Key Points
-
The analysis of unstable kernel phenotypes in maize led to the discovery and characterization of active class 2 DNA transposable elements (TEs).
-
These active elements are a very small fraction of the TEs found in plant genomes.
-
Access to all or part of the genomic sequence of an organism has led to the development of new techniques to analyse the life cycle of TEs and their interactions with the 'host' genome.
-
Two types of element — miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons — predominate in plant genomes.
-
MITEs are non-autonomous class 2 elements, but most can now be connected with two superfamilies of transposases: Tc1/mariner and PIF/harbinger.
-
LTR retrotransposons are the single largest component of plant genomes and are responsible for the recent genome expansion in some plants.
-
Despite evidence of recent activity, TEs that are present in high copy numbers in plant genomes are almost universally found to be defective and/or epigenetically silenced.
-
Some LTR retrotransposons are transcriptionally activated by various biotic and abiotic stresses.
-
Availability of mutant backgrounds that are deficient in epigenetic regulation offers the promise of activating previously silenced TEs and revealing new facets of their biology.
Abstract
Transposable elements are the single largest component of the genetic material of most eukaryotes. The recent availability of large quantities of genomic sequence has led to a shift from the genetic characterization of single elements to genome-wide analysis of enormous transposable-element populations. Nowhere is this shift more evident than in plants, in which transposable elements were first discovered and where they are still actively reshaping genomes.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
SanMiguel, P. & Bennetzen, J. L. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 81, 37–44 (1998).
Vicient, C. M. et al. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11, 1769–1784 (1999).
Meyers, B. C., Tingey, S. V. & Morgante, M. Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11, 1660–1676 (2001).A detailed survey of maize retrotransposons that combines random genomic sample sequencing, hybridization to bacterial artificial chromosomes and data obtained from a large collection of ESTs.
McClintock, B. Chromosome organization and genic expression. Cold Spring Harbor Symp. Quant. Biol. 16, 13–47 (1951).
Berg, D. E. & Howe, M. H. Mobile DNA (American Society for Microbiology Press, Washington, DC, 1989).
Wessler, S. R. Phenotypic diversity mediated by the maize transposable elements Ac and Spm. Science 242, 399–405 (1988).
Fedoroff, N. in Mobile DNA (eds Berg, D. E. & Howe, M. M.) 375–411 (American Society for Microbiology Press, Washington, DC, 1989).
Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, A. M. Mobile DNA II (American Society for Microbiology Press, Washington, DC, 2002).The newest edition of the transposable element bible.
McDonald, J. F. Transposable elements: possible catalysts of organismic evolution. Trends Ecol. Evol. 10, 123–126 (1995).
Kidwell, M. G. & Lisch, D. Transposable elements as sources of variation in animals and plants. Proc. Natl Acad. Sci. USA. 94, 7704–7711 (1997).
Johns, M. A., Mottinger, J. & Freeling, M. A low copy number, copia-like transposon in maize. EMBO J. 4, 1093–1102 (1985).
Varagona, M. J., Purugganan, M. & Wessler, S. R. Alternative splicing induced by insertion of retrotransposons into the maize waxy gene. Plant Cell 4, 811–820 (1992).
Vignols, F., Rigau, J., Torres, M. A., Capellades, M. & Puigdomenech, P. The brown midrib3 (bm3) mutation in maize occurs in the gene encoding caffeic acid O methyltransferase. Plant Cell 7, 407–416 (1995).
Britten, R. J., Graham, D. E. & Neufeld, B. R. Analysis of repeating DNA sequences by reassociation kinetics. Methods Enzymol. 29, 363–405 (1974).
Goldberg, R. B. DNA sequence organization in the soybean plant. Biochem. Genet. 16, 45–68 (1978).
Singer, M. F. SINEs and LINEs: highly repeated short and long interspersed sequences in mammals. Cell 28, 433–434 (1982).
Yoshioka, Y. et al. 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 (1993).
Leeton, P. R. J. & Smyth, D. R. An abundant LINE-like element amplified in the genome of Lilium speciosum. Mol. Gen. Genet. 237, 97–104 (1993).
Bureau, T. E. & Wessler, S. R. Tourist: a large family of inverted-repeat elements frequently associated with maize genes. Plant Cell 4, 1283–1294 (1992).
Bureau, T. E. & Wessler, S. R. Stowaway: a new family of inverted-repeat elements associated with genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6, 907–916 (1994).
Bureau, T. E., Ronald, P. C. & Wessler, S. R. A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl Acad. Sci. USA. 93, 8524–8529 (1996).
Wessler, S. R., Bureau, T. E. & White, S. E. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5, 814–821 (1995).
Oosumi, T., Garlick, B. & Belknap, W. R. Identification of putative nonautonomous transposable elements associated with several transposon families in Caenorhabditis elegans. J. Mol. Evol. 43, 11–18 (1996).
Tu, Z. Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti. Proc. Natl Acad. Sci. USA. 94, 7475–7480 (1997).
Tu, Z. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc. Natl Acad. Sci. USA. 98, 1699–1704 (2001).This paper reports the use of new software (available at the author's web site – see links box) that is designed to rapidly identify MITEs on the basis of their structural characteristics.
Feschotte, C. & Mouchès, C. Recent amplification of miniature inverted-repeat transposable elements in the vector mosquito Culex pipiens: characterization of the Mimo. family. Gene 250, 109–116 (2000).
Izsvak, Z. et al. Short inverted-repeat transposable elements in teleost fish and implications for a mechanism of their amplification. J. Mol. Evol. 48, 13–21 (1999).
Unsal, K. & Morgan, G. T. A novel group of families of short interspersed repetitive elements (SINEs) in Xenopus: evidence of a specific target site for DNA-mediated transposition of inverted-repeat SINEs. J. Mol. Biol. 248, 812–823 (1995).
Morgan, G. T. Identification in the human genome of mobile elements spread by DNA-mediated transposition. J. Mol. Biol. 254, 1–5 (1995).
Smit, A. F. A. & Riggs, A. D. Tiggers and DNA transposon fossils in the human genome. Proc. Natl Acad. Sci. USA. 93, 1443–1448 (1996).
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).
Turcotte, K., Srinivasan, S. & Bureau, T. Survey of transposable elements from rice genomic sequences. Plant J. 25, 169–179 (2001).
Jiang, N. & Wessler, S. R. Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements. Plant Cell 13, 2553–2564 (2001).
Zhang, Q., Arbuckle, J. & Wessler, S. R. Recent, extensive and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker. (Hbr) into genic regions of maize. Proc. Natl Acad. Sci. USA. 97, 1160–1165 (2000).
Feschotte, C., Zhang, X. & Wessler, S. R. in Mobile DNA II (eds Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, A. M.) (American Society of Microbiology Press, Washington, DC, in the press).
Feschotte, C. & Mouchès, C. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol. Biol. Evol. 17, 730–737 (2000).
Feschotte, C. & Wessler, S. R. Mariner-like transposases are widespread and diverse in flowering plants. Proc. Natl Acad. Sci. USA. 99, 280–285 (2002).Database searches and PCR experiments with plant-specific degenerate primers were combined to show that mariner -like TEs have successfully colonized many angiosperm genomes.
Walker, E. L., Eggleston, W. B., Demopulos, D., Kermicle, J. & Dellaporta, S. L. Insertions of a novel class of transposable elements with a strong target site preference at the r locus of maize. Genetics 146, 681–693 (1997).
Zhang, X. et al. P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc. Natl Acad. Sci. USA. 98, 12572–12577 (2001).Reports the first connection between an active maize DNA transposon system and a Tourist -like MITE family. Here, a 'top-down' approach was used in the isolation of an element that is required for transpositional activity and the identification of a new superfamily of eukaryotic transposases.
Kapitonov, V. V. & Jurka, J. Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107, 27–37 (1999).
Le, Q. H., Turcotte, K. & Bureau, T. Tc8, a Tourist-like transposon in Caenorhabditis elegans. Genetics 158, 1081–1088 (2001).
Engels, W. R., Johnson-Schlitz, D. M., Eggleston, W. B. & Sved, J. High-frequency P element loss in Drosophila is homolog dependent. Cell 62, 515–525 (1990).
Rubin, E. & Levy, A. A. Abortive gap repair: underlying mechanism for Ds element formation. Mol. Cell. Biol. 17, 6294–6302 (1997).
Casacuberta, E., Casacuberta, J. M., Puigdomenech, P. & Monfort, A. Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrant family of elements. Plant J. 16, 79–85 (1998).
Wessler, S. R., Nagel, A. & Casa, A. M. in Proceedings of the Fourth International Rice Genetics Symposium. (eds Khush, G. S., Brar, D. S. & Hardy, B.) 107–116 (International Rice Research Institute, Los Baños, the Philippines, 2001).
Casa, A. M. et al. The MITE family heartbreaker (Hbr): molecular markers in maize. Proc. Natl Acad. Sci. USA. 97, 10083–10089 (2000).
Casa, A. M. et al. Evaluation of Hbr. (MITE) markers for assessment of genetic relationships among maize (Zea mays. L.) inbred lines. Theor. Appl. Genet. 104, 104–110 (2002).
Kumar, A. & Bennetzen, J. L. Plant retrotransposons. Annu. Rev. Genet. 33, 479–532 (1999).
Grandbastien, M.-A., Spielmann, A. & Caboche, M. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337, 376–380 (1989).
Hirochika, H. et al. Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell 8, 725–734 (1996).
Marillonnet, S. & Wessler, S. R. Extreme structural heterogeneity among the members of a maize retrotransposon family. Genetics 150, 1245–1256 (1998).
Joseph, J. L., Sentry, J. W. & Smyth, D. R. Interspecies distribution of abundant DNA sequences in Lilium. J. Mol. Evol. 30, 146–154 (1990).
Thomas, C. A. The genetic organization of chromosomes. Annu. Rev. Genet. 5, 237–256 (1971).
SanMiguel, P. et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765–768 (1996).
SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. & Bennetzen, J. L. The paleontology of intergene retrotransposons of maize. Nature Genet. 20, 43–45 (1998).References 55 and 56 show that LTR retrotransposons make up more than half of the maize genome and that amplification of several families is responsible for doubling the genome in the past 5–6 million years.
Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E. & Schulman, A. H. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl Acad. Sci. USA. 97, 6603–6607 (2000).Along with reference 3 , this study documents large variations in the copy number of BARE-1 retrotransposons among and within Hordeum . species. By correlating this variation with intraspecific variation in genome size and with local changes in environmental conditions, the authors suggest that TE-mediated alterations might be adaptive.
Sassaman, D. M. et al. Many human L1 elements are capable of retrotransposition. Nature Genet. 16, 37–43 (1997).
Pouteau, S., Grandbastien, M. A. & Boccara, M. Microbial elicitors of plant defense responses activate transcription of a retrotransposon. Plant J. 5, 535–542 (1994).
Hirochika, H. Activation of tobacco retrotransposons during tissue culture. EMBO J. 12, 2521–2528 (1993).
Hirochika, H., Sugimoto, K., Otsuki, Y. & Kanda, M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl Acad. Sci. USA. 93, 7783–7788 (1996).
Grandbastien, M.-A. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3, 181–189 (1998).
Curcio, M. J. & Garfinkel, D. J. New lines of host defense: inhibition of Ty1 retrotransposition by Fus3p and NER/TFIIH. Trends Genet. 15, 43–45 (1999).
Melayah, D., Bonnivard, E., Chalhoub, B., Audeon, C. & Grandbastien, M. A. The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant J. 28, 159–168 (2001).Illustrates the use of transposon display to detect de novo insertions of a moderately high-copy-number retrotransposon following stress induction.
Waugh, R. et al. Genetic distribution of BARE1 retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253, 687–694 (1997).
Suoniemi, A., Narvanto, A. & Schulman, A. H. The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol. Biol. 31, 295–306 (1996).
Jaaskelainen, M. et al. Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J. 20, 413–422 (1999).
Kimura, Y. et al. OARE-1, a Ty1-copia retrotransposon in oat activated by abiotic and biotic stresses. Plant Cell Physiol. 42, 1345–1354 (2001).
McClintock, B. The Suppressor–Mutator system of control of gene action in maize. Carnegie Inst. Wash. Yearb. 57, 415–429 (1958).
McClintock, B. Components of action of the regulators Spm and Ac. Carnegie Inst. Wash. Yearb. 64, 527–534 (1965).
Chandler, V. L. & Walbot, V. DNA modification of a maize transposable element correlates with loss of activity. Proc. Natl Acad. Sci. USA. 83, 1767–1771 (1986).
Chomet, P., Wessler, S. R. & Dellaporta, S. L. Inactivation of the maize transposable element Activator. is associated with its DNA modification. EMBO J. 6, 295–302 (1987).
Banks, J. A., Masson, P. & Fedoroff, N. Molecular mechanisms in the developmental regulation of the maize Suppressor–Mutator transposable element. Genes Dev. 2, 1364–1380 (1988).
Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).
Kakutani, T., Jeddeloh, J. A., Flowers, S. K., Munakata, K. & Richards, E. J. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl Acad. Sci. USA. 93, 12406–12411 (1996).
Bestor, T. H. DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes. Phil. Trans. R. Soc. Lond. B Biol. Sci. 326, 179–187 (1990).
Flavell, R. B. Inactivation of gene expression in plants as a consequence of specific sequence duplication. Proc. Natl Acad. Sci. USA. 91, 3490–3496 (1994).
Voinnet, O. RNA silencing as a plant immune system against viruses. Trends Genet. 17, 449–459 (2001).
Vaucheret, H. & Fagard, M. Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet. 17, 29–35 (2001).
Matzke, M. A., Matzke, A. J., Pruss, G. J. & Vance, V. B. RNA-based silencing strategies in plants. Curr. Opin. Genet. Dev. 11, 221–227 (2001).
Jeong, B. R., Wu-Scharf, D., Zhang, C. & Cerutti, H. Suppressors of transcriptional transgenic silencing in Chlamydomonas are sensitive to DNA-damaging agents and reactivate transposable elements. Proc. Natl Acad. Sci. USA. 99, 1076–1081 (2002).
Singer, T., Yordan, C. & Martienssen, R. A. Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes Dev. 15, 591–602 (2001).
Miura, A. et al. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212–214 (2001).
Hirochika, H., Okamoto, H. & Kakutani, T. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12, 357–369 (2000).
Wright, D. A. & Voytas, D. F. Athila4 of Arabidopsis and calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res. 12, 122–131 (2002).References 82–85 show that a subset of Arabidopsis retrotransposons and DNA transposons are transcriptionally regulated by the SWI2/SNF2 chromatin-remodelling factor DDM1.
Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet. 22, 94–97 (1999).
Jin, Y. K. & Bennetzen, J. L. Structure and coding properties of Bs1, a maize retrovirus-like transposon. Proc. Natl Acad. Sci. USA. 86, 6235–6239 (1989).
Jiang, N. et al. Dasheng: a recently amplified non-autonomous LTR element that is a major component of pericentromeric regions in rice. Genetics (in the press).
Witte, C. P., Le, Q. H., Bureau, T. & Kumar, A. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc. Natl Acad. Sci. USA. 98, 13778–13783 (2001).
Ogiwara, I., Miya, M., Ohshima, K. & Okada, N. Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs. Mol. Biol. Evol. 16, 1238–1250 (1999).
Kapitonov, V. V. & Jurka, J. Rolling-circle transposons in eukaryotes. Proc. Natl Acad. Sci. USA. 98, 8714–8719 (2001).
Lampe, D. J., Churchill, M. E. & Robertson, H. M. A purified mariner transposase is sufficient to mediate transposition in vitro. EMBO J. 15, 5470–5479 (1996).
Ivics, Z., Hackett, P. B., Plasterk, R. H. & Izsvak, Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91, 501–510 (1997).References 92 and 93 emphasize the power of phylogenetic analyses to reconstruct an active transposase from a subset of inactive TE copies. Following these breakthrough studies, the reconstructed elements have been further developed into efficient transformation and mutagenic tools for a wide range of organisms.
Jordan, I. K. & McDonald, J. F. Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements. Genetica 107, 3–13 (1999).
Lerat, E., Brunet, F., Bazin, C. & Capy, P. Is the evolution of transposable elements modular? Genetica 107, 15–25 (1999).
Malik, H. S. & Eickbush, T. H. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 11, 1187–1197 (2001).
Bowen, N. J. & McDonald, J. F. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 11, 1527–1540 (2001).
Schwarz-Sommer, Z., Le Clercq, L., Gobel, E. & Saedler, H. Cin4, an insert altering the structure of the A1 gene in Zea mays, exhibits properties of nonviral retrotransposons. EMBO J. 6, 3873–3880 (1987).
Wright, D. et al. Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana. Genetics 142, 569–578 (1996).
Deragon, J. M. et al. An analysis of retroposition in plants based on a family of SINEs from Brassica napus. J. Mol. Evol. 39, 378–386 (1994).
White, S. E., Habera, L. F. & Wessler, S. R. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc. Natl Acad. Sci. USA. 91, 11792–11796 (1994).
Purugganan, M. D. & Wessler, S. R. Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon. Proc. Natl Acad. Sci. USA. 91, 11674–11678 (1994).
Konieczny, A., Voytas, D. F., Cummings, M. P. & Ausubel, F. M. A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127, 801–809 (1991).
Gierl, A. The En/Spm transposable element of maize. Curr. Top. Microbiol. Immunol. 204, 145–159 (1996).
Chandler, V., Rivin, C. & Walbot, V. Stable non-mutator stocks of maize have sequences homologous to the Mu1 transposable element. Genetics 114, 1007–1021 (1986).
Parsons, J. D. Miropeats: graphical DNA sequence comparisons. Comput. Appl. Biosci. 11, 615–619 (1995).
Kurtz, S. & Schleiermacher, C. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15, 426–427 (1999).
Jurka, J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418–420 (2000).
Lindroth, A. M. et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292, 2077–2080 (2001).
Tompa, R. et al. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12, 65–68 (2002).A new microarray technique for genome-wide mapping of cytosine methylation reveals that various retrotransposons are the preferential targets of CpNpG methylation in Arabidopsis.
Steimer, A. et al. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12, 1165–1178 (2000).
Amedeo, P., Habu, Y., Afsar, K., Scheid, O. M. & Paszkowski, J. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405, 203–206 (2000).
Ketting, R. F., Haverkamp, T. H., Van Luenen, H. G. & Plasterk, R. H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99, 133–141 (1999).
Wu-Scharf, D., Jeong, B., Zhang, C. & Cerutti, H. Transgene and transposon silencing in Chlamydomonas reinhardtii. by a DEAH-box RNA helicase. Science 290, 1159–1162 (2000).This paper and reference 81 show that the silencing of a DNA transposon and a LTR retrotransposon in Chlamydomonas involve enzymatic components of both PTGS and TGS, but do not seem to require DNA methylation.
Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).
Jensen, S., Gassama, M. P. & Heidmann, T. Taming of transposable elements by homology-dependent gene silencing. Nature Genet. 21, 209–212 (1999).
Djikeng, A., Shi, H., Tschudi, C. & Ullu, E. RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24–26-nucleotide RNAs. RNA 7, 1522–1530 (2001).
Acknowledgements
We thank members of the Wessler lab, Z. Bao and E. Pritham for suggestions on the manuscript and stimulating discussions, and H. Cerrutti, S. Eddy, M.-A. Grandbastien, R. Martienssen, J. Tu and D. Voytas for providing helpful information and unpublished data. This work was supported by grants from the National Science Foundation (Plant Genome Initiative), the National Institute of Health, the Department of Energy and the University of Georgia Research Foundation to S.R.W.
Author information
Authors and Affiliations
Corresponding author
Related links
Related links
DATABASES
MaizeDB
The <i>Arabidopsis</i> Information Resource
FURTHER INFORMATION
Encyclopedia of Life Sciences
Glossary
- ENDOSPERM
-
A triploid nutritive tissue in flowering plants.
- EPIGENETIC
-
Any heritable change in gene expression that is not caused by a change in DNA sequence.
- ORTHOLOGOUS GENES
-
Homologous genes that originated through speciation (for example, human and mouse β-globin).
- PARALOGOUS GENES
-
Homologous genes that originated by gene duplication (for example, human α-globin and β-globin).
- ABORTIVE GAP REPAIR
-
The double-stranded DNA break left at the site of excision of a class 2 transposon is repaired by the host machinery (gap repair). This gap is sometimes repaired by making an identical copy of the excised transposon, using the element still present on the sister chromatid or the homologous chromosome as a template. The process can be incomplete due to slippage and mispairing events. Such aberrant repairs are commonly responsible for the origin of an internally deleted copy of the excised transposon.
- PROTOPLAST
-
A cell after the removal of its cell wall.
- BREAKAGE–FUSION–BRIDGE CYCLE
-
In somatic cells, a cycle of chromosome breakage (at Ds, for example), DNA replication, chromatid fusion (forming a dicentric chromosome) and formation of a chromosome bridge occurs during mitotic anaphase. A new round follows when the chromosome breaks yet again as the two centromeres are pulled to opposite poles.
Rights and permissions
About this article
Cite this article
Feschotte, C., Jiang, N. & Wessler, S. Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3, 329–341 (2002). https://doi.org/10.1038/nrg793
Issue Date:
DOI: https://doi.org/10.1038/nrg793
This article is cited by
-
Effect of salicylic acid on retrotransposon polymorphism induced by salinity stress in wheat (Triticum aestivum L.)
Cereal Research Communications (2024)
-
Mobility of mPing and its associated elements is regulated by both internal and terminal sequences
Mobile DNA (2023)
-
Investigation of B-atp6-orfH79 distributing in Chinese populations of Oryza rufipogon and analysis of its chimeric structure
BMC Plant Biology (2023)
-
Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes
BMC Biology (2023)
-
Selection signatures and population dynamics of transposable elements in lima bean
Communications Biology (2023)