Skip to main content
SpringerLink
Log in

LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Retroelements and remnants thereof constitute a large fraction of the repetitive DNA of plant genomes. They include LTR (long terminal repeat) retrotransposons such as Ty1-copia and Ty3-gypsy retrotransposons, which are widespread in plant genomes and show structural similarity to retroviruses. Recently, non-LTR retrotransposons, lacking the long terminal repeats and subdivided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements), have been discovered as ubiquitous components of nuclear genomes in many species across the plant kingdom. LINEs are probably the most ancient class of retrotransposons in plant genomes, but the evolutionary borders between non-LTR retrotransposons, LTR retrotransposons and retroviruses are indistinct as shown by the detection of intermediate forms in other eukaryotic taxa. Transposition of non-LTR retrotransposons is only rarely observed in plants indicating that the majority of these retroelements are inactive and/or under regulation of the host genome. Transposition is poorly understood, but experimental evidence from other genetic systems, in particular from insect and mammalian species, shows that LINEs are able to transpose autonomously, while non-autonomous SINEs depend on the reverse transcription machinery of other retrotransposons. Fluorescence in situ hybridization demonstrated that different classes of retrotransposons differ largely in their chromosomal organization and are often excluded from blocks of rapidly homogenizing tandem repeats. In particular, LINEs contribute considerably to the repetitive DNA of nuclear plant genomes.

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

  • Bennetzen, J.L. and Kellogg, E.A. 1997. Do plants have a one-way ticket to genomic obesity? Plant Cell 9: 1509–1514.

    PubMed  Google Scholar 

  • Boeke, J.D. 1997. LINEs and Alus: the polyA connection. Nature Genet.16: 6–7.

    Google Scholar 

  • Danilevskaya, O.N., Arkhipova, I.R., Traverse, K.L. and Pardue, M.L. 1997. Promoting in tandem: the promotor for telomere transposons Het-Aand implications for the evolution of retroviral LTRs. Cell 88: 647–655.

    PubMed  Google Scholar 

  • Deragon, J.M., Gilbert, N., Rouquet, L., Lenoir, A., Arnaud, P. and Picard, G. 1996. A transcriptional analysis of the S1Bn (Brassica napus) family of SINE. Plant Mol. Biol. 32: 869–878.

    PubMed  Google Scholar 

  • Eickbush, T.H. 1994. Origin and evolutionary relationships of retroelements. In: S.S. Morse (Ed.), The Evolutionary Biology of Viruses, Raven Press, New York, pp. 121–157.

    Google Scholar 

  • Eickbush, T.H. 1997. Telomerase and retrotransposons: which came first? Science 277: 911–912.

    PubMed  Google Scholar 

  • Feng, Q., Moran, J.V., Kazazian, H.H. Jr. and Boeke, J.D. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for a retrotransposase required for retrotransposition. Cell 87: 905–916.

    PubMed  Google Scholar 

  • Feng, Q., Schumann, G. and Boeke, J.D. 1988. Retrotransposon R1Bm endonuclease cleaves the target sequence. Proc. Natl. Acad. Sci. USA 95: 2083–2088.

    Google Scholar 

  • Finnegan, D.J. 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103–107.

    Google Scholar 

  • Flavell, A.J., Pearce, S.R. and Kumar, A. 1994. Plant transposable elements and the genome. Curr. Opin. Genet. Dev. 4: 838–844.

    PubMed  Google Scholar 

  • Goubely, C., Arnaud, P., Tatout, C., Heslop-Harrison, J.S. and Deragon, J.M. 1999. S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in Brassica napus: identification of a preferred target site for asymmetrical methylation. Plant Mol. Biol. 39: 243–255.

    PubMed  Google Scholar 

  • Grandbastien, M.A. 1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3: 181–187.

    Article  Google Scholar 

  • Higashiyama, T., Noutoshi, Y., Fujie, M. and Yamada, T. 1997. Zepp, a LINE-like retrotransposon accumulated in the Chlorellatelomeric region. EMBO J 16: 3715–3723.

    PubMed  Google Scholar 

  • Knoop, V., Unseld, M., Marienfeld, J., Brandt, P., Sünkel, S., Ullrich, H. and Brennicke, A. 1996. copia-gypsy-and LINElike retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana. Genetics 142: 579–585.

    PubMed  Google Scholar 

  • Kubis, S., Heslop-Harrison, J.S., Desel, C. and Schmidt, T. 1998. The genomic organization of non-LTR retrotransposons (LINEs) from three Betaspecies and five other angiosperms. Plant Mol. Biol. 36: 821–831.

    PubMed  Google Scholar 

  • Kumar, A. 1998. The evolution of plant retroviruses: moving to green pastures. Trends Plant Sci. 3: 371–374.

    Google Scholar 

  • Kunze, R., Saedler, H. and Lönnig, W.E. 1997. Plant transposable elements. In: J.A. Callow (Ed.), Advances in Botanical Research, Vol. 27, Academic Press, San Diego/London etc., pp. 331–470.

    Google Scholar 

  • Leeton, P.R.J. and Smyth, D.R. 1993. An abundant LINE-like element amplified in the genome of Lilium speciosum. Mol. Gen. Genet. 237: 97–104.

    Google Scholar 

  • Lenoir, A., Cournoyer, B., Warwick, S., Picard, G. and Deragon, J.M. 1997. Evolution of SINE S1 retroposons in Cruciferae plant Species. Mol. Biol. Evol. 14: 934–941.

    PubMed  Google Scholar 

  • Luan, D.D., Korman, M.H., Jakubczak, J.L. and Eickbush, T.H. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72: 595–605.

    PubMed  Google Scholar 

  • Mochizuki, K., Umeda, M., Ohtsubo, H. and Ohtsubo, 1992. Characterization of a plant SINE, pSINE1, in rice genomes. Jpn. J. Genet. 57: 155–166.

    Google Scholar 

  • Moran, J.V., DeBerardinis, R.J. and Kazazian, H.H. Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530–1534.

    PubMed  Google Scholar 

  • Noma, K., Ohtsubo, E. and Ohtsubo, H. 1999. Non-LTR retrotransposons (LINEs) as ubiquitous components of plant genomes. Mol. Gen. Genet. 261: 71–79.

    PubMed  Google Scholar 

  • Noutoshi, Y., Arai, R., Fujie, M. and Yamada, T. 1998. Structure of the Chlorella Zeppretrotransposon: Zeppclusters in the genome. Mol. Gen. Genet. 259: 256–263.

    PubMed  Google Scholar 

  • Ohshima, K., Hamada, M., Terai, Y. and Okada, N. 1996. The 30-ends of tRNA-derived short interspersed repetitive elements are derived from the 30-ends of long interspersed repetitive elements. Mol. Cell. Biol. 16: 3756–3764.

    Google Scholar 

  • Pardue, M.L., Danilevskaya, O.N., Traverse, K.L. and Lowenhaupt, K. 1997. Evolutionary links between telomeres and transposable Elements. Genetica 100: 73–84.

    PubMed  Google Scholar 

  • SanMiguel, P., Tikhonov, A., Jin, Y.-K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., Avramova, Z., and Bennetzen, J.L. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765–768.

    Google Scholar 

  • Schmidt, T. and Heslop-Harrison, J.S. 1998. Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci. 3: 195–199.

    Google Scholar 

  • Schmidt, T., Kubis, S. and Heslop-Harrison, J.S. 1995. Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgarisL.): LINEs and Ly1-copia-like elements as major components of the genome. Chrom. Res. 3: 335–345.

    PubMed  Google Scholar 

  • Schwarz-Sommer, Z., Leclercq, L., Goebel, E. and Saedler, H. 1987. Cin4, an insert altering the structure of the A1gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 13: 3873–3880.

    Google Scholar 

  • Tatout, C., Lavie, L. and Deragon, J.M. 1998. Similar target site selection occurs in integration of plant and mammalian retroposons. J. Mol. Evol. 47: 463–470.

    PubMed  Google Scholar 

  • Wessler, S.R., Bureau, T.E. and White, S.E. 1995. LTRretrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814–821.

    PubMed  Google Scholar 

  • Wright, D.A., Ke, N., Smalle, J., Hauge, B.M., Goodman, H.M. and Voytas, D.F. 1996. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. Genetics 142: 569–578.

    PubMed  Google Scholar 

  • Xiong, Y. and Eickbush, T.H. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J.9: 3353–3362.

    PubMed  Google Scholar 

  • Yoshioka, Y., Matsumoto, S., Kojima, S., Ohshima, K., Okada, N. and Machida, Y. 1993. Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc. Natl. Acad. Sci. USA: 90: 6562–6566.

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Plant Molecular Cytogenetics Group, Institute of Crop Science and Plant Breeding, Christian Albrechts University of Kiel, Olshausenstr. 40, 24118, Kiel, Germany

    Thomas Schmidt

Authors
  1. Thomas Schmidt
    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

Schmidt, T. LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40, 903–910 (1999). https://doi.org/10.1023/A:1006212929794

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1006212929794

Search

Navigation