Bursts of retrotransposition reproduced in Arabidopsis

Nature

Volumn 461, Issue 7262, 2009, Pages 423-426

  Tsukahara, Sayuri ^a,b   Kobayashi, Akie ^a   Kawabe, Akira ^a   Mathieu, Olivier ^c,d   Miura, Asuka ^a   Kakutani, Tetsuji ^a,b  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c UNIVERSITY OF GENEVA   (Switzerland)

^d UNIVERSITÉ CLERMONT AUVERGNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; COMPARATIVE STUDY; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOME; MOLECULAR ECOLOGY; MUTATION; PROTEIN; RNA; SPECIES OCCURRENCE;

ARABIDOPSIS; ARTICLE; EPIGENETICS; EVOLUTION; GENE DELETION; GENE REARRANGEMENT; GENETIC VARIABILITY; LONG TERMINAL REPEAT; MOLECULAR BIOLOGY; MUTATION; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; REVERSE TRANSCRIPTION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CENTROMERE; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; DNA, SATELLITE; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENE DOSAGE; GENOME, PLANT; GENOMIC INSTABILITY; GENOMICS; MUTAGENESIS, INSERTIONAL; PHENOTYPE; PHYLOGENY; RECOMBINATION, GENETIC; RETROELEMENTS; STOCHASTIC PROCESSES; TRANSCRIPTION FACTORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 70349276670     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08351     Document Type: Article

References (30)

1. Kumar, A. & Bennetzen, J. L. Plant retrotransposons. Annu. Rev. Genet. 33, 479-532 (1999).
2. Havecker, E. R., Gao, X. & Voytas, D. F. The diversity of LTR retrotransposons. Genome Biol. 5, 225 (2004).
3. Vitte, C. & Bennetzen, J. L. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc. Natl Acad. Sci. USA 103, 17638-17643 (2006).
4. Hawkins, J. S., Kim, H. & Nason, J. D. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16, 1252-1261 (2006).
5. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815 (2000).
6. Le, Q. H., Wright, S., Yu, Z. & Bureau, T. Transposon diversity in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 97, 7376-7381 (2000).
7. Peterson-Burch, B. D., Nettleton, D. & Voytas, D. F. Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biol. 5, R78 (2004).
8. Steimer, A. et al. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12, 1165-1178 (2000).
9. Lippman, Z., May, B., Yordan, C., Singer, T. & Martienssen, R. Distinct mechanisms to determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1, E67 (2003).
10. Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926-1928 (1993).
11. 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).
12. Lucas, H., Feuerbach, F., Kunert, K., Grandbastien, M.-A. & Caboche, M. RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. EMBO J. 14, 2364-2373 (1995).
13. Hirochika, H., Okamoto, H. & Kakutani, T. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12, 357-369 (2000).
14. Finnegan, E., Peacock, J. & Dennis, E. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc. Natl Acad. Sci. USA 93, 8449-8454 (1996).
15. Bender, J. DNA methylation and epigenetics. Annu. Rev. Plant Biol. 55, 41-68 (2004).
16. Chan, S. W., Henderson, I. R. & Jacobsen, S. E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nature Rev. Genet. 6, 351-360 (2005).
17. Kakutani, T., Jeddeloh, J., Flowers, S., Munakata, K. & Richards, E. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc. Natl Acad. Sci. USA 93, 12406-12411 (1996).
18. Miura, A. et al. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212-214 (2001).
19. Kakutani, T. Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J. 12, 1447-1451 (1997).
20. Kaya, H. et al. FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems. Cell 104, 131-142 (2001).
21. Cokus, S. J. et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219 (2008).
22. Lister, R. et al. Highly integrated single-base resolution maps of epigenome in Arabidopsis. Cell 133, 523-536 (2008).
23. 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).
24. Yu, Z., Wright, S. I. & Bureau, T. E. Mutator-like elements in Arabidopsis thaliana: structure, diversity and evolution. Genetics 156, 2019-2031 (2000).
25. Mirouze, M. et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature doi:10.1038/nature08328 (this issue).
26. Kawabe, A. & Charlesworth, D. Patterns of DNA variation among three centromere satellite families in Arabidopsis halleri and A. lyrata. J. Mol. Evol. 64, 237-247 (2007).
27. Kankel, M. W. et al. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 1109-1122 (2003).
28. Bartee, L., Malagnac, F. & Bender, J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev. 15, 1753-1758 (2001).
29. Kato, M., Miura, A., Bender, J., Jacobsen, S. & Kakutani, T. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr. Biol. 13, 421-426 (2003).
30. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599 (2007).