Introns in gene evolution

Genetica

Volumn 118, Issue 2-3, 2003, Pages 123-131

  Fedorova, Larisa ^a   Fedorov, Alexei ^b  

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Evolution; Exons; Genes; Genome; Introns; Splicing

Indexed keywords

ALTERNATIVE SPLICING; CROSSING OVER, GENETIC; EVOLUTION, MOLECULAR; EXONS; GENE EXPRESSION REGULATION; INTRONS;

EUKARYOTA; INSERTION SEQUENCES; TRANSPOSONS;

EID: 0037630627     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1024145407467     Document Type: Review

References (85)

1. Akamatsu, W. & H. Okano, 2001. No to Hattatsu. Brain Dev. 33: 114-120.
2. Akopian, A.N., K. Okuse, V. Souslova, S. England, N. Ogata & J.N. Wood, 1999. Trans-splicing of a voltage-gated sodium channel is regulated by nerve growth factor. FEBS Lett. 445: 177-182.
3. Aoki, Y., Z. Huang, S.S. Thomas, P.G. Bhide, I. Huang, M.A. Moskowitz & S.A. Reeves, 2000. Increased susceptibility to ishemia-induced brain damage in transgenic mice over-expressing a dominant negative form of SHP2. FASEB J. 14: 1965-1973.
4. Belford, M. & P.S. Perlman, 1995. Mechanisms of intron mobility. J. Biol. Chem. 270: 30237-30240.
5. Berget, S.M., C. Moore & P.A. Sharp, 1977. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl. Acad. Sci. USA 74: 3171-3175.
6. Black, D.L., 2000. Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 103: 367-370.
7. Blake, C.C.F., 1978. Do genes-in-pieces imply proteins-in-pieces? Nature 273: 267.
8. Bonen, L. & J. Vogel, 2001. The ins and outs of group II introns. Trends Genet. 17: 322-331.
9. Brooks, A.R., B.P. Nagy, S. Taylor, W.S. Simonet, J.M. Taylor & B. Levy-Wilson, 1994. Sequences containing the second-intron enhancer are essential for transcription of the human apolipoprotein B gene in the livers of transgenic mice. Mol. Cell. Biol. 14: 2243-2256.
10. Carvalho, A.B. & A.G. Clark, 1999. Intron size and natural selection. Nature 401: 344.
11. Caudevilla, C., C. Codony, D. Serra, G. Plasencia, R. Roman, A. Graessmann, G. Asins, M. Bach-Elias & F.G. Hegardt, 2001, Localization of an exonic splicing enhancer responsible for mammalian natural trans-splicing. Nucl. Acids Res. 29: 3108-3115.
12. Cavaille, J., K. Buiting, M. Kiefmann, M. Lalande, C.I. Brannan, B. Horsthemke, J.-P. Bachellerie, J. Brosius & A. Huttenhofer, 2000. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad. Sci. USA 97: 14311-14316.
13. Cavalier-Smith, T., 1985. Selfish DNA and the origin of introns. Nature 315: 283-284.
14. Cavalier-Smith, T., 1991. Intron phylogeny: a new hypothesis. Trend. Genet. 7: 145-148.
15. Chow, L.T., R.E. Gelinas, J.R. Broker & R.J. Roberts, 1977. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12: 1-8.
16. Comeron, J.M. & M. Kreitman, 2000. The correlation between intron length and recombination in Drosophila: dynamic equilibrium between mutational and selective forces. Genetics 156: 1175-1190.
17. Crick, F., 1979. Split genes and RNA splicing. Science 204: 264-271.
18. Croft, L., S. Schandroff, F. Clark, K. Burrage, P. Arctander & J.S. Mattick, 2000. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat. Genet. 24: 340-341.
19. Darnel, J.E., 1978. Implications of RNA. RNA splicing in evolution of eukaryotic cells. Science 202: 1257-1260.
20. Domon, C. & A. Steinmetz, 1994. Exon shuffling in anther-specific genes from sunflower. Mol. Gen. Genet. 244: 312-317.
21. Doolittle, W.F., 1978. Genes in pieces: were they ever together? Nature 272: 581-582.
22. Doolittle, W.F., 1999. Lateral genomics. Trends Cell Biol. 9: M5-M8.
23. Dorit, R.L., L. Schoengach & W. Gilbert, 1990. How big is the universe of exons? Science 250: 1377-1382.
24. Dorn, R., G. Reuter & A. Loewendorf, 2001. Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila. Proc. Natl. Acad. Sci. USA 98: 9724-9729.
25. Douglas, S., S. Zauner, M. Fraunholz, M. Beaton, S. Penny, L.T. Deng, X. Wu, M. Reith, T. Cavalier-Smith & U.G. Maier, 2001. The highly reduced genome of an enslaved algal nucleus. Nature 410: 1091-1096.
26. Eddy, S.R., 1999. Noncoding RNA genes. Curr. Opin. Genet. Dev. 9: 695-699.
27. Evans, D. & T. Blumenthal, 2000. Trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: analysis of the SL2 RNA. Mol. Cell. Biol. 20: 6659-6667.
28. Fast, N.M., A.J. Roger, C.A. Richardson & W.F. Doolittle, 1998. U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome. Nucl. Acids Res. 26: 3202-3207.
29. Fast, N.M. & W.F. Doolittle, 1999. Trichomonas vaginalis possesses a gene encoding the essential spliceosomal component, PRP8.
30. Fedorov, A., G. Suboch, M. Bujakov & L. Fedorova, 1992. Analysis of nonuniformity in intron phase distribution. Nucl. Acids Res. 20: 2553-2557.
31. Fedorov, A., V. Starshenko, L. Fedorova, V. Filatov & E. Grigor'ev, 1998. Influence of exon duplication and shuffling on intron phase distribution. J. Mol. Evol. 46: 263-271.
32. Ferguson, K.C. & J.H. Rothman, 1999. Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. Mol. Cell. Biol. 19: 1892-1900.
33. Filipowicz, W., 2000. Imprinted expression of small nucleolar RNAs in brain: time for RNomics. Proc. Natl. Acad. Sci. USA 97: 14035-14037.
34. Gilbert, W., 1978. Why genes in pieces? Nature 271: 501.
35. Gilbert, W., 1987. The exon theory of genes. Cold Spring Harbor Symp. Quant. Biol. 52: 901-905.
36. Giroux, M.J., M. Clancy, J. Baier, L. Ingham, D. McCarty & C. Hannah, 1994. De novo synthesis of an intron by the maize transposable element Dissociation. Proc. Natl. Acad. Sci. USA 91: 12150-12154.
37. Hartman, H. & A. Fedorov, 2002. The origin of the eukaryotic cell - a genomic investigation. Proc. Natl. Acad. Sci. USA, 99: 1420-1425.
38. Hogenesch, J.B., K.A. Ching, S. Batalov, A.I. Su, J.R. Walker, Y.S.A. Zhou, Kay, P.G. Schultz & M.P. Cooke, 2001. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 106: 413-415.
39. Howell, M. & C.S. Hill, 1997. Xsmad2 directly activates the activin-inducible, dorsal mesoderm gene XFKH1 in Xenopus embryos. EMBO J. 16: 7411-7421.
40. Hural, J.A., M. Kwan, G. Henkel, M.B. Hock & M.A. Brown, 2000. An intron transcriptional enhancer element regulates IL-4 gene locus accessibility in mast cells. J. Immunol. 165: 3239-3249.
41. Jeffreys, A.J. & R.A. Flavell, 1977. The rabbit beta-globin gene contains a large insert in the coding sequence. Cell 12: 1097-1108.
42. Katinka, M.D., S. Duprat, E. Cornillot, G. Metenier, F. Thomarat, G. Prensier, V. Barbe, E. Peyretaillade, P. Brottier, P. Wincker, F. Delbac, H. El Alaoui, P. Peyret, W. Saurin, M. Gouy, J. Weissenbach & C.P. Vivares, 2001. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414: 450-453.
43. Kawasaki, T., S. Okumura, N. Kishimoto, H. Shimada & H. Ichikawa, 1999. RNA maturation of the rice SPK gene may involve trans-splicing. Plant J. 18: 625-632.
44. Krause, M. & D. Hirsh, 1987. A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 49: 753-761.
45. Lambowitz, A.M. & M. Belford, 1993. Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
46. Liu, J. & E.S. Maxwell, 1990. Mouse U14 snRNA is encoded in an intron of the mouse cognate hsc70 heat shock gene. Nucl. Acids Res. 18, 6565-6571.
47. Logsdom 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 intronslate theory. Proc. Natl. Acad. Sci. USA 92: 8507-8511.
48. Logsdon, J.M., 1998. The recent origin of spliceosomal introns revised. Curr. Opin. Genet. Dev. 8: 637-648.
49. Logsdon, J.M., A. Stoltzfus & W.F. Doolittle, 1998. Molecular evolution: recent cases of spliceosomal intron gain? Curr. Biol. 8: R560-R563.
50. Long, M. & C.H. Langley, 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
51. Long, M., C. Rosenberg & W. Gilbert, 1995. Intron phase correlations and the evolution of the intron-exon structure of genes. Proc. Natl. Acad. Sci. USA 92: 12495-12499.
52. Long, M., W. Wang & J. Zhang, 1999. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei in Drosophila. Gene 238: 135-141.
53. Long, M. & C. Rosenberg, 2000. Testing the 'proto-splice sites' model of intron origin: evidence from analysis of intron phase correlations. Mol. Biol. Evol. 17: 1789-1796.
54. Long, M., 2001. Evolution of novel genes. Curr. Opin. Genet. Dev. 11: 673-680.
55. Lopez, A.J., 1998. Alternative splicing of pre-mRNA: development consequences and mechanisms of regulation. Annu. Rev. Genet. 32: 279-305.
56. Lothian, C. & U. Lendahl, 1997. An evolutionary conserved region in the second intron of the human nestin gene directs gene expression to CNS progenitor cells and to early neural crest cells. Eur. J. Neurosci. 9: 452-462.
57. Lou, H., R.F. Gagel & S.M. Berget, 1996. An intron enhancer recognized by splicing factors activates polyadenylation. Genes Dev. 10: 208-219.
58. Maniatis, T. & R. Reed, 2002. An extensive network of coupling among gene expression machines. Nature 416: 499-506.
59. Martinez-Abarca, F. & N. Toro, 2000. Group II introns in the bacterial world. Mol. Microbiol. 38: 917-926.
60. Maxwell, E.S. & M.J. Fournier, 1995. The small nucleolar RNAs. Ann. Rev. Biochem. 35: 897-934.
61. Missler, M. & T.C. Sudhof, 1998. Neuroxins: three genes and 1001 products. Trends Genet. 14: 20-26.
62. Mitchell, J.R. & K. Collins, 2000. Human telomerase activation requires two independent interactions between telomerase RNA and telomerase reverse transcriptase. Mol. Cell 6: 361-371.
63. Muscarella, D.E. & V.M. Vogt, 1989. A mobile group I intron in the nuclear rDNA of Physarum polycephalum. Cell 56: 443-454.
64. Nikoh, N. & T. Fukatsu, 2001. Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic fungi of the genus Cordyceps. Mol. Biol. Evol. 81: 1631-1642.
65. Nilsen, T.W., 2001. Evolutionary origin of SL-addition trans-splicing: still an enigma. Trends Genet. 17: 678-680.
66. Nixon, J.E.J., A. Wang, H.G. Morrison, A.G. McArthur, M.L. Sogin, B.J. Loftus & J. Samuelson, 2002. A Spliceosomal intron in Giardia lamblia. Proc. Natl. Acad. Sci. USA 99: 3701-3705.
67. Nurminsky, D.I., M.V. Nurminskaya, D. DeAguiar & D.L. Hartl, 1998. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575.
68. Oshima, R.G., L. Abrams & D. Kulesh, 1990. Activation of an intron enhancer within the keratin 18 gene by expression of c-fos and c-jun in undifferentiated F9 embryonal carcinoma cells. Genes Dev. 4: 835-848.
69. Palmer, J.D. & J.M. Logsdon, 1991. The recent origin of introns. Curr. Opin. Genet. Dev. 1: 470-477.
70. Pan, Q. & R.U. Simpson, 1999. C-myc intron element-binding proteins are required for 1,25-dihydroxyvitamin D3 regulation of c-myc during HL-60 cell differentiation and the involvement of HOXB4. J. Biol. Chem. 274: 8437-8444.
71. Pankov, R., A. Umezawa, R. Maki, C.J. Der, C.A. Hauser & R.G. Oshima, 1994. Oncogene activation of human keratin 18 transcription via the Ras signal transduction pathway. Proc. Natl. Acad. Sci. USA 91: 873-877.
72. Patthy, L., 1999. Genome evolution and the evolution of exon-shuffling - a review. Gene 238: 103-114.
73. Peculis, B.A., 2000. RNA-binding proteins: if it looks like a sn(o)RNA. Curr Biol. 10: R916-R918.
74. Peng, Y., A. Genin, N.B. Spinner, R.H. Diamond & R. Taub, 1998. The gene encoding human nuclear protein tyrosine phosphatase, PRL-1. Cloning, chromosomal localization and identification of an intron enhancer. J. Biol. Chem. 273: 17286-17295.
75. Pogacic, V., F. Dragon & W. Filipowicz, 2000. Human H/ACA small nucleolar RNPs and telomerase share evolutionarily conserved proteins NHP2 and NOP10. Mol. Cell. Biol. 20: 9028-9040.
76. Reed, R. & K. Magni, 2001. A new view of mRNA export: separating the wheat from the chaff. Nat. Cell Biol. 3: E201-E204.
77. Rhodes, K. & R.G. Oshima, 1998. A regulatory element of the human keratin 18 gene with AP-I-dependent promoter activity. J. Biol. Chem. 273: 26534-26542.
78. Roger, A.J. & W.F. Doolittle, 1993. Why introns-in-pieces? Nature 364: 289-290.
79. Saxonov, S. & W. Gilbert, 2003. The universe of exons revisited. Genetica 118: 267-278.
80. Schmucker, D., J. Clemens, J. Shu, C. Worby, J. Xiao, M. Muda, J. Dixon & L. Zipursky, 2000. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101: 671-684.
81. Sharp, P.A., 1985. On the origin of RNA splicing and introns. Cell 42: 397-400.
82. Silvak, L.E., G. Pont-Kingdom K. Le, G. Mayr, K.F. Tai, B.T. Stevens & W.L. Carroll, 1999. A novel intron element operates posttranscriptionally to regulate human N-myc expression. Mol. Cell. Biol. 19: 155-163.
83. Simard, M.J. & B. Chabot, 2000. Control of hnRNP A1 alternative splicing: an intron element represses use of the common 3′ splice site. Mol. Cell. Biol. 20: 7353-7362.
84. Takahara, T., S.I. Kanazu, S. Yanagisawa & H. Akanuma, 2000. Heterogeneous Sp1 mRNAs in human HepG2 cells include a product of homotypic trans-splicing. J. Biol. Chem. 275: 38067-38072.
85. Weinsein, L.B. & J.A. Steitz, 1999. Guided tours: from precursor snoRNA to functional snoRNP. Curr. Opin. Cell Biol. 11: 378-384.