Preferential loss and gain of introns in 3′ portions of genes suggests a reverse-transcription mechanism of intron insertion

Gene

Volumn 338, Issue 1, 2004, Pages 85-91

  Sverdlov, Alexander V ^a   Babenko, Vladimir N ^a   Rogozin, Igor B ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Ag; Anopheles gambiae; Arabidopsis thaliana; At; Caenorhabditis elegans; Ce; Dm; Drosophila melanogaster; Duplication; Homo sapiens; Hs; Intron evolution; New introns; Old introns; Pf; Plasmodium falciparum; Saccharomyces cerevisiae; Sc; Sp; Splicing

Indexed keywords

COMPLEMENTARY DNA;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENE DUPLICATION; GENE INSERTION; GENETIC CODE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; HUMAN; INTRON; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCHIZOSACCHAROMYCES POMBE; STATISTICAL SIGNIFICANCE; TERMINAL SEQUENCE;

ANIMALS; ANOPHELES; ARABIDOPSIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENES; HUMANS; INTRONS; MODELS, GENETIC; PLASMODIUM FALCIPARUM; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; TRANSCRIPTION, GENETIC;

ANOPHELES GAMBIAE; ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; HOMO; HOMO SAPIENS; INSERTION SEQUENCES; MELANOGASTER; PLASMODIUM FALCIPARUM; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 4143150876     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.05.027     Document Type: Article

References (25)

1. Cavalier-Smith T. Selfish DNA and the origin of introns. Nature. 315:1985;283-284
2. Cavalier-Smith T. Intron phylogeny: a new hypothesis. Trends Genet. 7:1991;145-148
3. Dacks J.B., Doolittle W.F. Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help. Cell. 107:2001;419-425
4. Derr L.K. The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae. Genetics. 148:1998;937-945
5. Dibb N.J. Proto-splice site model of intron origin. J. Theor. Biol. 151:1991;405-416
6. Fedorov A., Merican A.F., Gilbert W. Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Natl. Acad. Sci. U. S. A. 99:2002;16128-16133
7. Fedorov A., Roy S., Fedorova L., Gilbert W. Mystery of intron gain. Genome Res. 13:2003;2236-2241
8. Fink G.R. Pseudogenes in yeast? Cell. 49:1987;5-6
9. Gilbert W. The exon theory of genes. Cold Spring Harbor Symp. Quant. Biol. 52:1987;901-905
10. Gilbert W., Glynias M. On the ancient nature of introns. Gene. 135:1993;137-144
11. Huang X. On global sequence alignment. Comput. Appl. Biosci. 10:1994;227-235
12. Kondrashov F.A., Koonin E.V. Origin of alternative splicing by tandem exon duplication. Hum. Mol. Genet. 10:2001;2661-2669
13. Lamond A.I. RNA splicing. Running rings around RNA. Nature. 397:1999;655-656
14. Letunic I., Copley R.R., Bork P. Common exon duplication in animals and its role in alternative splicing. Hum. Mol. Genet. 11:2002;1561-1567
15. Logsdon J.M. Jr. The recent origins of spliceosomal introns revisited. Curr. Opin. Genet. Dev. 8:1998;637-648
16. Lynch M. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. U. S. A. 99:2002;6118-6123
17. Lynch M., Richardson A.O. The evolution of spliceosomal introns. Curr. Opin. Genet. Dev. 12:2002;701-710
18. Maniatis T., Reed R. An extensive network of coupling among gene expression machines. Nature. 416:2002;499-506
19. Menendez-Arias L. Molecular basis of fidelity of DNA synthesis and nucleotide specificity of retroviral reverse transcriptases. Prog. Nucleic Acid Res. Mol. Biol. 71:2002;91-147
20. Mourier T., Jeffares D.C. Eukaryotic intron loss. Science. 300:2003;1393
21. Rogozin I.B., Wolf Y.I., Sorokin A.V., Mirkin B.G., Koonin E.V. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13:2003;1512-1517
22. Roy S.W., Fedorov A., Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc. Natl. Acad. Sci. U. S. A. 100:2003;7158-7162
23. Sakurai A., Fujimori S., Kochiwa H., Kitamura-Abe S., Washio T., Saito R., Carninci P., Hayashizaki Y., Tomita M. On biased distribution of introns in various eukaryotes. Gene. 300:2002;89-95
24. Stephens R.M., Schneider T.D. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228:1992;1124-1136
25. Sverdlov A.V., Rogozin I.B., Babenko V.N., Koonin E.V. Evidence of splice signal migration from exon to intron during intron evolution. Curr. Biol. 13:2003;2170-2174