Skip to main content
SpringerLink
Log in

Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L.

  • Research Article
  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Methylation with respect to its degree and distribution throughout the 18S, 5.8S and 25S rRNA gene clusters (rDNA) and within single rDNA repeats in seedlings of the higher plant Cucurbita pepo L. (zucchini) was investigated. In this plant, which is characterized by several thousand repeats, at least 70% are completely or nearly completely methylated in CpGs and to a lower degree in CpNpGs. Detailed methylation analysis revealed that a fraction of about 3–4% of all repeats is hypomethylated near the transcription initiation site (TIS) which may indicate the fraction of active repeats in C. pepo. However, a different fraction (3–4% of all repeats) which is not methylated in all sites tested (including those at the TIS) is present in C. pepo and may thus represent active but differentially methylated rDNA. The results are discussed in context of recent models on methylation and gene activity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Blundy KS, Cullis CA, Hepburn AG: Ribosomal DNA methylation in a flax genotroph and a crown gall tumor. Plant Mol Biol 8: 217–225 (1987).

    Google Scholar 

  2. Boyes J, Bird A: DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64: 1123–1134 (1991).

    Article  PubMed  Google Scholar 

  3. Chaconas G, van der Sande J: 5′ 32P labelling of RNA and DNA restriction fragments. Meth Enzymol 65: 75–35 (1980).

    PubMed  Google Scholar 

  4. Delseny M, Laroche M, Penon P: Methylation pattern of radish (Raphanus sativus) nuclear ribosomal RNA genes. Plant Physiol 76: 627–1532 (1984).

    Google Scholar 

  5. Deltour R, Mosen H: Proposals for the macromolecular organization of the higher plant nucleolonema. Biol Cell 60: 75–86 (1987).

    Google Scholar 

  6. Doerfler W: DNA methylation and gene activity. Annu Rev Biochem 52: 93–124 (1983).

    Article  PubMed  Google Scholar 

  7. Echeverria M, Delcasso-Tremousaygue D, Delseny M: A nuclear protein binding to dA/dT-rich sequences upstream from the radish DNA promoter. Plant J 2: 211–219 (1992).

    Article  PubMed  Google Scholar 

  8. Ellis THN, Delseny M, Lee D, Burcham KWG: Methylated and undermethylated rDNA repeats are interspersed at random in two higher plant species. Plant Mol Biol 14: 73–80 (1989).

    Article  Google Scholar 

  9. Ellis THN, Goldsbrough PB, Castleton JA: Transcription and methylation of flax rDNA. Nucl Acids Res 11: 3047–3064 (1983).

    PubMed  Google Scholar 

  10. Feinberg AP, Vogelstein B: A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6–13 (1983).

    PubMed  Google Scholar 

  11. Flavell RB, O'Dell M, Thompson WF: Cytosine methylation of ribosomal RNA genes and nucleolus organiser activity in wheat. In: Bradham P, Bennet M (eds) Kew Chromosome Conference II, pp. 11–17. George Allen and Unwin, London (1983).

    Google Scholar 

  12. Flavell RB, O'Dell M, Thompson WF, Vincentz M, Sardana R, Barker RF: The differential expression of ribosomal RNA genes. Phil Trans R Soc Lond B 314: 385–397 (1986).

    Google Scholar 

  13. Flavell RB, O'Dell M, Thompson WF: Regulation of cytosine methylation in ribosomal DNA and nucleolus organizer expression in wheat. J Mol Biol 204: 523–534 (1988).

    Article  PubMed  Google Scholar 

  14. Ganal M, Hemleben V: Comparison of ribosomal RNA genes in four closely related Cucurbitaceae. Plant Syst Evol 154: 63–77 (1986).

    Google Scholar 

  15. Ganal M, Torres RA, Hemleben V: Complex structure of the ribosomal DNA spacer of Cucumis sativus (cucumber). Mol Gen Genet 212: 548–554 (1988).

    Article  PubMed  Google Scholar 

  16. Givens JF, Phillips RL: The nucleolus organizer region of maize (Zea mays L.). Chromosoma 57: 103–117 (1976).

    Article  Google Scholar 

  17. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A: Sequence specificity of methylation in higher plant DNA. Nature 292: 860–862 (1981).

    PubMed  Google Scholar 

  18. Gründler P, Unfried I, Pascher K, Schweizer D: rDNA intergenic region from Arabidopsis thaliana. Structural analysis, intraspecific variation and functional implications. J Mol Biol 221: 1209–1222 (1991).

    Article  PubMed  Google Scholar 

  19. Hemleben V, Leweke B, Roth A, Stadler J: Organization of highly repetitive satellite DNA from two Cucurbitaceae species (Cucumis melo and Cucumis sativus). Nucl Acids Res 10: 631–644 (1982).

    PubMed  Google Scholar 

  20. Hemleben V, Ganal M, Gerstner J, Schiebel K, Torres RA: Organization and length heterogeneity of plant ribosomal RNA genes. In: Kahl G (ed) Architecture of Eukaryotic Genes, pp. 371–383. VCH, Weinheim (1988).

    Google Scholar 

  21. Ingle J, Timmis JN, Sinclair J: The relationship between satellite DNA, ribosomal RNA gene redundancy, and genome size in plants. Plant Physiol 55: 496–501 (1975).

    Google Scholar 

  22. Jaenisch R, Jähner D: Methylation, expression and chromosomal position of genes in mammals. Biochim Biophys Acta 782: 1–9 (1984).

    PubMed  Google Scholar 

  23. Jupe ER, Zimmer EA: Unmethylated regions in the intergenic spacer of maize and teosinte ribosomal RNA genes. Plant Mol Biol 14: 333–347 (1990).

    Article  PubMed  Google Scholar 

  24. Kelly RJ, Siegel A: The Cucurbita maxima ribosomal DNA intergenic spacer has a complex structure. Gene 80: 239–248 (1990).

    Google Scholar 

  25. King K, Torres RA, Zentgraf U, Hemleben V: Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of Cucurbitaceae. J Mol Evol 36: 144–152 (1993).

    PubMed  Google Scholar 

  26. Long EO, Dawid IB: Repeated genes in eukaryotes. Annu Rev Biochem 49: 727–764 (1980).

    Article  PubMed  Google Scholar 

  27. Maniatis T, Fritsch EF, Sambrook J: Molecular Cloning, A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1982).

    Google Scholar 

  28. Martini G, O'Dell M, Flavell RB: Partial inactivation of wheat nucleolus organisers by the nucleolus organiser chromosomes from Aegilops umbellulata. Chromosoma 84: 687–700 (1982).

    Article  Google Scholar 

  29. Olmedilla A, Delcasso D, Delseny M: Methylation pattern of nuclear ribosomal RNA genes from rice (Oryzasativa). Plant Sci Lett 37: 123–127 (1984).

    Article  Google Scholar 

  30. Pennock DG, Reeder RH: In vitro methylation of Hpa II sites in Xenopus laevis rDNA does not affect its transcription in oocytes. Nucl Acids Res 12: 2225–2232 (1984).

    PubMed  Google Scholar 

  31. Razin A, Szyf M: DNA methylation patterns. Formation and function. Biochim Biophys Acta 782: 331–342 (1984).

    PubMed  Google Scholar 

  32. Rigby P, Dickmann M, Rhodes C, Berg P: Labelling desoxyribonucleic acid to high specific activity in vitro by nicktranslation with DNA polymerase I. Nucl Acids Res 7: 1263–1281 (1977).

    Google Scholar 

  33. Rogers SO, Bendich AJ: Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol 9: 509–520 (1987).

    Google Scholar 

  34. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989).

    Google Scholar 

  35. Schiebel K, von Waldburg G, Gerstner J, Hemleben V: Termination of transcription of ribosomal RNA genes of mung bean occurs within a 175 bp repetitive element of the spacer region. Mol Gen Genet 218: 302–307 (1989).

    Article  PubMed  Google Scholar 

  36. Schmitz ML, Maier UG, Brown JWS, Feix G: Specific binding of nuclear proteins to the promoter region of a maize nuclear rRNA gene unit. J Biol Chem 264: 1467–1472 (1989).

    PubMed  Google Scholar 

  37. Selker EU: DNA methylation and chromatin structure: a view from below. Trends Biochem Sci 15: 103–107 (1990).

    Article  PubMed  Google Scholar 

  38. Siegel A, Kolacz K: Heterogeneity in pumpkin ribosomal DNA. Plant Physiol 72: 166–171 (1983).

    Google Scholar 

  39. Sollner-Webb B, Mougey EB: News from the nucleolus: rRNA gene expression. Trends Biochem Sci 16: 58–62 (1991).

    Article  PubMed  Google Scholar 

  40. Taylor JH: DNA methylation and cellular differentiation. Springer-Verlag, Wien/New York (1984).

    Google Scholar 

  41. Thompson WF, Flavell RB: DNaseI sensitivity of ribosomal RNA genes in chromatin and nucleolar dominance in wheat. J Mol Biol 204: 535–548 (1988).

    Google Scholar 

  42. Timmis J, Ingle J: Quantitative regulation of gene activity in plants. Plant Physiol 56: 255–258 (1975).

    Google Scholar 

  43. Torres-Ruiz RA, Hemleben V: Use of ribosomal DNA spacer probes to distinguish cultivars of Cucurbita pepo L. and other Cucurbitaceae. Euphytica 53: 11–17 (1991).

    Google Scholar 

  44. Torres RA, Zentgraf U, Hemleben V: Species and genus specificity of the intergenic spacer (IGS) in the ribosomal RNA genes of Cucurbitaceae. Z Naturforsch 44c: 1029–1034 (1989).

    Google Scholar 

  45. Torres RA, Ganal M, Hemleben V: GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes. J Mol Evol 30: 170–181 (1990).

    PubMed  Google Scholar 

  46. von Kalm L, Vize PD, Smyth DR: An under-methylated region in the spacer of ribosomal RNA genes of Lilium henryi. Plant Mol Biol 6: 33–39 (1986).

    Google Scholar 

  47. Waterhouse RN, Boulter D, Gatehouse JA: An organspecific hypomethylation of cotyledon genomic rDNA in Pisum sativum L. FEBS Lett 209: 223–226 (1986).

    Article  Google Scholar 

  48. Watson JC, Kaufman LS, Thompson WF: Developmental regulation of cytosin methylation in the nuclear ribosomal RNA genes of Pisum sativum. J Mol Biol 193: 15–26 (1987).

    PubMed  Google Scholar 

  49. Zentgraf U, Ganal M, Hemleben V: Length heterogeneity of the rRNA precursor in cucumber (Cucumis sativus). Plant Mol Biol 15: 465–474 (1990).

    PubMed  Google Scholar 

  50. Zentgraf U, Hemleben V: Complex formation of nuclear proteins with the RNA polymerase I promoter and repeated elements in the external transcribed spacer of Cucumis sativus ribosomal DNA. Nucl Acids Res 14: 3685–3691 (1992).

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Lehrstuhl für Genetik, Institut für Mikrobiologie und Genetik, Ludwig Maximilians Universität München, Maria Ward Strasse 1a, 80638, München, FRG

    Ramon A. Torres-Ruiz

  2. Lehrstuhl für Allgemeine Genetik, Biologisches Institut der Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 7400, Tübingen, Germany

    Vera Hemleben

Authors
  1. Ramon A. Torres-Ruiz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vera Hemleben
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Torres-Ruiz, R.A., Hemleben, V. Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L.. Plant Mol Biol 26, 1167–1179 (1994). https://doi.org/10.1007/BF00040697

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00040697

Key words

Search

Navigation