David N Cooper, Cardiff University, Cardiff, UK
Published online: September 2007
DOI: 10.1002/9780470015902.a0005088.pub2
During the evolution of human genes, exons have been both acquired and lost. The study of the structure of orthologous mammalian genes provides numerous examples of the gain or loss of exons by a variety of different mechanisms.
Keywords: exon deletion; exon insertion; exon duplication/amplification; exon shuffling; LINE element-mediated recombination; alternative splicing; pseudoexons
| References | |
| Alekseyenko AV, Kim N and Lee CJ (2007) Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA 13: 661–670. | |
| Björklund AK, Ekman D and Elofsson A (2006) Expansion of protein domain repeats. PLoS Computational Biology 2: e114. | |
| Blumenfeld OO and Huang C-H (1995) Molecular genetics of the glycophorin gene family, the antigens for the MNSs blood groups: multiple gene rearrangements and modulation of splice site usage result in extensive diversification. Human Mutation 6: 199–209. | |
| Bottenus RE, Ichinose A and Davie EW (1990) Nucleotide sequence of the gene for the b-subunit of human factor XIII. Biochemistry 29: 11195–11209. | |
| Courseaux A and Nahon J-L (2001) Birth of two chimeric genes in the Hominidae lineage. Science 291: 1293–1297. | |
| Coy JF, Dubel S, Kioschis P et al. (1996) Molecular cloning of tissue-specific transcripts of a transketolase-related gene: implications for the evolution of new vertebrate genes. Genomics 32: 309–316. | |
| Doolittle RF (1995) The multiplicity of domains in proteins. Annual Review of Biochemistry 64: 287–314. | |
| Dorit RL, Schoenbach L and Gilbert W (1990) How big is the universe of exons? Science 250: 1377–1382. | |
| Ejima Y and Yang L (2003) Trans mobilization of genomic DNA as a mechanism for retrotransposon-mediated exon shuffling. Human Molecular Genetics 12: 1321–1328. | |
| Fedorov A, Fedorova L, Starshenko V, Filatov V and Grigorev E (1998) Influence of exon duplication on intron and exon phase distribution. Journal of Molecular Evolution 46: 263–271. | |
| Furuno N, Nakagawa K, Eguchi U et al. (1991) Complete nucleotide sequence of the human RCC1 gene involved in coupling between DNA replication and mitosis. Genomics 11: 459–461. | |
| Goodier JL, Ostertag EM and Kazazian HH (2000) Transduction of 3¢-flanking sequences is common in L1 retrotransposition. Human Molecular Genetics 9: 653–657. | |
| Harrington ED, Boue S, Valcarcel J, Reich JG and Bork P (2004) Estimating rates of alternative splicing in mammals and invertebrates. Nature Genetics 36: 915–917. | |
| Hawkins JD (1988) A survey on intron and exon lengths. Nucleic Acids Research 16: 9893–9908. | |
| Holguin MH, Kurtz CB, Parker CJ, Weis JJ and Weis JH (1990) Loss of human CR1- and murine Crry-like exons in human CR2 transcripts due to CR2 gene mutations. Journal of Immunology 145: 1776–1781. | |
| Huang CH, Xie SS, Socha W and Blumenfeld OO (1995) Sequence diversification and exon inactivation in the glycophorin A gene family from chimpanzee to human. Journal of Molecular Evolution 41: 478–486. | |
| Hughes AL (1994) Evolution of the ATP-binding cassette transmembrane transporters of vertebrates. Molecular Biology and Evolution 11: 899–910. | |
| Jaworski CJ and Piatigorsky J (1989) A pseudo-exon in the functional human A-crystallin gene. Nature 337: 752–754. | |
| Kaessmann H, Zollner S, Nekrutenko A and Li WH (2002) Signatures of domain shuffling in the human genome. Genome Research 12: 1642–1650. | |
| Kim H-J, Kim D-H, Magoori K, Saeki S and Yamamoto TT (1998) Evolution of the apolipoprotein E receptor 2 gene by exon loss. Journal of Biochemistry 124: 451–456. | |
| Kim SJ, Ruiz N, Bezouska K and Drickamer K (1992) Organization of the gene encoding the human macrophage mannose receptor (MRC1). Genomics 14: 721–727. | |
| Kondrashov FA and Koonin EV (2001) Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics 10: 2661–2669. | |
| Krull M, Brosius J and Schmitz J (2005) Alu-SINE exonization: en route to protein-coding function. Molecular Biology and Evolution 22: 1702–1711. | |
| Kudo S and Fukuda M (1989) Structural organization of glycophorins A and B genes: glycophorin B gene evolved by homologous recombination at Alu repeat sequence. Proceedings of the National Academy of Sciences of the USA 86: 4619–4623. | |
| Kudo S and Fukuda M (1990) Identification of a novel human glycophorin, glycophorin E, by isolation of genomic clones and complementary DNA clones utilizing polymerase chain reaction. Journal of Biological Chemistry 265: 1102–1110. | |
| Lev-Maor G, Sorek R, Shomron N and Ast G (2003) The birth of an alternatively spliced exon: 3¢ splice-site selection in Alu exons. Science 300: 1288–1291. | |
| Lev-Maor G, Sorek R, Levanon EY et al. (2007) RNA-editing-mediated exon evolution. Genome Biology 8: R29. | |
| Liu M and Grigoriev A (2004) Protein domains correlate strongly with exons in multiple eukaryotic genomes – evidence of exon shuffling? Trends in Genetics 20: 399–403. | |
| Mayer WE, O'Huigin C and Klein J (1993) Resolution of the HLA-DRB6 puzzle: a case of grafting a de novo-generated exon on an existing gene. Proceedings of the National Academy of Sciences of the USA 90: 10720–10724. | |
| Miyazaki H, Fukamizu A, Hirose S et al. (1984) Structure of the human renin gene. Proceedings of the National Academy of Sciences of the USA 81: 5999–6003. | |
| Modrek B and Lee CJ (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genetics 34: 177–180. | |
| Mola G, Vela E, Fernandez-Figueras MT et al. (2007) Exonization of Alu-generated splice variants in the surviving gene of human and non-human primates. Journal of Molecular Biology 366: 1055–1063. | |
| Moran JV, DeBerardinis RJ and Kazazian HH (1999) Exon shuffling by L1 retrotransposition. Science 283: 1530–1534. | |
| Park I, Schaeffer E, Sidoli A et al. (1985) Organization of the human transferrin gene: direct evidence that it originated by gene duplication. Proceedings of the National Academy of Sciences of the USA 82: 3149–3153. | |
| Patthy L (1991) Modular exchange principles in proteins. Current Opinion in Structural Biology 1: 351–361. | |
| book Patthy L (1995) Protein Evolution by Exon Shuffling. New York: Springer-Verlag. | |
| Rozmahel R, Heng HH, Duncan AM et al. (1997) Amplification of CFTR exon 9 sequences to multiple locations in the human genome. Genomics 45: 554–561. | |
| Sorek R, Lev-Maor G, Reznik M et al. (2004) Minimal conditions for exonization of intronic sequences: 5¢ splice site formation in Alu exons. Molecular Cell 14: 221–231. | |
| Sorek R, Dror G and Shamir R (2006) Assessing the number of ancestral alternatively spliced exons in the human genome. BMC Genomics 7: 273. | |
| Südhof TC, Goldstein JL, Brown MS and Russell DW (1985a) The LDL receptor gene: a mosaic of exons shared with different proteins. Science 228: 815–819. | |
| Südhof TC, Russell DW, Goldstein JL et al. (1985b) Cassette of eight exons shared by genes for LDL receptor and EGF precursor. Science 228: 893–897. | |
| Wang W, Zheng H, Yang S et al. (2005) Origin and evolution of new exons in rodents. Genome Research 15: 1258–1264. | |
| Wyatt K, White HE, Wang L et al. (2006) Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. Structure 14: 1823–1834. | |
| Xie SS, Huang CH, Reid ME, Blancher A and Blumenfeld OO (1997) The glycophorin A gene family in gorillas: structure, expression, and comparison with the human and chimpanzee homologues. Biochemical Genetics 35: 59–76. | |
| Xing J, Wang H, Belancio VP et al. (2006) Emergence of primate genes by retrotransposon-mediated sequence transduction. Proceedings of the National Academy of Sciences of the USA 103: 17608–17613. | |
| Zhang XH-F and Chasin LA (2006) Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proceedings of the National Academy of Sciences of the USA 103: 13427–13432. | |
| Further Reading | |
| book Cooper DN (1999) Human Gene Evolution. Oxford: BIOS Scientific. | |
| Kolkman JA and Stemmer WP (2001) Directed evolution of proteins by exon shuffling. Nature Biotechnology 19: 423–428. | |
| Long M (2001) Evolution of novel genes. Current Opinion in Genetics and Development 11: 673–680. | |
| Vilches C, Pando MJ and Parham P (2000) Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain. Immunogenetics 51: 639–646. | |
| Web Links | |
| ePath Chromosome condensation 1 (CHC1); LocusID: 1104. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=1104 | |
| ePath Chromosome condensation 1 (CHC1); MIM number: 179710. OMIM: http://www.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?179710 | |
| ePath Cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (CFTR); LocusID: 1080. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=1080 | |
| ePath Cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (CFTR); MIM number: 602421. OMIM: http://www.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?602421 | |
| ePath Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor (LRP8); LocusID: 7804. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=7804 | |
| ePath Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor (LRP8); MIM number: 602600. OMIM: http://www.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?602600 | |
| ePath Major histocompatibility complex, class II, DR beta 6 (HLA-DRB6); LocusID: 3128. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=3128 | |
| ePath Renin (REN); MIM number: 179820. OMIM: http://www.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?179820 | |
| ePath Renin (REN); LocusID: 5972. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=5972 | |
| ePath Transferrin (TF); LocusID: 7018. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=7018 | |
| ePath Transferrin (TF); MIM number: 190000. OMIM http://www.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?190000 | |
| ePath Vertebrate exon evolution database: http://www.bioinformatics.ucla.edu/VEEDB | |
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