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. 1993 Mar 11;21(5):1273–1279. doi: 10.1093/nar/21.5.1273

Identification and characterization of new human medium reiteration frequency repeats.

J Jurka 1, D J Kaplan 1, C H Duncan 1, J Walichiewicz 1, A Milosavljevic 1, G Murali 1, J F Solus 1
PMCID: PMC309293  PMID: 8464711

Abstract

We report nine new families of human medium reiteration frequency interspersed repetitive elements (MER elements). They were identified by computer-assisted analyses. Six of them were independently confirmed as repetitive families by DNA-DNA hybridization, and the number of elements for each of these families was estimated by plaque hybridization assay. The involvement of some of the reported MER elements in genetic rearrangements is demonstrated.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  2. Akahori Y., Handa H., Imai K., Abe M., Kameyama K., Hibiya M., Yasui H., Okamura K., Naito M., Matsuoka H. Sigma region located between C mu and C delta genes of human immunoglobulin heavy chain: possible involvement of tRNA-like structure in RNA splicing. Nucleic Acids Res. 1988 Oct 25;16(20):9497–9511. doi: 10.1093/nar/16.20.9497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Altruda F., Cervella P., Tarone G., Botta C., Balzac F., Stefanuto G., Silengo L. A human integrin beta 1 subunit with a unique cytoplasmic domain generated by alternative mRNA processing. Gene. 1990 Nov 15;95(2):261–266. doi: 10.1016/0378-1119(90)90369-3. [DOI] [PubMed] [Google Scholar]
  4. Batzer M. A., Kilroy G. E., Richard P. E., Shaikh T. H., Desselle T. D., Hoppens C. L., Deininger P. L. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11;18(23):6793–6798. doi: 10.1093/nar/18.23.6793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  6. Bottenus R. E., Ichinose A., Davie E. W. Nucleotide sequence of the gene for the b subunit of human factor XIII. Biochemistry. 1990 Dec 25;29(51):11195–11209. doi: 10.1021/bi00503a007. [DOI] [PubMed] [Google Scholar]
  7. Brini A. T., Lee G. M., Kinet J. P. Involvement of Alu sequences in the cell-specific regulation of transcription of the gamma chain of Fc and T cell receptors. J Biol Chem. 1993 Jan 15;268(2):1355–1361. [PubMed] [Google Scholar]
  8. Calabi F., Jarvis J. M., Martin L., Milstein C. Two classes of CD1 genes. Eur J Immunol. 1989 Feb;19(2):285–292. doi: 10.1002/eji.1830190211. [DOI] [PubMed] [Google Scholar]
  9. Chamberlain J. S., Gibbs R. A., Ranier J. E., Nguyen P. N., Caskey C. T. Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res. 1988 Dec 9;16(23):11141–11156. doi: 10.1093/nar/16.23.11141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Chen S. J., Chen Z., d'Auriol L., Le Coniat M., Grausz D., Berger R. Ph1+bcr- acute leukemias: implication of Alu sequences in a chromosomal translocation occurring in the new cluster region within the BCR gene. Oncogene. 1989 Feb;4(2):195–202. [PubMed] [Google Scholar]
  11. Collins F. S., Weissman S. M. The molecular genetics of human hemoglobin. Prog Nucleic Acid Res Mol Biol. 1984;31:315–462. doi: 10.1016/s0079-6603(08)60382-7. [DOI] [PubMed] [Google Scholar]
  12. Edwards A., Voss H., Rice P., Civitello A., Stegemann J., Schwager C., Zimmermann J., Erfle H., Caskey C. T., Ansorge W. Automated DNA sequencing of the human HPRT locus. Genomics. 1990 Apr;6(4):593–608. doi: 10.1016/0888-7543(90)90493-e. [DOI] [PubMed] [Google Scholar]
  13. Ewulonu U. K., Ravi L., Medof M. E. Characterization of the decay-accelerating factor gene promoter region. Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4675–4679. doi: 10.1073/pnas.88.11.4675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  15. Fields C. A., Grady D. L., Moyzis R. K. The human THE-LTR(O) and MstII interspersed repeats are subfamilies of a single widely distributed highly variable repeat family. Genomics. 1992 Jun;13(2):431–436. doi: 10.1016/0888-7543(92)90264-s. [DOI] [PubMed] [Google Scholar]
  16. Fujii J., Zarain-Herzberg A., Willard H. F., Tada M., MacLennan D. H. Structure of the rabbit phospholamban gene, cloning of the human cDNA, and assignment of the gene to human chromosome 6. J Biol Chem. 1991 Jun 25;266(18):11669–11675. [PubMed] [Google Scholar]
  17. Gibbs P. E., Zielinski R., Boyd C., Dugaiczyk A. Structure, polymorphism, and novel repeated DNA elements revealed by a complete sequence of the human alpha-fetoprotein gene. Biochemistry. 1987 Mar 10;26(5):1332–1343. doi: 10.1021/bi00379a020. [DOI] [PubMed] [Google Scholar]
  18. Gnarra J. R., Otani H., Wang M. G., McBride O. W., Sharon M., Leonard W. J. Human interleukin 2 receptor beta-chain gene: chromosomal localization and identification of 5' regulatory sequences. Proc Natl Acad Sci U S A. 1990 May;87(9):3440–3444. doi: 10.1073/pnas.87.9.3440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Higuchi K., Law S. W., Hoeg J. M., Schumacher U. K., Meglin N., Brewer H. B., Jr Tissue-specific expression of apolipoprotein A-I (ApoA-I) is regulated by the 5'-flanking region of the human ApoA-I gene. J Biol Chem. 1988 Dec 5;263(34):18530–18536. [PubMed] [Google Scholar]
  20. Horn G. T., Richards B., Merrill J. J., Klinger K. W. Characterization and rapid diagnostic analysis of DNA polymorphisms closely linked to the cystic fibrosis locus. Clin Chem. 1990 Sep;36(9):1614–1619. [PubMed] [Google Scholar]
  21. Jurka J., Milosavljevic A. Reconstruction and analysis of human Alu genes. J Mol Evol. 1991 Feb;32(2):105–121. doi: 10.1007/BF02515383. [DOI] [PubMed] [Google Scholar]
  22. Jurka J. Novel families of interspersed repetitive elements from the human genome. Nucleic Acids Res. 1990 Jan 11;18(1):137–141. doi: 10.1093/nar/18.1.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jurka J., Walichiewicz J., Milosavljevic A. Prototypic sequences for human repetitive DNA. J Mol Evol. 1992 Oct;35(4):286–291. doi: 10.1007/BF00161166. [DOI] [PubMed] [Google Scholar]
  24. Kaplan D. J., Jurka J., Solus J. F., Duncan C. H. Medium reiteration frequency repetitive sequences in the human genome. Nucleic Acids Res. 1991 Sep 11;19(17):4731–4738. doi: 10.1093/nar/19.17.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kimura S., Hong Y. S., Kotani T., Ohtaki S., Kikkawa F. Structure of the human thyroid peroxidase gene: comparison and relationship to the human myeloperoxidase gene. Biochemistry. 1989 May 16;28(10):4481–4489. doi: 10.1021/bi00436a054. [DOI] [PubMed] [Google Scholar]
  26. Labuda D., Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 1989 Apr 11;17(7):2477–2491. doi: 10.1093/nar/17.7.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Loftus J. C., Plow E. F., Frelinger A. L., 3rd, D'Souza S. E., Dixon D., Lacy J., Sorge J., Ginsberg M. H. Molecular cloning and chemical synthesis of a region of platelet glycoprotein IIb involved in adhesive function. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7114–7118. doi: 10.1073/pnas.84.20.7114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ludwig E. H., Blackhart B. D., Pierotti V. R., Caiati L., Fortier C., Knott T., Scott J., Mahley R. W., Levy-Wilson B., McCarthy B. J. DNA sequence of the human apolipoprotein B gene. DNA. 1987 Aug;6(4):363–372. doi: 10.1089/dna.1987.6.363. [DOI] [PubMed] [Google Scholar]
  29. Mackman N., Morrissey J. H., Fowler B., Edgington T. S. Complete sequence of the human tissue factor gene, a highly regulated cellular receptor that initiates the coagulation protease cascade. Biochemistry. 1989 Feb 21;28(4):1755–1762. doi: 10.1021/bi00430a050. [DOI] [PubMed] [Google Scholar]
  30. Matera A. G., Hellmann U., Schmid C. W. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 1990 Oct;10(10):5424–5432. doi: 10.1128/mcb.10.10.5424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nomiyama H., Tsuzuki T., Wakasugi S., Fukuda M., Shimada K. Interruption of a human nuclear sequence homologous to mitochondrial DNA by a member of the KpnI 1.8 kb family. Nucleic Acids Res. 1984 Jul 11;12(13):5225–5234. doi: 10.1093/nar/12.13.5225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Pittler S. J., Baehr W., Wasmuth J. J., McConnell D. G., Champagne M. S., vanTuinen P., Ledbetter D., Davis R. L. Molecular characterization of human and bovine rod photoreceptor cGMP phosphodiesterase alpha-subunit and chromosomal localization of the human gene. Genomics. 1990 Feb;6(2):272–283. doi: 10.1016/0888-7543(90)90567-e. [DOI] [PubMed] [Google Scholar]
  33. Poncz M., Schwartz E., Ballantine M., Surrey S. Nucleotide sequence analysis of the delta beta-globin gene region in humans. J Biol Chem. 1983 Oct 10;258(19):11599–11609. [PubMed] [Google Scholar]
  34. Rettenmeier R., Natt E., Zentgraf H., Scherer G. Isolation and characterization of the human tyrosine aminotransferase gene. Nucleic Acids Res. 1990 Jul 11;18(13):3853–3861. doi: 10.1093/nar/18.13.3853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Rogan P. K., Pan J., Weissman S. M. L1 repeat elements in the human epsilon-G gamma-globin gene intergenic region: sequence analysis and concerted evolution within this family. Mol Biol Evol. 1987 Jul;4(4):327–342. doi: 10.1093/oxfordjournals.molbev.a040448. [DOI] [PubMed] [Google Scholar]
  36. Rotter M., Zimmerman K., Poustka A., Soussi-Yanicostas N., Starzinski-Powitz A. The human embryonic myosin alkali light chain gene: use of alternative promoters and 3' non-coding regions. Nucleic Acids Res. 1991 Apr 11;19(7):1497–1504. doi: 10.1093/nar/19.7.1497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ryan S. C., Zielinski R., Dugaiczyk A. Structure of the gorilla alpha-fetoprotein gene and the divergence of primates. Genomics. 1991 Jan;9(1):60–72. doi: 10.1016/0888-7543(91)90221-y. [DOI] [PubMed] [Google Scholar]
  38. Samia J. A., Alexander S. J., Horton K. W., Auron P. E., Byers M. G., Shows T. B., Webb A. C. Chromosomal organization and localization of the human urokinase inhibitor gene: perfect structural conservation with ovalbumin. Genomics. 1990 Jan;6(1):159–167. doi: 10.1016/0888-7543(90)90461-3. [DOI] [PubMed] [Google Scholar]
  39. Shapiro L. H., Ashmun R. A., Roberts W. M., Look A. T. Separate promoters control transcription of the human aminopeptidase N gene in myeloid and intestinal epithelial cells. J Biol Chem. 1991 Jun 25;266(18):11999–12007. [PubMed] [Google Scholar]
  40. Skalnik D. G., Strauss E. C., Orkin S. H. CCAAT displacement protein as a repressor of the myelomonocytic-specific gp91-phox gene promoter. J Biol Chem. 1991 Sep 5;266(25):16736–16744. [PubMed] [Google Scholar]
  41. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  42. Stanford D. R., Holicky E. L., Perry C. A., Rehder K., Jr, Harvey S. E., Rohleder A. M., Wieben E. D. The snRNP E protein multigene family contains five pseudogenes with common mutations. DNA Seq. 1991;1(5):357–363. doi: 10.3109/10425179109020790. [DOI] [PubMed] [Google Scholar]
  43. Ueda S., Washio K., Kurosaki K. Human-specific sequences: isolation of species-specific DNA regions by genome subtraction. Genomics. 1990 Sep;8(1):7–12. doi: 10.1016/0888-7543(90)90219-k. [DOI] [PubMed] [Google Scholar]
  44. Vidal F., Mougneau E., Glaichenhaus N., Vaigot P., Darmon M., Cuzin F. Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):208–212. doi: 10.1073/pnas.90.1.208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Woods-Samuels P., Kazazian H. H., Jr, Antonarakis S. E. Nonhomologous recombination in the human genome: deletions in the human factor VIII gene. Genomics. 1991 May;10(1):94–101. doi: 10.1016/0888-7543(91)90489-2. [DOI] [PubMed] [Google Scholar]
  46. Yen P. H., Marsh B., Allen E., Tsai S. P., Ellison J., Connolly L., Neiswanger K., Shapiro L. J. The human X-linked steroid sulfatase gene and a Y-encoded pseudogene: evidence for an inversion of the Y chromosome during primate evolution. Cell. 1988 Dec 23;55(6):1123–1135. doi: 10.1016/0092-8674(88)90257-7. [DOI] [PubMed] [Google Scholar]
  47. Zucchi I., Schlessinger D. Distribution of moderately repetitive sequences pTR5 and LF1 in Xq24-q28 human DNA and their use in assembling YAC contigs. Genomics. 1992 Feb;12(2):264–275. doi: 10.1016/0888-7543(92)90373-z. [DOI] [PubMed] [Google Scholar]
  48. van der Feltz M. J., Shivji M. K., Allen P. B., Heisterkamp N., Groffen J., Wiedemann L. M. Nucleotide sequence of both reciprocal translocation junction regions in a patient with Ph positive acute lymphoblastic leukaemia, with a breakpoint within the first intron of the BCR gene. Nucleic Acids Res. 1989 Jan 11;17(1):1–10. doi: 10.1093/nar/17.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]

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