Epigenetic variation in the FWA gene within the genus Arabidopsis

Plant Journal

Volumn 66, Issue 5, 2011, Pages 831-843

  Fujimoto, Ryo ^a   Sasaki, Taku ^b,d   Kudoh, Hiroshi ^c   Taylor, Jennifer M ^a   Kakutani, Tetsuji ^b   Dennis, Elizabeth S ^a  

^a CSIRO   (Australia)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d GREGOR MENDEL INSTITUTE OF MOLECULAR PLANT BIOLOGY   (Austria)

Author keywords

Arabidopsis; DNA methylation; epigenetics; flowering time; natural variation; silencing

Indexed keywords

ARABIDOPSIS; DNA METHYLATION; EPIGENETICS; FLOWERING TIME; NATURAL VARIATION; SILENCING;

DNA; DNA SEQUENCES; GENES; METHYLATION; PLANTS (BOTANY); TISSUE; TRANSCRIPTION;

ALKYLATION;

ARABIDOPSIS PROTEIN; FWA PROTEIN, ARABIDOPSIS; HOMEODOMAIN PROTEIN; PLANT DNA; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; CROSS BREEDING; DNA METHYLATION; FLOWER; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC EPIGENESIS; GENETIC VARIABILITY; GENETICS; METABOLISM; PHYSIOLOGY; TANDEM REPEAT; TRANSCRIPTION INITIATION SITE; TRANSGENE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CROSSES, GENETIC; DNA METHYLATION; DNA, PLANT; EPIGENESIS, GENETIC; FLOWERS; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; GENETIC VARIATION; HOMEODOMAIN PROTEINS; TANDEM REPEAT SEQUENCES; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; TRANSGENES;

ARABIDOPSIS; ARABIDOPSIS LYRATA; ARABIDOPSIS THALIANA;

EID: 79957612014     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2011.04549.x     Document Type: Article

References (31)

1. Cao, X., and, Jacobsen, S.E., (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138-1144. (Pubitemid 34766938)
2. Chan, S.W., Zilberman, D., Xie, Z., Johansen, L.K., Carrington, J.C., and, Jacobsen, S.E., (2004) RNA silencing genes control de novo DNA methylation. Science, 303, 1336. (Pubitemid 38269419)
3. Chan, S.W., Zhang, X., Bernatavichute, Y.V., and, Jacobsen, S.E., (2006) Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol. 4, e363.
4. Clough, S.J., and, Bent, A.F., (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743.
5. Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M., and, Jacobsen, S.E., (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219. (Pubitemid 351380251)
6. Cubas, P., Vincent, C., and, Coen, E., (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature, 401, 157-161. (Pubitemid 29436317)
7. Daxinger, L., Kanno, T., Bucher, E., van der Winden, J., Naumann, U., Matzke, A.J., and, Matzke, M., (2009) A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J. 28, 48-57.
8. Fahlgren, N., Jogdeo, S., Kasschau, K.D., et al. (2010) MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell, 22, 1074-1089.
9. Fujimoto, R., Kinoshita, Y., Kawabe, A., Kinoshita, T., Takashima, K., Nordborg, M., Nasrallah, M.E., Shimizu, K.K., Kudoh, H., and, Kakutani, T., (2008) Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet. 4, e1000048.
10. Gehring, M., Bubb, K.L., and, Henikoff, S., (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science, 324, 1447-1451.
11. Hsieh, T.F., Ibarra, C.A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R.L., and, Zilberman, D., (2009) Genome-wide demethylation of Arabidopsis endosperm. Science, 324, 1451-1454.
12. Ikeda, Y., Kobayashi, Y., Yamaguchi, A., Abe, M., and, Araki, T., (2007) Molecular basis of late-flowering phenotype caused by dominant epi-alleles of the FWA locus in Arabidopsis. Plant Cell Physiol. 48, 205-220.
13. Jullien, P.E., and, Berger, F., (2009) Gamete-specific epigenetic mechanisms shape genomic imprinting. Curr. Opin. Plant Biol. 12, 637-642.
14. Kakutani, T., (1997) Genetic characterization of late-flowering traits induced by DNA hypomethylation mutation in Arabidopsis thaliana. Plant J. 12, 1447-1451. (Pubitemid 28042700)
15. Kardailsky, I., Shukla, V.K., Ahn, J.H., Dagenais, N., Christensen, S.K., Nguyen, J.T., Chory, J., Harrison, M.J., and, Weigel, D., (1999) Activation tagging of the floral inducer FT. Science, 286, 1962-1965. (Pubitemid 129515906)
16. Kinoshita, T., Miura, A., Choi, Y., Cao, X., Jacobsen, S.E., Fischer, R.L., and, Kakutani, T., (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science, 303, 521-523. (Pubitemid 38120849)
17. Kinoshita, Y., Saze, H., Kinoshita, T., Miura, A., Soppe, W.J., Koornneef, M., and, Kakutani, T., (2007) Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. 49, 38-45. (Pubitemid 44952696)
18. Kinoshita, T., Ikeda, Y., and, Ishikawa, R., (2008) Genomic imprinting: a balance between antagonistic roles of parental chromosome. Semin. Cell Dev. Biol. 19, 574-579.
19. Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M., and, Araki, T., (1999) A pair of related genes with antagonistic roles in mediating flowering signals. Science, 286, 1960-1962. (Pubitemid 129515905)
20. Koornneef, M., Hanhart, C.J., and, van der Veen, J.H., (1991) A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol. Gen. Genet. 229, 57-66.
21. Lippman, Z., Gendrel, A.V., Black, M., et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430, 471-476. (Pubitemid 38987911)
22. Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H., and, Ecker, J.R., (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523-536.
23. Ma, Z., Coruh, C., and, Axtell, M.J., (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell, 22, 1090-1103.
24. Manning, K., Tör, M., Poole, M., Hong, Y., Thompson, A.J., King, G.J., Giovannoni, J.J., and, Seymour, G.B., (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38, 948-952. (Pubitemid 44141665)
25. Miura, K., Agetsuma, M., Kitano, H., Yoshimura, A., Matsuoka, M., Jacobsen, S.E., and, Ashikari, M., (2009) A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proc. Natl. Acad. Sci. USA, 106, 11218-11223.
26. Paulin, R., Grigg, G.W., Davey, M.W., and, Piper, A.A., (1998) Urea improves efficiency of bisulphite-mediated sequencing of 5â-methylcytosine in genomic DNA. Nucleic Acids Res. 26, 5009-5010. (Pubitemid 28491185)
27. Richards, E.J., (2008) Population genetics. Curr. Opin. Genet. Dev. 18, 221-226.
28. Shimizu-Inatsugi, R., Lihova, J., Iwanaga, H., Kudoh, H., Marhold, K., Savolainen, O., Watanabe, K., Yakubov, V.V., and, Shimizu, K.K., (2009) The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Mol. Ecol. 18, 4024-4028.
29. Soppe, W.J., Jacobsen, S.E., Alonso-Blanco, C., Jackson, J.P., Kakutani, T., Koornneef, M., and, Peeters, A.J., (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell, 6, 791-802.
30. Vaughn, M.W., Tanurdzic, M., Lippman, Z., et al. (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 5, e174.
31. Waterhouse, P.M., and, Helliwell, C.A., (2003) Exploring plant genomes by RNA-induced gene silencing. Nat. Rev. Genet. 4, 29-38. (Pubitemid 36043213)