Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1984 May 25;12(10):4127–4138. doi: 10.1093/nar/12.10.4127

Simple sequences are ubiquitous repetitive components of eukaryotic genomes.

D Tautz, M Renz
PMCID: PMC318821  PMID: 6328411

Abstract

Simple sequences are stretches of DNA which consist of only one, or a few tandemly repeated nucleotides, for example poly (dA) X poly (dT) or poly (dG-dT) X poly (dC-dA). These two types of simple sequence have been shown to be repetitive and interspersed in many eukaryotic genomes. Several other types have been found by sequencing eukaryotic DNA. In this report we have undertaken a systematical survey for simple sequences. We hybridized synthetical simple sequence DNA to genome blots of phylogenetically different organisms. We found that many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes. We propose therefore that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression. This latter inference is supported by the fact that we have detected simple sequences only in the metabolically inactive micronucleus of the protozoan Stylonychia, but not in the metabolically active macronucleus which is derived from the micronucleus by chromosome diminution.

Full text

PDF
4127

Images in this article

4130Image
on p.4130

Selected References

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

  1. Ammermann D., Steinbrück G., von Berger L., Hennig W. The development of the macronucleus in the ciliated protozoan Stylonychia mytilus. Chromosoma. 1974 May 10;45(4):401–429. doi: 10.1007/BF00283386. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Chandrasekaran R., Birdsall D. L., Leslie A. G., Ratliff R. L. Left-handed DNA helices. Nature. 1980 Feb 21;283(5749):743–745. doi: 10.1038/283743a0. [DOI] [PubMed] [Google Scholar]
  3. Bishop J. O., Rosbash M. Polynucleotide sequences in eukaryotic DNA and RNA that form ribonuclease-resistant complexes with polyuridylic acid. J Mol Biol. 1974 May 5;85(1):75–86. doi: 10.1016/0022-2836(74)90130-2. [DOI] [PubMed] [Google Scholar]
  4. Denhardt D. T. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966 Jun 13;23(5):641–646. doi: 10.1016/0006-291x(66)90447-5. [DOI] [PubMed] [Google Scholar]
  5. Deugau K. V., Mitchel R. E., Birnboim H. C. Nucleotide sequence of polypyrimidines from cloned mouse DNA as determined by base-specific blockage of exonuclease action. Anal Biochem. 1983 Feb 15;129(1):88–97. doi: 10.1016/0003-2697(83)90056-8. [DOI] [PubMed] [Google Scholar]
  6. Dover G. Molecular drive: a cohesive mode of species evolution. Nature. 1982 Sep 9;299(5879):111–117. doi: 10.1038/299111a0. [DOI] [PubMed] [Google Scholar]
  7. Epplen J. T., McCarrey J. R., Sutou S., Ohno S. Base sequence of a cloned snake W-chromosome DNA fragment and identification of a male-specific putative mRNA in the mouse. Proc Natl Acad Sci U S A. 1982 Jun;79(12):3798–3802. doi: 10.1073/pnas.79.12.3798. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Flavell R. A., Van den Berg F. M., Grosveld G. C. Isolation and characterization of the oligo(dA-dT) clusters and their flanking DNA segments in the rabbit genome. J Mol Biol. 1977 Oct 5;115(4):715–735. doi: 10.1016/0022-2836(77)90111-5. [DOI] [PubMed] [Google Scholar]
  9. Gebhard W., Zachau H. G. Simple DNA sequences and dispersed repetitive elements in the vicinity of mouse immunoglobulin K light chain genes. J Mol Biol. 1983 Oct 25;170(2):567–573. doi: 10.1016/s0022-2836(83)80161-2. [DOI] [PubMed] [Google Scholar]
  10. Hamada H., Petrino M. G., Kakunaga T. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6465–6469. doi: 10.1073/pnas.79.21.6465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hamada H., Petrino M. G., Kakunaga T. Molecular structure and evolutionary origin of human cardiac muscle actin gene. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5901–5905. doi: 10.1073/pnas.79.19.5901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hentschel C. C. Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nuclease. Nature. 1982 Feb 25;295(5851):714–716. doi: 10.1038/295714a0. [DOI] [PubMed] [Google Scholar]
  13. Höchtl J., Zachau H. G. A novel type of aberrant recombination in immunoglobulin genes and its implications for V-J joining mechanism. Nature. 1983 Mar 17;302(5905):260–263. doi: 10.1038/302260a0. [DOI] [PubMed] [Google Scholar]
  14. Johnson D., Morgan A. R. Unique structures formed by pyrimidine-purine DNAs which may be four-stranded. Proc Natl Acad Sci U S A. 1978 Apr;75(4):1637–1641. doi: 10.1073/pnas.75.4.1637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kafatos F. C., Jones C. W., Efstratiadis A. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res. 1979 Nov 24;7(6):1541–1552. doi: 10.1093/nar/7.6.1541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kedes L. H. Histone genes and histone messengers. Annu Rev Biochem. 1979;48:837–870. doi: 10.1146/annurev.bi.48.070179.004201. [DOI] [PubMed] [Google Scholar]
  17. Kvist S., Roberts L., Dobberstein B. Mouse histocompatibility genes: structure and organisation of a Kd gene. EMBO J. 1983;2(2):245–254. doi: 10.1002/j.1460-2075.1983.tb01413.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lauth M. R., Spear B. B., Heumann J., Prescott D. M. DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of Oxytricha. Cell. 1976 Jan;7(1):67–74. doi: 10.1016/0092-8674(76)90256-7. [DOI] [PubMed] [Google Scholar]
  19. Lipps H. J., Nordheim A., Lafer E. M., Ammermann D., Stollar B. D., Rich A. Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus. Cell. 1983 Feb;32(2):435–441. doi: 10.1016/0092-8674(83)90463-4. [DOI] [PubMed] [Google Scholar]
  20. Loening U. E. The fractionation of high-molecular-weight ribonucleic acid by polyacrylamide-gel electrophoresis. Biochem J. 1967 Jan;102(1):251–257. doi: 10.1042/bj1020251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Miesfeld R., Krystal M., Arnheim N. A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is found between the human delta and beta globin genes. Nucleic Acids Res. 1981 Nov 25;9(22):5931–5947. doi: 10.1093/nar/9.22.5931. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Morgan A. R., Coulter M. B., Flintoff W. F., Paetkau V. H. Enzymatic synthesis of deoxyribonucleic acids with repeating sequences. A new repeating trinucleotide deoxyribonucleic acid, d(T-C-C)n-d(G-G-A)n. Biochemistry. 1974 Apr 9;13(8):1596–1603. doi: 10.1021/bi00705a007. [DOI] [PubMed] [Google Scholar]
  23. Nikaido T., Nakai S., Honjo T. Switch region of immunoglobulin Cmu gene is composed of simple tandem repetitive sequences. Nature. 1981 Aug 27;292(5826):845–848. doi: 10.1038/292845a0. [DOI] [PubMed] [Google Scholar]
  24. Nishioka Y., Leder P. Organization and complete sequence of identical embryonic and plasmacytoma kappa V-region genes. J Biol Chem. 1980 Apr 25;255(8):3691–3694. [PubMed] [Google Scholar]
  25. Ohno S., Epplen J. T. The primitive code and repeats of base oligomers as the primordial protein-encoding sequence. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3391–3395. doi: 10.1073/pnas.80.11.3391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Richards J. E., Gilliam A. C., Shen A., Tucker P. W., Blattner F. R. Unusual sequences in the murine immunoglobulin mu-delta heavy-chain region. Nature. 1983 Dec 1;306(5942):483–487. doi: 10.1038/306483a0. [DOI] [PubMed] [Google Scholar]
  27. Rogers J. Molecular biology. CACA sequences - the ends and the means? Nature. 1983 Sep 8;305(5930):101–102. doi: 10.1038/305101a0. [DOI] [PubMed] [Google Scholar]
  28. Russell D. W., Smith M., Cox D., Williamson V. M., Young E. T. DNA sequences of two yeast promoter-up mutants. Nature. 1983 Aug 18;304(5927):652–654. doi: 10.1038/304652a0. [DOI] [PubMed] [Google Scholar]
  29. Saffer J. D., Lerman M. I. Unusual class of Alu sequences containing a potential Z-DNA segment. Mol Cell Biol. 1983 May;3(5):960–964. doi: 10.1128/mcb.3.5.960. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Schaffner W., Kunz G., Daetwyler H., Telford J., Smith H. O., Birnstiel M. L. Genes and spacers of cloned sea urchin histone DNA analyzed by sequencing. Cell. 1978 Jul;14(3):655–671. doi: 10.1016/0092-8674(78)90249-0. [DOI] [PubMed] [Google Scholar]
  31. Sederoff R., Lowenstein L. Polypyrimidine segments in Drosophila melanogaster DNA: II. Chromosome location and nucleotide sequence. Cell. 1975 Jun;5(2):183–194. doi: 10.1016/0092-8674(75)90026-4. [DOI] [PubMed] [Google Scholar]
  32. Sharp P. A. Conversion of RNA to DNA in mammals: Alu-like elements and pseudogenes. Nature. 1983 Feb 10;301(5900):471–472. doi: 10.1038/301471a0. [DOI] [PubMed] [Google Scholar]
  33. Shen S. H., Smithies O. Human globin psi B2 is not a globin-related sequence. Nucleic Acids Res. 1982 Dec 11;10(23):7809–7818. doi: 10.1093/nar/10.23.7809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Shenkin A., Burdon R. H. Deoxyadenylate-rich and deoxyguanylate-rich regions in mammalian DNA. J Mol Biol. 1974 May 5;85(1):19–39. doi: 10.1016/0022-2836(74)90126-0. [DOI] [PubMed] [Google Scholar]
  35. Shenkin A., Burdon R. H. Deoxyadenylate-rich sequences in mammalian DNA. FEBS Lett. 1972 May 1;22(2):157–160. doi: 10.1016/0014-5793(72)80033-4. [DOI] [PubMed] [Google Scholar]
  36. Skinner D. M., Bonnewell V., Fowler R. F. Sites of divergence in the sequence of a complex satellite DNA and several cloned variants. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1151–1157. doi: 10.1101/sqb.1983.047.01.130. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. 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]
  39. Straus N. A., Birnboim H. C. Polypyrimidine sequences found in eukaryotic DNA have been conserved during evolution. Biochim Biophys Acta. 1976 Dec 13;454(3):419–428. doi: 10.1016/0005-2787(76)90268-9. [DOI] [PubMed] [Google Scholar]
  40. Stringer J. R. DNA sequence homology and chromosomal deletion at a site of SV40 DNA integration. Nature. 1982 Mar 25;296(5855):363–366. doi: 10.1038/296363a0. [DOI] [PubMed] [Google Scholar]
  41. Sures I., Lowry J., Kedes L. H. The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions. Cell. 1978 Nov;15(3):1033–1044. doi: 10.1016/0092-8674(78)90287-8. [DOI] [PubMed] [Google Scholar]
  42. Tautz D., Renz M. An optimized freeze-squeeze method for the recovery of DNA fragments from agarose gels. Anal Biochem. 1983 Jul 1;132(1):14–19. doi: 10.1016/0003-2697(83)90419-0. [DOI] [PubMed] [Google Scholar]
  43. Tautz D., Renz M. Simple DNA sequences of Drosophila virilis isolated by screening with RNA. J Mol Biol. 1984 Jan 15;172(2):229–235. doi: 10.1016/s0022-2836(84)80041-8. [DOI] [PubMed] [Google Scholar]
  44. Walmsley R. M., Szostak J. W., Petes T. D. Is there left-handed DNA at the ends of yeast chromosomes? Nature. 1983 Mar 3;302(5903):84–86. doi: 10.1038/302084a0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES