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. 1984 Feb 10;12(3):1641–1655. doi: 10.1093/nar/12.3.1641

Ruminant globin gene structures suggest an evolutionary role for Alu-type repeats.

J C Schimenti, C H Duncan
PMCID: PMC318605  PMID: 6322113

Abstract

Bovine fetal and adult globin genes were cloned and subjected to DNA sequence analysis. Both of these genes contained insertions of Alu-type repetitive DNA within their introns. Comparison of cow and goat beta-type globin genes indicates that intragenic DNA insertions played a role in their evolution. These data support the theory that Alu-type repeats maintain genetic diversity by inhibiting gene conversion.

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Selected References

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  1. Babin D. R., Schroeder W. A., Shelton J. R., Shelton J. B., Robberson B. The amino acid sequence of the gamma chain of bovine fetal hemoglobin. Biochemistry. 1966 Apr;5(4):1297–1310. doi: 10.1021/bi00868a025. [DOI] [PubMed] [Google Scholar]
  2. Barsh G. S., Seeburg P. H., Gelinas R. E. The human growth hormone gene family: structure and evolution of the chromosomal locus. Nucleic Acids Res. 1983 Jun 25;11(12):3939–3958. doi: 10.1093/nar/11.12.3939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bell G. I., Pictet R., Rutter W. J. Analysis of the regions flanking the human insulin gene and sequence of an Alu family member. Nucleic Acids Res. 1980 Sep 25;8(18):4091–4109. doi: 10.1093/nar/8.18.4091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bentley D. L., Rabbitts T. H. Evolution of immunoglobulin V genes: evidence indicating that recently duplicated human V kappa sequences have diverged by gene conversion. Cell. 1983 Jan;32(1):181–189. doi: 10.1016/0092-8674(83)90508-1. [DOI] [PubMed] [Google Scholar]
  5. Calabretta B., Robberson D. L., Barrera-Saldaña H. A., Lambrou T. P., Saunders G. F. Genome instability in a region of human DNA enriched in Alu repeat sequences. Nature. 1982 Mar 18;296(5854):219–225. doi: 10.1038/296219a0. [DOI] [PubMed] [Google Scholar]
  6. Cleary M. L., Haynes J. R., Schon E. A., Lingrel J. B. Identification by nucleotide sequence analysis of a goat pseudoglobin gene. Nucleic Acids Res. 1980 Oct 24;8(20):4791–4802. doi: 10.1093/nar/8.20.4791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cleary M. L., Schon E. A., Lingrel J. B. Two related pseudogenes are the result of a gene duplication in the goat beta-globin locus. Cell. 1981 Oct;26(2 Pt 2):181–190. doi: 10.1016/0092-8674(81)90301-9. [DOI] [PubMed] [Google Scholar]
  8. Congote L. F., Solomon S. Hormonal regulation of hemoglobin synthesis in cells of fetal calf liver cultured in a serum-free medium. Biochemistry. 1978 Apr 4;17(7):1160–1165. doi: 10.1021/bi00600a004. [DOI] [PubMed] [Google Scholar]
  9. Dhruva B. R., Shenk T., Subramanian K. N. Integration in vivo into simian virus 40 DNA of a sequence that resembles a certain family of genomic interspersed repeated sequences. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4514–4518. doi: 10.1073/pnas.77.8.4514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Di Segni G., Carrara G., Tocchini-Valentini G. R., Shoulders C. C., Baralle F. E. Selective in vitro transcription of one of the two Alu family repeats present in the 5' flanking region of the human epsilon-globin gene. Nucleic Acids Res. 1981 Dec 21;9(24):6709–6722. doi: 10.1093/nar/9.24.6709. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Duncan C. H., Jagadeeswaran P., Wang R. R., Weissman S. M. Structural analysis of templates and RNA polymerase III transcripts of Alu family sequences interspersed among the human beta-like globin genes. Gene. 1981 Mar;13(2):185–196. doi: 10.1016/0378-1119(81)90007-x. [DOI] [PubMed] [Google Scholar]
  12. Duncan C., Biro P. A., Choudary P. V., Elder J. T., Wang R. R., Forget B. G., de Riel J. K., Weissman S. M. RNA polymerase III transcriptional units are interspersed among human non-alpha-globin genes. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5095–5099. doi: 10.1073/pnas.76.10.5095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fink G. R., Styles C. A. Gene conversion of deletions in the his4 region of yeast. Genetics. 1974 Jun;77(2):231–244. doi: 10.1093/genetics/77.2.231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fristensky B., Lis J., Wu R. Portable microcomputer software for nucleotide sequence analysis. Nucleic Acids Res. 1982 Oct 25;10(20):6451–6463. doi: 10.1093/nar/10.20.6451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gabuzda T. G., Silver R. K., Chui L. C., Lewis H. B. The formation of foetal and adult haemoglobin in cell cultures of neonatal calf marrow. Br J Haematol. 1970 Nov;19(5):621–633. doi: 10.1111/j.1365-2141.1970.tb01646.x. [DOI] [PubMed] [Google Scholar]
  16. Grimaldi G., Queen C., Singer M. F. Interspersed repeated sequences in the African green monkey genome that are homologous to the human Alu family. Nucleic Acids Res. 1981 Nov 11;9(21):5553–5568. doi: 10.1093/nar/9.21.5553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Haynes J. R., Rosteck P., Jr, Lingrel J. B. Unusual sequence homology at the 5-ends of the developmentally regulated beta A-, beta C-, and gamma-globin genes of the goat. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7127–7131. doi: 10.1073/pnas.77.12.7127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Haynes S. R., Toomey T. P., Leinwand L., Jelinek W. R. The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element. Mol Cell Biol. 1981 Jul;1(7):573–583. doi: 10.1128/mcb.1.7.573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hess J. F., Fox M., Schmid C., Shen C. K. Molecular evolution of the human adult alpha-globin-like gene region: insertion and deletion of Alu family repeats and non-Alu DNA sequences. Proc Natl Acad Sci U S A. 1983 Oct;80(19):5970–5974. doi: 10.1073/pnas.80.19.5970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Houck C. M., Rinehart F. P., Schmid C. W. A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol. 1979 Aug 15;132(3):289–306. doi: 10.1016/0022-2836(79)90261-4. [DOI] [PubMed] [Google Scholar]
  21. Houck C. M., Schmid C. W. The evolution of a family of short interspersed repeats in primate DNA. J Mol Evol. 1981;17(3):148–155. doi: 10.1007/BF01733908. [DOI] [PubMed] [Google Scholar]
  22. Huisman T. H. The in vivo production of hemoglobin C in ruminants. Ann N Y Acad Sci. 1974 Nov 29;241(0):549–555. doi: 10.1111/j.1749-6632.1974.tb21911.x. [DOI] [PubMed] [Google Scholar]
  23. Jagadeeswaran P., Forget B. G., Weissman S. M. Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts? Cell. 1981 Oct;26(2 Pt 2):141–142. doi: 10.1016/0092-8674(81)90296-8. [DOI] [PubMed] [Google Scholar]
  24. Jagadeeswaran P., Tuan D., Forget B. G., Weissman S. M. A gene deletion ending at the midpoint of a repetitive DNA sequence in one form of hereditary persistence of fetal haemoglobin. Nature. 1982 Apr 1;296(5856):469–470. doi: 10.1038/296469a0. [DOI] [PubMed] [Google Scholar]
  25. Jelinek W. R., Schmid C. W. Repetitive sequences in eukaryotic DNA and their expression. Annu Rev Biochem. 1982;51:813–844. doi: 10.1146/annurev.bi.51.070182.004121. [DOI] [PubMed] [Google Scholar]
  26. Jelinek W. R., Toomey T. P., Leinwand L., Duncan C. H., Biro P. A., Choudary P. V., Weissman S. M., Rubin C. M., Houck C. M., Deininger P. L. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1398–1402. doi: 10.1073/pnas.77.3.1398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kalb V. F., Glasser S., King D., Lingrel J. B. A cluster of repetitive elements within a 700 base pair region in the mouse genome. Nucleic Acids Res. 1983 Apr 11;11(7):2177–2184. doi: 10.1093/nar/11.7.2177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kitchen H., Brett I. Embryonic and fetal hemoglobin in animals. Ann N Y Acad Sci. 1974 Nov 29;241(0):653–671. doi: 10.1111/j.1749-6632.1974.tb21921.x. [DOI] [PubMed] [Google Scholar]
  29. Kominami R., Muramatsu M., Moriwaki K. A mouse type 2 Alu sequence (M2) is mobile in the genome. Nature. 1983 Jan 6;301(5895):87–89. doi: 10.1038/301087a0. [DOI] [PubMed] [Google Scholar]
  30. Krawinkel U., Zoebelein G., Brüggemann M., Radbruch A., Rajewsky K. Recombination between antibody heavy chain variable-region genes: evidence for gene conversion. Proc Natl Acad Sci U S A. 1983 Aug;80(16):4997–5001. doi: 10.1073/pnas.80.16.4997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Krayev A. S., Kramerov D. A., Skryabin K. G., Ryskov A. P., Bayev A. A., Georgiev G. P. The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res. 1980 Mar 25;8(6):1201–1215. doi: 10.1093/nar/8.6.1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Krayev A. S., Markusheva T. V., Kramerov D. A., Ryskov A. P., Skryabin K. G., Bayev A. A., Georgiev G. P. Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. Nucleic Acids Res. 1982 Dec 11;10(23):7461–7475. doi: 10.1093/nar/10.23.7461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Lauer J., Shen C. K., Maniatis T. The chromosomal arrangement of human alpha-like globin genes: sequence homology and alpha-globin gene deletions. Cell. 1980 May;20(1):119–130. doi: 10.1016/0092-8674(80)90240-8. [DOI] [PubMed] [Google Scholar]
  34. Lavrijsen K., Verwilghen R. L. The synthesis of adult hemoglobins during hepatic erythropoiesis in the calf fetus. Hemoglobin. 1983;7(2):159–179. doi: 10.3109/03630268309048644. [DOI] [PubMed] [Google Scholar]
  35. Lawrence C. W., Sherman F., Jackson M., Gilmore R. A. Mapping and gene conversion studies with the structural gene for iso-1-cytochrome C in yeast. Genetics. 1975 Dec;81(4):615–629. doi: 10.1093/genetics/81.4.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Liebhaber S. A., Goossens M., Kan Y. W. Homology and concerted evolution at the alpha 1 and alpha 2 loci of human alpha-globin. Nature. 1981 Mar 5;290(5801):26–29. doi: 10.1038/290026a0. [DOI] [PubMed] [Google Scholar]
  37. Maeda N., Bliska J. B., Smithies O. Recombination and balanced chromosome polymorphism suggested by DNA sequences 5' to the human delta-globin gene. Proc Natl Acad Sci U S A. 1983 Aug;80(16):5012–5016. doi: 10.1073/pnas.80.16.5012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Miyake T., Migita K., Sakaki Y. Some KpnI family members are associated with the Alu family in the human genome. Nucleic Acids Res. 1983 Oct 11;11(19):6837–6846. doi: 10.1093/nar/11.19.6837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Nijhof W., Ronda G. J., Jonxis J. H. The synthesis of haemoglobins A and F in the calf. Biol Neonate. 1972;21(1):120–129. doi: 10.1159/000240502. [DOI] [PubMed] [Google Scholar]
  41. Ollo R., Rougeon F. Gene conversion and polymorphism: generation of mouse immunoglobulin gamma 2a chain alleles by differential gene conversion by gamma 2b chain gene. Cell. 1983 Feb;32(2):515–523. doi: 10.1016/0092-8674(83)90471-3. [DOI] [PubMed] [Google Scholar]
  42. Page G. S., Smith S., Goodman H. M. DNA sequence of the rat growth hormone gene: location of the 5' terminus of the growth hormone mRNA and identification of an internal transposon-like element. Nucleic Acids Res. 1981 May 11;9(9):2087–2104. doi: 10.1093/nar/9.9.2087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Pease L. R., Schulze D. H., Pfaffenbach G. M., Nathenson S. G. Spontaneous H-2 mutants provide evidence that a copy mechanism analogous to gene conversion generates polymorphism in the major histocompatibility complex. Proc Natl Acad Sci U S A. 1983 Jan;80(1):242–246. doi: 10.1073/pnas.80.1.242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Reisner A. H., Bucholtz C. A. Apparent relatedness of the main component of ovine 1.714 satellite DNA to bovine 1.715 satellite DNA. EMBO J. 1983;2(7):1145–1149. doi: 10.1002/j.1460-2075.1983.tb01559.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Rinehart F. P., Ritch T. G., Deininger P. L., Schmid C. W. Renaturation rate studies of a single family of interspersed repeated sequences in human deoxyribonucleic acid. Biochemistry. 1981 May 26;20(11):3003–3010. doi: 10.1021/bi00514a003. [DOI] [PubMed] [Google Scholar]
  46. Robbins J., Rosteck P., Jr, Haynes J. R., Freyer G., Cleary M. L., Kalter H. D., Smith K., Lingrel J. B. The isolation and partial characterization of recombinant DNA containing genomic globin sequences from the goat. J Biol Chem. 1979 Jul 10;254(13):6187–6195. [PubMed] [Google Scholar]
  47. Romero-Herrera A. E., Lehmann H., Joysey K. A., Friday A. E. Molecular evolution of myoglobin and the fossil record: a phylogenetic synthesis. Nature. 1973 Dec 14;246(5433):389–395. doi: 10.1038/246389a0. [DOI] [PubMed] [Google Scholar]
  48. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Schmid C. W., Jelinek W. R. The Alu family of dispersed repetitive sequences. Science. 1982 Jun 4;216(4550):1065–1070. doi: 10.1126/science.6281889. [DOI] [PubMed] [Google Scholar]
  50. Schon E. A., Cleary M. L., Haynes J. R., Lingrel J. B. Structure and evolution of goat gamma-, beta C- and beta A-globin genes: three developmentally regulated genes contain inserted elements. Cell. 1981 Dec;27(2 Pt 1):359–369. doi: 10.1016/0092-8674(81)90419-0. [DOI] [PubMed] [Google Scholar]
  51. Schon E. A., Wernke S. M., Lingrel J. B. Gene conversion of two functional goat alpha-globin genes preserves only minimal flanking sequences. J Biol Chem. 1982 Jun 25;257(12):6825–6835. [PubMed] [Google Scholar]
  52. Schreier P. H., Bothwell A. L., Mueller-Hill B., Baltimore D. Multiple differences between the nucleic acid sequences of the IgG2aa and IgG2ab alleles of the mouse. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4495–4499. doi: 10.1073/pnas.78.7.4495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Schroeder W. A., Shelton J. R., Shelton J. B., Apell G., Huisman T. H., Smith L. L., Carr W. R. Amino acid sequences in the -chains of adult bovine hemoglobins C-Rhodesia and D-Zambia. Arch Biochem Biophys. 1972 Sep;152(1):222–232. doi: 10.1016/0003-9861(72)90210-x. [DOI] [PubMed] [Google Scholar]
  54. Schroeder W. A., Shelton J. R., Shelton J. B., Robberson B., Babin D. R. A comparison of amino acid sequences in the beta-chains of adult bovine hemoglobins A and B. Arch Biochem Biophys. 1967 Apr;120(1):124–135. doi: 10.1016/0003-9861(67)90606-6. [DOI] [PubMed] [Google Scholar]
  55. Shafit-Zagardo B., Maio J. J., Brown F. L. KpnI families of long, interspersed repetitive DNAs in human and other primate genomes. Nucleic Acids Res. 1982 May 25;10(10):3175–3193. doi: 10.1093/nar/10.10.3175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Shapiro S. G., Schon E. A., Townes T. M., Lingrel J. B. Sequence and linkage of the goat epsilon I and epsilon II beta-globin genes. J Mol Biol. 1983 Sep 5;169(1):31–52. doi: 10.1016/s0022-2836(83)80174-0. [DOI] [PubMed] [Google Scholar]
  57. Shen C. K., Maniatis T. The organization of repetitive sequences in a cluster of rabbit beta-like globin genes. Cell. 1980 Feb;19(2):379–391. doi: 10.1016/0092-8674(80)90512-7. [DOI] [PubMed] [Google Scholar]
  58. Shen S. H., Slightom J. L., Smithies O. A history of the human fetal globin gene duplication. Cell. 1981 Oct;26(2 Pt 2):191–203. doi: 10.1016/0092-8674(81)90302-0. [DOI] [PubMed] [Google Scholar]
  59. Slightom J. L., Blechl A. E., Smithies O. Human fetal G gamma- and A gamma-globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes. Cell. 1980 Oct;21(3):627–638. doi: 10.1016/0092-8674(80)90426-2. [DOI] [PubMed] [Google Scholar]
  60. Suske G., Wenz M., Cato A. C., Beato M. The uteroglobin gene region: hormonal regulation, repetitive elements and complete nucleotide sequence of the gene. Nucleic Acids Res. 1983 Apr 25;11(8):2257–2271. doi: 10.1093/nar/11.8.2257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Van Arsdell S. W., Denison R. A., Bernstein L. B., Weiner A. M., Manser T., Gesteland R. F. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell. 1981 Oct;26(1 Pt 1):11–17. doi: 10.1016/0092-8674(81)90028-3. [DOI] [PubMed] [Google Scholar]
  62. Watanabe Y., Tsukada T., Notake M., Nakanishi S., Numa S. Structural analysis of repetitive DNA sequences in the bovine corticotropin-beta-lipotropin precursor gene region. Nucleic Acids Res. 1982 Mar 11;10(5):1459–1469. doi: 10.1093/nar/10.5.1459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Weiner A. M., Denison R. A. Either gene amplification or gene conversion may maintain the homogeneity of the multigene family encoding human U1 small nuclear RNA. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1141–1149. doi: 10.1101/sqb.1983.047.01.129. [DOI] [PubMed] [Google Scholar]
  64. Weiss E. H., Mellor A., Golden L., Fahrner K., Simpson E., Hurst J., Flavell R. A. The structure of a mutant H-2 gene suggests that the generation of polymorphism in H-2 genes may occur by gene conversion-like events. Nature. 1983 Feb 24;301(5902):671–674. doi: 10.1038/301671a0. [DOI] [PubMed] [Google Scholar]
  65. Zimmer E. A., Martin S. L., Beverley S. M., Kan Y. W., Wilson A. C. Rapid duplication and loss of genes coding for the alpha chains of hemoglobin. Proc Natl Acad Sci U S A. 1980 Apr;77(4):2158–2162. doi: 10.1073/pnas.77.4.2158. [DOI] [PMC free article] [PubMed] [Google Scholar]

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