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Unmethylated regions in the intergenic spacer of maize and teosinte ribosomal RNA genes

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Abstract

The restriction endonucleases Hpa II and Msp I were used to examine cytosine methylation in the ribosomal RNA genes (rDNA) of inbred lines of maize and species of teosinte. In all of the rDNAs examined, Msp I (not sensitive to mCpG) digestion yielded a distribution of lower molecular weight fragments indicative of multiple recognition sites. The majority of the rDNA arrays in an individual were inaccessible to Hpa II (sensitive to mCpG) cleavage, but a significant fraction (10–25%) was cleaved at least once by Hpa II into repeat unit length fragments (9.1 kbp). In some maize inbred lines, one or two additional fragment populations (less than 9.1 kbp in length) were also produced by Hpa II digestion. All of the unmethylated Hpa II sites mapped to the intergenic spacer (IGS), and the major unmethylated site was located approximately 800 bp 5′ to the start of the 18S RNA coding sequence. An Eco RI polymorphism, present in the 26S gene of certain inbred lines and hybrids, was utilized to investigate the organization of unmethylated repeat units in the rDNA array. In double digest experiments with Hpa II/Eco RI, the fragments from repeat units with two Eco RI sites were sensitive to Hpa II digestion, whereas, the fragments from repeat units with a single Eco RI site were almost completely resistant to Hpa II digestion. Similar digestion patterns were also observed in Eco RII (sensitive to mCNG)/Eco RI digests. These results suggest that unmethylated and Eco RI polymorphic sites occur in the same repeat units.

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References

  1. Appels R, Honeycutt RL: rDNA evolution over a billion years. In: DuttaSK (ed) DNA Systematics II. Plants, pp. 81–135. CRC Press, Boca Raton (1986).

    Google Scholar 

  2. Bedbrook J, Gerlach WL, Thompson RD, Jones J, Flavell RB. Molecular cloning of higher plant DNA. In: Rubenstein I, Gengenbach B, Phillips RL (eds) Genetic Improvement of Crops, pp. 93–114. University of Minnesota Press (1978).

  3. Bennetzen JL: Covalent DNA modification and the regulation of mutator element transposition in maize. Mol Gen Genet 208: 45–51 (1987).

    Article  Google Scholar 

  4. Bennetzen JL, Brown WE, Springer PS: The state of DNA modification within and flanking maize transposable elements. In: Nelson O (ed) Plant Transposable Elements, pp. 237–250. Plenum Press (1988).

  5. Bianchi MW, Viotti A: DNA methylation and tissue-specific transcription of the storage protein genes of maize. Plant Mol Biol 11: 203–214 (1988).

    Google Scholar 

  6. Bird AP: Methylation of the genes coding for the 18S, 28S and 5S ribosomal RNA. In: TrautnerTA (ed) Methylation of DNA, pp. 129–141. Springer-Verlag, Berlin (1984);

    Google Scholar 

  7. Bird AP, Taggart MH, Gehring CA: Methylated and unmethylated ribosomal RNA genes in the mouse. J Mol Biol 152: 1–17 (1981).

    Article  PubMed  Google Scholar 

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

    Google Scholar 

  9. Chandler VL, Walbot V: DNA modification of a maize transposable element correlates with loss of activity. Proc Natl Acad Sci USA 83: 1767–1771 (1986).

    PubMed  Google Scholar 

  10. Delsney M, Larouche M, Penon P: Methylation pattern of radish (Raphanus sativus) nuclear ribosomal RNA genes. Plant Physiol 76: 627–632 (1984).

    Google Scholar 

  11. Deumling B: Sequence arrangement of a highly methylated satellite DNA of a plant, Scilla: A tandemly repeated inverted repeat. Proc Natl Acad Sci USA 78: 338–342 (1981).

    Google Scholar 

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

    PubMed  Google Scholar 

  13. Ellis THN, Goldsborough PB, Castleton JA: Transcription and methylation of flax rDNA. Nucleic Acids Res 11: 3047–3064 (1983).

    PubMed  Google Scholar 

  14. Flavell RB: The structure and control of expression of ribosomal RNA genes. Oxf Surv Plant Mol Cell Biol 3: 252–274 (1986).

    Google Scholar 

  15. Flavell RB, O'Dell M, Thompson WF: Cytosine methylation of ribosomal RNA genes and nucleolus organizer activity in wheat. In: Brandham PE, Bennett MD (eds) Kew Chromosome Conference II, pp. 11–17. George Allen and Unwin, London (1983).

    Google Scholar 

  16. Flavell RB, O'Dell MO, 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 

  17. Gama-Sosa MA, Wang R, Kuo KC, Gehrke CW, Ehrlich M: The 5-methylcytosine content of highly repeat sequences in human DNA. Nucleic Acids Res 11: 3087–3095 (1983).

    PubMed  Google Scholar 

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

    Google Scholar 

  19. 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 

  20. Laskey RA, Mills AD: Enhanced autoradiographic detection of 32P and 125I using intensifying screens and hypersensitized film. FEBS Lett 82: 314–316 (1977).

    PubMed  Google Scholar 

  21. Messing J, Carlson J, Hagen G, Rubenstein I, Oleson A: Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region. DNA 3: 31–40 (1984).

    PubMed  Google Scholar 

  22. McClelland M, Nelson M: The effect of site specific methylation on restriction endonuclease digestion. Nucleic Acids Res 13 Supp: r201-r207 (1985).

    PubMed  Google Scholar 

  23. McMullen MD, Hunter B, Phillips RL, Rubenstein I: The structure of the maize ribosomal DNA spacer region. Nucleic Acids Res 14: 4953–4968 (1984).

    Google Scholar 

  24. Nick H, Bowen B, Ferl RJ, Gilbert W: Detection of cytosine methylation in the maize alcohol dehydrogenase gene by genomic sequencing. Nature 319: 243–246 (1986).

    Google Scholar 

  25. Olmedilla A, Delcusso D, Delseny M: Methylation pattern of nuclear ribosomal RNA genes from rice (Oryza sativa). Plant Sci Lett 37: 123–127 (1984).

    Google Scholar 

  26. Perry RP: Processing of RNA. Ann Rev Biochem 45: 605–629 (1976).

    PubMed  Google Scholar 

  27. Phillips RL: Molecular cytogenetics of the nucleolus organizer region. In: WaldenDB (ed) Maize Breeding and Genetics, pp. 711–741. John Wiley and Sons, New York (1978).

    Google Scholar 

  28. Phillips RL, Kowles RV, McMullen MD, Enomoto S, Rubenstein I: Developmentally-timed changes in maize endosperm DNA. In: FreelingM (ed) Plant Genetics, pp. 739–754. Alan R. Liss, New York (1985).

    Google Scholar 

  29. Phillips RL, McMullen MD, Enomoto S, Rubenstein I: Ribosomal DNA in maize. In: Gustafson JP, Appels R (eds) Chromosome Structure and Function; Impact of New Concepts, pp. 201–214. Plenum Press, New York (1988).

    Google Scholar 

  30. Phillips RL, Wang AS, Kowles RV: Molecular and developmental cytogenetics of gene multiplicity in maize. Stadler Symp 15: 105–118 (1983).

    Google Scholar 

  31. Rivin CJ, Cullis CA, Walbot V: Evaluating quantitative variation in the genome of Zea mays. Genetics 113: 1009–1019 (1986).

    PubMed  Google Scholar 

  32. Rivin CJ, Zimmer EA, Cullis CA, Walbot V, Huynh T, Davis RW: Evaluation of genomic variability at the nucleic acid level. Plant Mol Biol Rep 1: 9–16 (1983).

    Google Scholar 

  33. Rivin CJ, Zimmer EA, Walbot V: Isolation of DNA and DNA recombinants from maize. In: SheridanWF (ed) Maize for Biological Research, pp. 161–164. Plant Molecular Biology Association, Charlottesville, VA (1982).

    Google Scholar 

  34. 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 

  35. Schwartz D, Dennis E: Transposase activity of the Ac controlling element in maize is regulated by its degree of methylation. Mol Gen Genet 205: 476–482 (1986).

    Google Scholar 

  36. Steele-Scott N, Kavanagh TA, Timmis JN: Methylation of rRNA genes in some higher plants. Plant Sci Let 35: 213–217 (1984).

    Article  Google Scholar 

  37. Takaiwa F, Oona K, Iada Y, Sugiura M: The complete sequence of a rice rRNA gene. Gene 37: 255–289 (1985).

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  39. Toloczyki C, FeixG: Occurrence of 9 homologous repeat units in the external spacer region of a nuclear maize rRNA gene unit. Nucleic Acids Res 14: 4969–4986 (1986).

    PubMed  Google Scholar 

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

    Google Scholar 

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

    PubMed  Google Scholar 

  42. Wu C: The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286: 854–860 (1980).

    PubMed  Google Scholar 

  43. Zimmer EA, Jupe ER, Walbot V: Ribosomal gene structure, variation and inheritance in maize and its ancestors. Genetics 120: 1125–1136 (1988).

    PubMed  Google Scholar 

  44. Zimmer EA, Newton KJ: A simple method for the isolation of high molecular weight DNA from individual maize seedlings and tissues. In: SheridanWF (ed) Maize for Biological Research, pp. 165–168. Plant Molecular Biology Association, Charlottesville, VA (1982).

    Google Scholar 

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  1. Eldon R. Jupe

    Present address: Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, 45267, Cincinnati, OH, USA

Authors and Affiliations

  1. Department of Biochemistry, Louisiana State University, USA

    Eldon R. Jupe & Elizabeth A. Zimmer

  2. Department of Botany, Louisiana State University, USA

    Elizabeth A. Zimmer

  3. Louisiana Agricultural Experiment Station, LSU Agricultural Center, 70803, Baton Rouge, LA, USA

    Elizabeth A. Zimmer

Authors
  1. Eldon R. Jupe
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  2. Elizabeth A. Zimmer
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Jupe, E.R., Zimmer, E.A. Unmethylated regions in the intergenic spacer of maize and teosinte ribosomal RNA genes. Plant Mol Biol 14, 333–347 (1990). https://doi.org/10.1007/BF00028770

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  • DOI: https://doi.org/10.1007/BF00028770

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