Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity

Scientific Reports

Volumn 3, Issue , 2013, Pages

  Tsuchiya, Tokuji ^a   Eulgem, Thomas ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; EDM2 PROTEIN, ARABIDOPSIS; TRANSCRIPTION FACTOR; TRANSPOSON;

ADAPTATION; ARABIDOPSIS; ARTICLE; GENE SILENCING; GENETIC ENHANCEMENT; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MUTATION; SITE DIRECTED MUTAGENESIS; TRANSPOSON; PROCEDURES;

ADAPTATION, PHYSIOLOGICAL; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA TRANSPOSABLE ELEMENTS; GENE SILENCING; GENETIC ENHANCEMENT; MUTAGENESIS, SITE-DIRECTED; MUTATION; TRANSCRIPTION FACTORS;

EID: 84877764664     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep01701     Document Type: Article

References (58)

1. Rando, O. J. Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev 22, 148-55 (2012).
2. Saze, H., Tsugane, K., Kanno, T. & Nishimura, T. DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol 53, 766-84 (2012).
3. Huff, J. T. & Zilberman, D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Curr Opin Genet Dev 22, 132-8 (2012).
4. Mirouze, M. & Paszkowski, J. Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14, 267-74 (2011).
5. Dooner, H. K. & Weil, C. F. Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev 17, 486-92 (2007). (Pubitemid 350184304)
6. Bestor, T. H. DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes. Philos Trans R Soc Lond B Biol Sci 326, 179-87 (1990).
7. Flavell, A. J. Retroelements, reverse transcriptase and evolution. Comp Biochem Physiol B Biochem Mol Biol 110, 3-15 (1995).
8. Saze, H. & Kakutani, T. Differentiation of epigenetic modifications between transposons and genes. Curr Opin Plant Biol 14, 81-7 (2011).
9. Jacob, Y. et al. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16, 763-8 (2009).
10. Schulze, S. R. Wallrath, L. L. Gene regulation by chromatin structure: paradigms established in Drosophila melanogaster. Annu Rev Entomol 52, 171-92 (2007). (Pubitemid 46133567)
11. Jackson, J. P., Lindroth, A.M., Cao, X. & Jacobsen, S. E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556-60 (2002). (Pubitemid 34288860)
12. Johnson, L., Cao, X. & Jacobsen, S. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12, 1360-7 (2002). (Pubitemid 34915537)
13. Jasencakova, Z. et al. Histone modifications in Arabidopsis-high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J 33, 471-80 (2003). (Pubitemid 36251188)
14. Ebbs, M. L., Bartee, L. & Bender, J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 25, 10507-15 (2005). (Pubitemid 41681971)
15. Ebbs, M. L. & Bender, J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18, 1166-76 (2006). (Pubitemid 43956123)
16. Miura, A. et al. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411, 212-4 (2001).
17. Lippman, Z., May, B., Yordan, C., Singer, T. & Martienssen, R. Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1, E67 (2003).
18. Tsukahara, S. et al. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461, 423-6 (2009).
19. Finnegan, E. J. & Kovac, K. A. Plant DNA methyltransferases. Plant Mol Biol 43, 189-201 (2000).
20. Cao, X. & Jacobsen, S. E. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99 Suppl 4, 16491-8 (2002). (Pubitemid 35470998)
21. Cao, X. & Jacobsen, S. E. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12, 1138-44 (2002). (Pubitemid 34766938)
22. Cao, X. et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13, 2212-7 (2003). (Pubitemid 38024949)
23. Matzke, M., Kanno, T., Daxinger, L., Huettel, B. & Matzke, A. J. RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21, 367-76 (2009).
24. Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126, 1189-201 (2006). (Pubitemid 44380289)
25. Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M. & Jacobsen, S. E. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3, e3156 (2008).
26. Soppe, W. J. et al. DNA methylation controls histone H3 lysine 9methylation and heterochromatin assembly in Arabidopsis. EMBO J 21, 6549-59 (2002). (Pubitemid 35448432)
27. Tariq, M. et al. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. ProcNatl Acad SciUS A100, 8823-7 (2003). (Pubitemid 36899182)
28. Johnson, L. M. et al. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17, 379-84 (2007). (Pubitemid 46241885)
29. Roudier, F. et al. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30, 1928-38 (2011).
30. Eulgem, T. et al. EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels. Plant J 49, 829-39 (2007). (Pubitemid 46279266)
31. Tsuchiya, T. & Eulgem, T. The Arabidopsis defense component EDM2 affects the floral transition in an FLC-dependent manner. Plant J 62, 518-28 (2010).
32. Tsuchiya, T. & Eulgem, T. Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development. BMC Plant Biol 10, 203 (2010).
33. Tsuchiya, T. & Eulgem, T. EMSY-like genes are required for full RPP7-mediated race-specific immunity and basal defense in Arabidopsis. Mol Plant Microbe Interact 24, 1573-81 (2011).
34. Sanchez, R. & Zhou,M.M. The PHD finger: a versatile epigenome reader. Trends Biochem Sci 36, 364-72 (2011).
35. Lisch, D. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60, 43-66 (2009).
36. Steimer, A. et al. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12, 1165-78 (2000). (Pubitemid 30622720)
37. Soppe, W. J. et al. The late flowering phenotype of fwa mutants is caused by gainof-function epigenetic alleles of a homeodomain gene. Mol Cell 6, 791-802 (2000).
38. May, B. P., Lippman, Z. B., Fang, Y., Spector, D. L. & Martienssen, R. A. Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet 1, e79 (2005).
39. Vaillant, I., Schubert, I., Tourmente, S. & Mathieu, O. MOM1 mediates DNAmethylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep 7, 1273-8 (2006). (Pubitemid 44835097)
40. Saze, H. & Kakutani, T. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factorDDM1. EMBO J 26, 3641-52 (2007). (Pubitemid 47236873)
41. Tanurdzic, M. et al. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol 6, 2880-95 (2008).
42. Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461-72 (2009).
43. Ito, H. et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472, 115-9 (2011).
44. 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 8, e1002474 (2012).
45. 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, 12406-11 (1996). (Pubitemid 26367156)
46. Kakutani, T. Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J 12, 1447-51 (1997). (Pubitemid 28042700)
47. Kankel, M. W. et al. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 1109-22 (2003). (Pubitemid 36417951)
48. Mathieu, O., Reinders, J., Caikovski, M., Smathajitt, C. & Paszkowski, J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130, 851-62 (2007). (Pubitemid 47334929)
49. Rigal, M., Kevei, Z., Pélissier, T. & Mathieu, O. DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. EMBO J 31, 2981-93 (2012).
50. Meyer, P.DNAmethylation systems and targets in plants. FEBS Lett 585, 2008-15 (2011).
51. Richards, E. J. Inherited epigenetic variation-revisiting soft inheritance. Nat Rev Genet 7, 395-401 (2006).
52. Alonso, J. M. et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301, 653-7 (2003). (Pubitemid 36927950)
53. Curtis, M. D. Grossniklaus, U.Agateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133, 462-9 (2003). (Pubitemid 37325657)
54. Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacteriummediated transformation of Arabidopsis thaliana. Plant J 16, 735-43 (1998).
55. Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29, e45 (2001).
56. Gruntman, E. et al. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics 9, 371 (2008).
57. Saleh, A., Alvarez-Venegas, R. & Avramova, Z. An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc 3, 1018-25 (2008). (Pubitemid 351818690)
58. Yuan, J. S., Reed, A., Chen, F. & Stewart, C. N. Statistical analysis of real-time PCR data. BMC Bioinformatics 7, 85 (2006).