Gene Deletions in Evolution

Abstract

Gross gene deletions and microdeletions have occurred during primate evolution. A number of gene deletions occur as polymorphic variants in human populations. The generative mechanisms underlying evolutionarily significant gene deletions appear to be similar to those responsible for pathological gene deletions, suggesting a predisposing role for the local DNA sequence environment.

Keywords: deletion; microdeletion; breakpoint; gene evolution, polymorphisms

Figure 1.

Model for homologous recombination between 4.2 kb repeats (open boxes) flanking the human glutathione S‐transferase M1 (GSTM1) gene leading to gene deletion (Xu et al., ). M1, M2, M4 and M5 denote the GSTM1, GSTM2, GSTM4 and GSTM5 genes respectively. Vertical lines denote EcoR I and Hind III restriction sites. The sizes of the EcoR I/Hind III fragments are shown. (Figure from Cooper DN Human Gene Evolution with the kind permission of BIOS Scientific Publishers, Oxford.)

Figure 2.

Examples of deletions flanked by short direct repeats within noncoding sequences of mammalian β‐globin genes. (From Efstratiadis et al..) Pairwise alignments of sequences within noncoding regions of mammalian β‐globin genes are shown. A deletion is assumed in the upper sequence with respect to the lower sequence. Dashes denote the nucleotides not present in the upper sequence. Short direct repeats are underlined. The two aligned human Aγ large intron sequences are those of two different alleles. (Figure from Cooper DN Human Gene Evolution with the kind permission of BIOS Scientific Publishers, Oxford.)

Figure 3.

Alignment of δ‐globin gene sequences from colobus monkey (C), rhesus macaque (R), baboon (B), spider monkey (S) and human (H). (After Vincent and Wilson ) Transcribed sequences are denoted by upper case letters, flanking regions are in lower case letters. +1 denotes the site of trancriptional initiation. Underlined bases represent an imperfect inverted repeat which may contribute to the formation of a hairpin loop. (Figure from Cooper DN Human Gene Evolution with the kind permission of BIOS Scientific Publishers, Oxford.)

close

References

Board P, Coggan M, Johnston P, et al. (1990) Genetic heterogeneity of the human glutathione transferases: a complex of gene families. Pharmacology and Therapeutics 48: 357–369.

Cooper DN (1999) Human Gene Evolution. Oxford, UK: BIOS Scientific Publishers.

Cooper DN and Krawczak M (1993) Human Gene Mutation. Oxford, UK: BIOS Scientific Publishers.

Deeb SS, Alvarez A, Malkki M and Motolsky AG (1995) Molecular patterns and sequence polymorphisms in the red and green visual pigment genes of Japanese men. Human Genetics 95: 501–506.

Efstratiadis A, Posakony JW, Maniatis T, et al. (1980) The structure and evolution of the human β‐globin gene family. Cell 21: 653–668.

Funkhouser W, Koop BF, Charmley P, et al. (1997) Evolution and selection of primate T cell antigen receptor BV8 gene subfamily. Molecular Phylogenetics and Evolution 8: 51–64.

Galili U and Swanson K (1991) Gene sequences suggest inactivation of α‐1,3‐galactosyltransferase in catarrhines after the divergence of apes from monkeys. Proceedings of the National Academy of Sciences of the United States of America 88: 7401–7404.

Hunt DM, Cowing JA, Patel R, et al. (1995) Sequence and evolution of the blue cone pigment gene in Old and New World primates. Genomics 27: 535–538.

Larsen RD, Rivera‐Marrero CA, Ernst LK, Cummings RD and Lowe JB (1990) Frameshift and nonsense mutations in a genomic sequence homologous to a murine UDP‐Gal:beta‐D‐Gal(1,4)‐D‐GlcNAc alpha (1,3)‐galactosyltransferase cDNA. Journal of Biological Chemistry 265: 7055–7061.

Lundwall A (1998) The cotton‐top tamarin carries an extended semenogelin I gene but no semenogelin II gene. European Journal of Biochemistry 255: 45–51.

McEvoy SM and Maeda N (1988) Complex events in the evolution of the haptoglobin gene cluster in primates. Journal of Biological Chemistry 263: 15740–15747.

Meireles CM, Schneider MP, Sampaio MI, et al. (1995) Fate of a redundant gamma‐globin gene in the atelid clade of New World monkeys: implications concerning fetal globin gene expression. Proceedings of the National Academy of Sciences of the United States of America 92: 2607–2611.

Pemble S, Schroeder KR, Spenser SR, et al. (1994) Human glutathione S‐transferase theta (GSTT1):cDNA cloning and the characterization of a genetic polymorphism. Biochemical Journal 300: 271–276.

Toyosawa S, O'hUigin C, Figueroa F, Tichy H and Klein J (1998) Identification and characterization of amelogenin genes in monotremes, reptiles, and amphibians. Proceedings of the National Academy of Sciences of the United States of America 95: 13056–13061.

Vincent KA and Wilson AC. (1989) Evolution and transcription of Old World monkey globin genes. Journal of Molecular Biology 207: 465–479.

Wu XW, Muzny DM, Lee CC and Caskey CT (1992) Two independent mutational events in the loss of urate oxidase during hominoid evolution. Journal of Molecular Evolution 34: 78–84.

Xu S‐J, Wang Y‐P, Roe B and Pearson WR (1998) Characterization of the human class mu glutathione S‐transferase gene cluster and the GSTM1 deletion. Journal of Biological Chemistry 273: 3517–3527.

Further Reading

Colin Y, Cherif‐Zahar B, Le Van Kim C, et al. (1991) Genetic basis of the RhD‐positive and RhD‐negative blood group polymorphism as determined by Southern analysis. Blood 78: 2747–2752.

Felice AE, Cleek MP, Marino EM, et al. (1986) Different ζ‐globin gene deletions among black Americans. Human Genetics 73: 221–224.

Ghanem N, Buresi C, Moisan J‐P, et al. (1989) Deletion, insertion, and restriction site polymorphism of the T‐cell receptor gamma variable locus in French, Lebanese, Tunisian, and Black African populations. Immunogenetics 30: 350–360.

Li W‐H, Gu Z, Wang H and Nekrutenko A (2001) Evolutionary analyses of the human genome. Nature 409: 847–849.

Mitchell RJ, Howlett S, White NG, et al. (1999) Deletion polymorphism in the human COL1A2 gene: genetic evidence of a non‐African population whose descendants spread to all continents. Human Biology 71: 901–914.

Rabbani H, Pan Q, Kondo N, Smith CIE and Hammarström L (1996) Duplications and deletions of the human IGHC locus: evolutionary implications. Immunogenetics 45: 136–141.

Rowen L, Koop BF and Hood L (1996) The complete 685‐kilobase DNA sequence of the human β T cell receptor locus. Science 272: 1755–1762.

Saitou N and Ueda S (1994) Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates. Molecular Biology and Evolution 11: 504–512.

Teisberg P, Jonassen R, Mevag B, Gedde‐Dahl T and Olaisen B (1988) Restriction fragment length polymorphisms of the complement component C4 loci on chromosome 6: studies with emphasis on the determination of gene number. Annals of Human Genetics 52: 77–84.

Weaver DT and DePamphilis ML (1982) Specific sequences in native DNA that arrest synthesis by DNA polymerase α. Journal of Biological Chemistry 257: 2075–2086.

Web Links

Glutathione S‐transferase M1 (GSTM1); Locus ID: 2944. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=2944

Glycoprotein, alpha‐galactosyltransferase 1 (GGTA1); Locus ID: 2681. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=2681

Opsin 1 (cone pigments), long‐wave‐sensitive (color blindness, protan) (OPN1LW); Locus ID: 5956. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=5956

Opsin 1 (cone pigments), medium‐wave‐sensitive (color blindness, deutan) (OPN1MW); Locus ID: 2652. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=2652

T cell receptor beta locus (TRB@); Locus ID: 6957. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=6957

Glutathione S‐transferase M1 (GSTM1); MIM number: 138350. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?138350

Glycoprotein, alpha‐galactosyltransferase 1 (GGTA1); MIM number: 104175. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?104175

Opsin 1 (cone pigments), long‐wave‐sensitive (color blindness, protan) (OPN1LW); MIM number: 303900. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?303900

Opsin 1 (cone pigments), medium‐wave‐sensitive (color blindness, deutan) (OPN1MW); MIM number: 303800. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?303800

T cell receptor beta locus (TRB@); MIM number: 186930. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?186930

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Cooper, David N(Jul 2006) Gene Deletions in Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005094]