Skip to main content
PMC home page
The Plant Cell logoLink to The Plant Cell
. 1995 Nov;7(11):1823–1833. doi: 10.1105/tpc.7.11.1823

The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes.

A V Vershinin 1, T Schwarzacher 1, J S Heslop-Harrison 1
PMCID: PMC161041  PMID: 8535136

Abstract

Repetitive DNA sequences in the terminal heterochromatin of rye (Secale cereale) chromosomes have consequences for the structural and functional organization of chromosomes. The large-scale genomic organization of these regions was studied using the telomeric repeat from Arabidopsis and clones of three nonhomologous, tandemly repeated, subtelomeric DNA families with complex but contrasting higher order structural organizations. Polymerase chain reaction analysis with a single primer showed a fraction of the repeat units of one family organized in a "head-to-head" orientation. Such structures suggest evolution of chromosomes by chromatid-type breakage-fusion-bridge cycles. In situ hybridization and pulse field gel electrophoresis showed the order of the repeats and the heterogeneity in the lengths of individual arrays. After Xbal digestion and pulse field gel electrophoresis, the telomeric and two subtelomeric clones showed strong hybridization signals from 40 to 100 kb, with a maximum at 50 to 60 kb. We suggest that these fragments define a basic higher order structure and DNA loop domains of regions of rye chromosomes consisting of arrays of tandemly organized sequences.

Full Text

The Full Text of this article is available as a PDF (2.5 MB).

Selected References

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

  1. Bedbrook J. R., Jones J., O'Dell M., Thompson R. D., Flavell R. B. A molecular description of telometic heterochromatin in secale species. Cell. 1980 Feb;19(2):545–560. doi: 10.1016/0092-8674(80)90529-2. [DOI] [PubMed] [Google Scholar]
  2. Bendich A. J., McCarthy B. J. DNA Comparisons among Barley, Oats, Rye, and Wheat. Genetics. 1970 Aug;65(4):545–565. doi: 10.1093/genetics/65.4.545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Biessmann H., Mason J. M. Telomeric repeat sequences. Chromosoma. 1994 Jun;103(3):154–161. doi: 10.1007/BF00368007. [DOI] [PubMed] [Google Scholar]
  4. Britten R. J., Kohne D. E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science. 1968 Aug 9;161(3841):529–540. doi: 10.1126/science.161.3841.529. [DOI] [PubMed] [Google Scholar]
  5. Cheung W. Y., Gale M. D. The isolation of high molecular weight DNA from wheat, barley and rye for analysis by pulse-field gel electrophoresis. Plant Mol Biol. 1990 May;14(5):881–888. doi: 10.1007/BF00016525. [DOI] [PubMed] [Google Scholar]
  6. Cross S. H., Allshire R. C., McKay S. J., McGill N. I., Cooke H. J. Cloning of human telomeres by complementation in yeast. Nature. 1989 Apr 27;338(6218):771–774. doi: 10.1038/338771a0. [DOI] [PubMed] [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dod B., Mottez E., Desmarais E., Bonhomme F., Roizés G. Concerted evolution of light satellite DNA in genus Mus implies amplification and homogenization of large blocks of repeats. Mol Biol Evol. 1989 Sep;6(5):478–491. doi: 10.1093/oxfordjournals.molbev.a040564. [DOI] [PubMed] [Google Scholar]
  9. Espinás M. L., Carballo M. Pulsed-field gel electrophoresis analysis of higher-order chromatin structures of Zea mays. Highly methylated DNA in the 50 kb chromatin structure. Plant Mol Biol. 1993 Mar;21(5):847–857. doi: 10.1007/BF00027116. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Ganal M. W., Broun P., Tanksley S. D. Genetic mapping of tandemly repeated telomeric DNA sequences in tomato (Lycopersicon esculentum). Genomics. 1992 Oct;14(2):444–448. doi: 10.1016/s0888-7543(05)80239-3. [DOI] [PubMed] [Google Scholar]
  12. Ganal M. W., Lapitan N. L., Tanksley S. D. Macrostructure of the tomato telomeres. Plant Cell. 1991 Jan;3(1):87–94. doi: 10.1105/tpc.3.1.87. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Manuelidis L. A view of interphase chromosomes. Science. 1990 Dec 14;250(4987):1533–1540. doi: 10.1126/science.2274784. [DOI] [PubMed] [Google Scholar]
  14. McClintock B. The Stability of Broken Ends of Chromosomes in Zea Mays. Genetics. 1941 Mar;26(2):234–282. doi: 10.1093/genetics/26.2.234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Murata M., Ogura Y., Motoyoshi F. Centromeric repetitive sequences in Arabidopsis thaliana. Jpn J Genet. 1994 Aug;69(4):361–370. doi: 10.1266/jjg.69.361. [DOI] [PubMed] [Google Scholar]
  16. Nelson W. G., Pienta K. J., Barrack E. R., Coffey D. S. The role of the nuclear matrix in the organization and function of DNA. Annu Rev Biophys Biophys Chem. 1986;15:457–475. doi: 10.1146/annurev.bb.15.060186.002325. [DOI] [PubMed] [Google Scholar]
  17. Peacock W. J., Dennis E. S., Rhoades M. M., Pryor A. J. Highly repeated DNA sequence limited to knob heterochromatin in maize. Proc Natl Acad Sci U S A. 1981 Jul;78(7):4490–4494. doi: 10.1073/pnas.78.7.4490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Reeves R., Nissen M. S. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem. 1990 May 25;265(15):8573–8582. [PubMed] [Google Scholar]
  19. Richards E. J., Ausubel F. M. Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell. 1988 Apr 8;53(1):127–136. doi: 10.1016/0092-8674(88)90494-1. [DOI] [PubMed] [Google Scholar]
  20. Richards E. J., Goodman H. M., Ausubel F. M. The centromere region of Arabidopsis thaliana chromosome 1 contains telomere-similar sequences. Nucleic Acids Res. 1991 Jun 25;19(12):3351–3357. doi: 10.1093/nar/19.12.3351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Röder M. S., Lapitan N. L., Sorrells M. E., Tanksley S. D. Genetic and physical mapping of barley telomeres. Mol Gen Genet. 1993 Apr;238(1-2):294–303. doi: 10.1007/BF00279558. [DOI] [PubMed] [Google Scholar]
  22. SCHILDKRAUT C. L., MARMUR J., DOTY P. Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol. 1962 Jun;4:430–443. doi: 10.1016/s0022-2836(62)80100-4. [DOI] [PubMed] [Google Scholar]
  23. Smith G. P. Evolution of repeated DNA sequences by unequal crossover. Science. 1976 Feb 13;191(4227):528–535. doi: 10.1126/science.1251186. [DOI] [PubMed] [Google Scholar]
  24. Toledo F., Le Roscouet D., Buttin G., Debatisse M. Co-amplified markers alternate in megabase long chromosomal inverted repeats and cluster independently in interphase nuclei at early steps of mammalian gene amplification. EMBO J. 1992 Jul;11(7):2665–2673. doi: 10.1002/j.1460-2075.1992.tb05332.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Wang K., Koop B. F., Hood L. A simple method using T4 DNA polymerase to clone polymerase chain reaction products. Biotechniques. 1994 Aug;17(2):236–238. [PubMed] [Google Scholar]
  26. Wevrick R., Willard H. F. Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: high-frequency array-length polymorphism and meiotic stability. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9394–9398. doi: 10.1073/pnas.86.23.9394. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wevrick R., Willard V. P., Willard H. F. Structure of DNA near long tandem arrays of alpha satellite DNA at the centromere of human chromosome 7. Genomics. 1992 Dec;14(4):912–923. doi: 10.1016/s0888-7543(05)80112-0. [DOI] [PubMed] [Google Scholar]
  28. Willard H. F., Waye J. S., Skolnick M. H., Schwartz C. E., Powers V. E., England S. B. Detection of restriction fragment length polymorphisms at the centromeres of human chromosomes by using chromosome-specific alpha satellite DNA probes: implications for development of centromere-based genetic linkage maps. Proc Natl Acad Sci U S A. 1986 Aug;83(15):5611–5615. doi: 10.1073/pnas.83.15.5611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Wu K. S., Tanksley S. D. PFGE analysis of the rice genome: estimation of fragment sizes, organization of repetitive sequences and relationships between genetic and physical distances. Plant Mol Biol. 1993 Oct;23(2):243–254. doi: 10.1007/BF00029001. [DOI] [PubMed] [Google Scholar]

Articles from The Plant Cell are provided here courtesy of Oxford University Press

RESOURCES