M. Glynias, 1993. On the ancient nature of introns. Gene 135(1-2): 137-144.
20. Go, M., 1981. Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature 291: 90-92.
21. Go, M. & M. Nosaka, 1987. Protein architecture and the origin of introns. Cold Spring Harb. Symp. Quant. Biol. 52: 915-924.
22. Jensen, E.O., K. Paludan, J.J. Hyldignielsen, P. Jorgensen & K.A. Marcker, 1981. The structure of a chromosomal leghemoglobin gene from soybean. Nature 291: 677-679.
23. Kwiatowski, J., M. Krawczyk, M. Kornacki, K. Bailey & F.J. Ayala, 1995. Evidence against the exon theory of genes derived from the triose-phosphate isomerase gene. PNAS 92: 8503-8506.
24. Logsdon Jr., JM., 1998. The recent origin of spliceosomal introns revisited. Curr. Opin. Gen. Dev. 8: 637-648.
25. Logsdon Jr., J.M., M.G. Tyshenko, C. Dixon, J.D. Jafari, V.K. Walker & J.D. Palmer, 1995. Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. PNAS 92: 8507-8511.
26. Long, M., C. Rosenberg & W. Gilbert, 1995. Intron phase correlations and the evolution of the intron/exon structure of genes. PNAS 92: 12495-12499.
27. Long, M., S.J. De Souza, C. Rosenberg & W. Gilbert, 1998. Relationship between 'proto-splice sites' and intron phases: evidence from dicodon analysis. PNAS 95: 219-223.
28. Marchionni, M. & W. Gilbert, 1986. The triosephosphate isomerase gene from maize: introns antedate the plant-animal divergence. Cell 46(1): 133-141.
29. Moens, L., J. Vanfleteren, I. Debaere, A.M. Jellie, W. Tate & C.N. Trotman, 1992. Unexpected intron location in nonvertebrate globin genes. FEBS Lett. 312: 105-109.
30. Palmer, J.D. & Logsdon Jr., J.M., 1991. The recent origin of introns. Curr. Opin. Genet. Dev. 1(4): 470-477.
31. Paquette, S.M., S. Bak & R. Feyereisen, 2000. Intron-exon organization and phylogeny in a large superfamily, the paralogous cytochrome P450 genes of Arabidopsis thaliana. DNA Cell Biol. 19(5): 307-317.
32. Parnes, J.R. & J.G. Seidman, 1982. Structure of wild-type and mutant mouse beta-2-microglobulin genes. Cell 29(2): 661-669.
33. Perler, F., A. Efstratiadis, P. Lomedico, W. Gilbert, R. Kolodner & J. Dodgson, 1980. The evolution of genes - the chicken preproinsulin gene. Cell 20(2): 555-556.
34. Rogozin, I.B., J. Lyons-Weiler & E.V. Koonin, 2000. Intron sliding in conserved gene families. Trends Genet. 16(10): 430-432.
35. Roy, S.W., A. Fedorov & W. Gilbert, 2002. The signal of ancient introns is obscured by intron density and homolog number. PNAS 99(24): 15513-15517.
36. Roy, S.W., M. Nosaka, S.J. De Souza & W. Gilbert, 1999. Centripetal modules and ancient introns. Gene 238: 95-91.
37. Roy, S.W., B.P. Lewis, A. Fedorov & W. Gilbert, 2001. Footprints of primordial introns on the eukaryotic genome. Trends Genet. 17(9): 496-498.
38. Sakharkar, M.K., T.W. Tan & S.J. De Souza, 2001. Generation of a database containing discordant intron positions in eukaryotic genes (MIDB). Bioinformatics 17(8): 671-675.
39. Sato, Y., Y. Nimura, K. Yra & M. Go, 1999. Module-intron correlation and intron sliding in family F/10 xylanase genes. Gene 238: 93-101.
40. Stoltzfus, A., 1994. Origin of introns - early or late? Nature 369: 526-527.
41. Stoltzfus, A., D.F. Spencer, M. Zuker, J.M. Logsdon & W.F. Doolittle, 1994. Testing the exon theory of genes - the evidence from protein structure. Science 265: 202-207.
42. Stoltzfus, A., J.M. Logsdon Jr., J.D. Palmer & W.F. Doolittle, 1997. Intron 'sliding' and the diversity of intron positions. PNAS 94: 10739-10744.
43. Stone, E.M., K.N. Rothblum & R.J. Schwartz, 1985. Intron-dependent evolution of chicken glyceraldehyde phosphate dehydrogenase gene. Nature 313: 498-500.
44. Stone, E.M., K.N. Rothblum, M.C. Alevy, T.M. Kuo & R.J. Schwartz, 1985. Complete sequence of the chicken glyceraldehyde-3-phosphate dehydrogenase gene. PNAS 82(6): 1628-1632.
45. Straus, D. & W. Gilbert, 1985. Genetic engineering in the precambrian - structure of the chicken triosephosphate isomerase gene. Mol. Cell Biol. 5(12): 3497-3506.
46. Sudhof, T.C., J.L. Goldstein, M.S. Brown & D.W. Russell, 1985a. The LDL receptor gene - a mosaic of exons shared with different proteins. Science 228: 815-822.
47. Sudhof, T.C., D.W. Russell, J.L. Goldstein, M.S. Brown, R. Sanchezpescador & G.I. Bell, 1985b. Cassette of 8 exons shared by genes for LDL receptor and EGF precursor. Science 228: 893-895.
48. Tittiger, C., S. Whyard & V.K. Walker, 1993. A novel intron site in the triopsephosphate isomerase gene from the mosquito Culex tarsalis. Nature 361: 470-472.
49. Tyshenko, M.G. & V.K. Walker, 1997. Towards a reconciliation of the introns early or late views: triosephosphate isomerase genes from insects. Biochim. Biophys. Acta 1353: 131-136.
50. Wolf, Y.I., F.A. Kondrashov & E.V. Koonin, 2000. No footprints of primordial introns in a eukaryotic genome. Trends Genet. 16(8): 333-334.
51. Wolf, Y.I., F.A. Kondrashov & E.V. Koonin, 2001a. No footprints of primordial introns in a eukaryotic genome [Author Correction]. Trends Genet. 17(3): 146.
52. Wolf, Y.I., F.A. Kondrashov & E.V. Koonin, 2001b. Footprints of primordial introns on the eukaryotic genome: still no clear traces. Trends Genet. 17(9): 499-501.