Controlled activation of retrotransposition for plant breeding

Current Opinion in Biotechnology

Volumn 32, Issue , 2015, Pages 200-206

  Paszkowski, Jerzy ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ENVIRONMENTAL REGULATIONS; GENES;

CROP IMPROVEMENT; GENETIC VARIATION; PHENOTYPIC DIVERSITY; PHENOTYPIC TRAITS; PLANT BREEDING; REGULATORY ORGANIZATIONS; RETROTRANSPOSITION; TRANSPOSABLE ELEMENTS;

AGRICULTURE;

ARABIDOPSIS; CROP MANAGEMENT; DNA METHYLATION; EPIGENETICS; GENE ACTIVATION; GENE FUNCTION; GENETIC VARIABILITY; NONHUMAN; PHENOTYPIC VARIATION; PLANT BREEDING; REGULATORY MECHANISM; RETROPOSON; REVIEW; ANIMAL; BREEDING; GENETICS; HUMAN; PHENOTYPE; PLANT; PLANT GENOME;

RETROPOSON;

ANIMALS; BREEDING; GENETIC VARIATION; GENOME, PLANT; HUMANS; PHENOTYPE; PLANTS; RETROELEMENTS;

EID: 84922620312     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2015.01.003     Document Type: Review

References (62)

1. Kapitonov V.V., Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 2008, 9:411-412. [author reply 414].
2. Gao D., Chen J., Chen M., Meyers B.C., Jackson S. A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLOS ONE 2012, 7:e32010.
3. Tenaillon M.I., Hollister J.D., Gaut B.S. A triptych of the evolution of plant transposable elements. Trends Plant Sci 2010, 15:471-478.
4. Du J., Tian Z., Hans C.S., Laten H.M., Cannon S.B., Jackson S.A., Shoemaker R.C., Ma J. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 2010, 63:584-598.
5. Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., Zhang J., Fulton L., Graves T.A., et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326:1112-1115.
6. Naito K., Zhang F., Tsukiyama T., Saito H., Hancock C.N., Richardson A.O., Okumoto Y., Tanisaka T., Wessler S.R. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 2009, 461:1130-1134.
7. Liu R., Vitte C., Ma J., Mahama A.A., Dhliwayo T., Lee M., Bennetzen J.L. A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A 2007, 104:11844-11849.
8. Ammiraju J.S., Zuccolo A., Yu Y., Song X., Piegu B., Chevalier F., Walling J.G., Ma J., Talag J., Brar D.S., et al. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 2007, 52:342-351.
9. Lisch D. How important are transposons for plant evolution?. Nat Rev Genet 2013, 14:49-61.
10. Johns M.A., Mottinger J., Freeling M. A low copy number, copia-like transposon in maize. EMBO J 1985, 4:1093-1101.
11. McClintock B. The significance of responses of the genome to challenge. Science 1984, 226:792-801.
12. Pumplin N., Voinnet O. RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 2013, 11:745-760.
13. Grandbastien M.A., Spielmann A., Caboche M. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 1989, 337:376-380.
14. Steimer A., Amedeo P., Afsar K., Fransz P., Mittelsten Scheid O., Paszkowski J. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 2000, 12:1165-1178.
15. Cheng X., Wang M., Lee H.K., Tadege M., Ratet P., Udvardi M., Mysore K.S., Wen J. An efficient reverse genetics platform in the model legume Medicago truncatula. New Phytol 2014, 201:1065-1076.
16. Yarce J.C., Lee H.K., Tadege M., Ratet P., Mysore K.S. Forward genetics screening of Medicago truncatula Tnt1 insertion lines. Methods Mol Biol 2013, 1069:93-100.
17. Duangpan S., Zhang W., Wu Y., Jansky S.H., Jiang J. Insertional mutagenesis using Tnt1 retrotransposon in potato. Plant Physiol 2013, 163:21-29.
18. Cui Y., Barampuram S., Stacey M.G., Hancock C.N., Findley S., Mathieu M., Zhang Z., Parrott W.A., Stacey G. Tnt1 retrotransposon mutagenesis: a tool for soybean functional genomics. Plant Physiol 2013, 161:36-47.
19. Grandbastien M.A., Audeon C., Bonnivard E., Casacuberta J.M., Chalhoub B., Costa A.P., Le Q.H., Melayah D., Petit M., Poncet C., et al. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res 2005, 110:229-241.
20. Anca I.A., Fromentin J., Bui Q.T., Mhiri C., Grandbastien M.A., Simon-Plas F. Different tobacco retrotransposons are specifically modulated by the elicitor cryptogein and reactive oxygen species. J Plant Physiol 2014, 171:1533-1540.
21. Takeda S., Sugimoto K., Kakutani T., Hirochika H. Linear DNA intermediates of the Tto1 retrotransposon in Gag particles accumulated in stressed tobacco and Arabidopsis thaliana. Plant J 2001, 28:307-317.
22. Bohmdorfer G., Tramontano A., Luxa K., Bachmair A. A synthetic biology approach allows inducible retrotransposition in whole plants. Syst Synth Biol 2010, 4:133-138.
23. Hirochika H., Sugimoto K., Otsuki Y., Tsugawa H., Kanda M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci U S A 1996, 93:7783-7788.
24. Ding Y., Wang X., Su L., Zhai J., Cao S., Zhang D., Liu C., Bi Y., Qian Q., Cheng Z., et al. SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice. Plant Cell 2007, 19:9-22.
25. Miyao A., Tanaka K., Murata K., Sawaki H., Takeda S., Abe K., Shinozuka Y., Onosato K., Hirochika H. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 2003, 15:1771-1780.
26. Fukai E., Dobrowolska A.D., Madsen L.H., Madsen E.B., Umehara Y., Kouchi H., Hirochika H., Stougaard J. Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. Plant Mol Biol 2008, 68:653-663.
27. Tsukahara S., Kobayashi A., Kawabe A., Mathieu O., Miura A., Kakutani T. Bursts of retrotransposition reproduced in Arabidopsis. Nature 2009, 461:423-426.
28. Grandbastien M.A. LTR retrotransposons, handy hitchhikers of plant regulation and stress response. Biochim Biophys Acta 2014, In press. 10.1016/j.bbagrm.2014.07.017.
29. Miguel C., Marum L. An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond. J Exp Bot 2011, 62:3713-3725.
30. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010, 11:204-220.
31. Reinders J., Wulff B.B., Mirouze M., Mari-Ordonez A., Dapp M., Rozhon W., Bucher E., Theiler G., Paszkowski J. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 2009, 23:939-950.
32. Lindroth A.M., Cao X., Jackson J.P., Zilberman D., McCallum C.M., Henikoff S., Jacobsen S.E. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 2001, 292:2077-2080.
33. Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002, 416:556-560.
34. Jeddeloh J.A., Stokes T.L., Richards E.J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 1999, 22:94-97.
35. Lisch D. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 2009, 60:43-66.
36. Lisch D., Slotkin R.K. Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts. Int Rev Cell Mol Biol 2011, 292:119-152.
37. Slotkin R.K., Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 2007, 8:272-285.
38. Mirouze M., Reinders J., Bucher E., Nishimura T., Schneeberger K., Ossowski S., Cao J., Weigel D., Paszkowski J., Mathieu O. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 2009, 461:427-430.
39. Pecinka A., Dinh H.Q., Baubec T., Rosa M., Lettner N., Mittelsten Scheid O. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 2010, 22:3118-3129.
40. Tittel-Elmer M., Bucher E., Broger L., Mathieu O., Paszkowski J., Vaillant I. Stress-induced activation of heterochromatic transcription. PLoS Genet 2010, 6:e1001175.
41. Ito H., Gaubert H., Bucher E., Mirouze M., Vaillant I., Paszkowski J. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 2011, 472:115-119.
42. Cavrak V.V., Lettner N., Jamge S., Kosarewicz A., Bayer L.M., Mittelsten Scheid O. How a retrotransposon exploits the plant's heat stress response for its activation. PLoS Genet 2014, 10:e1004115.
43. El Baidouri M., Panaud O. Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biol Evol 2013, 5:954-965.
44. Cui X., Cao X. Epigenetic regulation and functional exaptation of transposable elements in higher plants. Curr Opin Plant Biol 2014, 21c:83-88.
45. Song X., Wang D., Ma L., Chen Z., Li P., Cui X., Liu C., Cao S., Chu C., Tao Y., et al. Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development. Plant J 2012, 71:378-389.
46. Wei L., Gu L., Song X., Cui X., Lu Z., Zhou M., Wang L., Hu F., Zhai J., Meyers B.C., et al. Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A 2014, 111:3877-3882.
47. Cui X., Jin P., Cui X., Gu L., Lu Z., Xue Y., Wei L., Qi J., Song X., Luo M., et al. Control of transposon activity by a histone H3K4 demethylase in rice. Proc Natl Acad Sci U S A 2013, 110:1953-1958.
48. Erhard K.F., Parkinson S.E., Gross S.M., Barbour J.E., Lim J.P., Hollick J.B. Maize RNA polymerase IV defines trans-generational epigenetic variation. Plant Cell 2013, 25:808-819.
49. Barbour J.E., Liao I.T., Stonaker J.L., Lim J.P., Lee C.C., Parkinson S.E., Kermicle J., Simon S.A., Meyers B.C., Williams-Carrier R., et al. Required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. Plant Cell 2012, 24:1761-1775.
50. Erhard K.F., Stonaker J.L., Parkinson S.E., Lim J.P., Hale C.J., Hollick J.B. RNA polymerase IV functions in paramutation in Zea mays. Science 2009, 323:1201-1205.
51. Alleman M., Sidorenko L., McGinnis K., Seshadri V., Dorweiler J.E., White J., Sikkink K., Chandler V.L. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006, 442:295-298.
52. Schornack S., Moscou M.J., Ward E.R., Horvath D.M. Engineering plant disease resistance based on TAL effectors. Annu Rev Phytopathol 2013, 51:383-406.
53. Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346:1258096.
54. Mirouze M., Vitte C. Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. J Exp Bot 2014, 65:2801-2812.
55. Cowley M., Oakey R.J. Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet 2013, 9:e1003234.
56. McCue A.D., Nuthikattu S., Slotkin R.K. Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs. RNA Biol 2013, 10:1379-1395.
57. McCue A.D., Nuthikattu S., Reeder S.H., Slotkin R.K. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet 2012, 8:e1002474.
58. McCue A.D., Slotkin R.K. Transposable element small RNAs as regulators of gene expression. Trends Genet 2012, 28:616-623.
59. Nosaka M., Itoh J., Nagato Y., Ono A., Ishiwata A., Sato Y. Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS Genet 2012, 8:e1002953.
60. Mari-Ordonez A., Marchais A., Etcheverry M., Martin A., Colot V., Voinnet O. Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet 2013, 45:1029-1039.
61. Sarazin A., Voinnet O. Exploring new models of easiRNA biogenesis. Nat Genet 2014, 46:530-531.
62. Creasey K.M., Zhai J., Borges F., Van Ex F., Regulski M., Meyers B.C., Martienssen R.A. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 2014, 508:411-415.