Temporal and Spatial Downregulation of Arabidopsis MET1 Activity Results in Global DNA Hypomethylation and Developmental Defects

  • Kim, Minhee (Department of Biological Sciences, Seoul National University) ;
  • Ohr, Hyonhwa (Department of Biological Sciences, Seoul National University) ;
  • Lee, Jee Woong (Department of Biological Sciences, Seoul National University) ;
  • Hyun, Youbong (Department of Biological Sciences, Seoul National University) ;
  • Fischer, Robert L. (Department of Plant and Microbial Biology, University of California at Berkeley) ;
  • Choi, Yeonhee (Department of Biological Sciences, Seoul National University)
  • Received : 2008.09.24
  • Accepted : 2008.09.29
  • Published : 2008.12.31


DNA methylation is an epigenetic mechanism for gene silencing. In Arabidopsis, MET1 is the primary DNA methyltransferase that maintains CG DNA methylation. Plants having an overall reduction of MET1 activity, caused by a met1 mutation or a constitutively expressed MET1 antisense gene, display genome hypomethylation, inappropriate gene and transposon transcription, and developmental abnormalities. However, the effect of a transient reduction in MET1 activity caused by inhibiting MET1 expression in a restricted set of cells is not known. For this reason, we generated transgenic plants with a MET1 antisense gene fused to the DEMETER (DME) promoter (DME:MET1 a/s). Here we show that DME is expressed in leaf primordia, lateral root primoridia, in the region distal to the primary root apical meristem, which are regions that include proliferating cells. Endogenous MET1 expression was normal in organs where the DME:MET1 a/s was not expressed. Although DME promoter is active only in a small set of cells, these plants displayed global developmental abnormalities. Moreover, centromeric repeats were hypomethylated. The developmental defects were accumulated by the generations. Thus, not maintaining CG methylation in a small population of proliferating cells flanking the meristems causes global developmental and epigenetic abnormalities that cannot be rescued by restoring MET1 activity. These results suggest that during plant development there is little or no short-term molecular memory for reestablishing certain patterns of CG methylation that are maintained by MET1. Thus, continuous MET1 activity in dividing cells is essential for proper patterns of CG DNA methylation and development.




Supported by : Korea Research Foundation, Korea Science and Engineering Foundation, National Institute of Health, United States Department of Agriculture


  1. Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, CD., 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 https://doi.org/10.1038/nature06745
  2. Doerner, P., Jorgensen, J.E., You, R., Steppuhn, J., and Lamb, C. (1996). Control of root growth and development by cyclin expression. Nature 380, 520-523 https://doi.org/10.1038/380520a0
  3. Jullien, PE., Kinoshita, T., Ohad, N., and Berger, F. (2006). Maintenance of DNA methylation during the Arabidopsis life cycle Is essential for parental imprinting. Plant Cell 18, 1360-1372 https://doi.org/10.1105/tpc.106.041178
  4. Kinoshita, T., Miura, A, Choi, Y., Kinoshita, 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 https://doi.org/10.1126/science.1089835
  5. Morales-Ruiz, T., Ortega-Galisteo, AP., Ponferrada-Marin, M.I., Martinez-Macias, R.R., Ariza, R.R., and Roldan-Arjona, T. (2006). DEMETER and REPRESSOR OF SILENCING1 encode 5methylcytosine DNA glycosylases. Proc. Natl. Acad. Sci. USA 103, 6853-6858
  6. Ortega-Galisteo, AP., Morales-Ruiz, T., Ariza, R.R., and RoldanAriona, T. (2008). Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol. BioI. 67, 671-681 https://doi.org/10.1007/s11103-008-9346-0
  7. Penterman, J., Zilberman, D., Huh, J.H., Ballinger, T., Henikoff, S., and Fischer, R.L. (2007). DNA demethylation in the Arabidopsis genome. Proc. Natl. Acad. Sci. USA 104,6752-6757
  8. Scott, R.J., and Spielman, M. (2006). Genomic imprinting in plants and mammals: how life history constrains convergence. Cytogenet Genome Res. 113,53-67 https://doi.org/10.1159/000090815
  9. Sutherland, D., Coe, L., and Raleigh, E.A. (1992). McrBC: A Multisubunit GTP-dependent restriction endonuclease. J. Mol. BioI. 225, 327-348 https://doi.org/10.1016/0022-2836(92)90925-A
  10. Yadegari, R., Kinoshita, T., Lotan, 0., Cohen, G., Katz, A, Choi, Y., Katz, A, Nakashima, K., Harada, J.J., Goldberg, R.B., et al. (2000). Mutations in the FIE and MEA genes that encode interacting polycomb proteins cause parent-of-origin effects on seed development by distinct mechanisms. Plant Cell 12, 2367-2381 https://doi.org/10.1105/tpc.12.12.2367
  11. Zilberman, D., Gehring, M., Tran, RK, Ballinger, T., and Henikoff, S. (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61-69 https://doi.org/10.1038/ng1929
  12. Lippman, Z., May, B., Yordan, C., Singer, T., and Martienssen, R. (2003). Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS BioI. 1, E67 https://doi.org/10.1371/journal.pbio.0000067
  13. Saze, H., SCheid, O.M., and Paszkowski, J. (2003). Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 34, 65-69 https://doi.org/10.1038/ng1138
  14. Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, an, Berry, C.C., Millar, AH., and Ecker, J.R. (2008). Highly integrated Single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 https://doi.org/10.1016/j.cell.2008.03.029
  15. Ronemus, M.J., Galbiati, M., Ticknor, C., Chen, J., and Dellaporta, S.L. (1996). Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273, 654-657 https://doi.org/10.1126/science.273.5275.654
  16. Bender, J. (2004). DNA Methylation and Epigenetics. Annu. Rev. Plant BioI. 55, 41-68 https://doi.org/10.1146/annurev.arplant.55.031903.141641
  17. Xiao, w., Gehring, M., Choi, Y., Margossian, L., Pu, H., Harada, J.J., Goldberg, R.B., Pennell, R.I., and Fischer, R.L. (2003). Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell 5, 891-901 https://doi.org/10.1016/S1534-5807(03)00361-7
  18. Barkoulas, M., Galinha, C., Grigg, S.P., and Tsiantis, M. (2007). From genes to shape: regulatory interactions in leaf development. Curro Opin. Plant BioI. 10, 660-666 https://doi.org/10.1016/j.pbi.2007.07.012
  19. Ferreira, P.C., Hemerly, A.S., Engler, JD., van Montagu, M., Engler, G., and Inze, D. (1994). Developmental expression of the arabidopsis cyclin gene cyc1At. Plant Cell 6, 1763-1774 https://doi.org/10.1105/tpc.6.12.1763
  20. Chan, S.w., Henderson, I.R., and Jacobsen, S.E. (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6,351-360 https://doi.org/10.1038/nrg1601
  21. Gehring, M., Huh, J.H., Hsieh, T.F., Penterman, J., Choi, Y., Harada, J.J., Goldberg, R.B., and Fischer, R.L. (2006). DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124, 495-506 https://doi.org/10.1016/j.cell.2005.12.034
  22. Kankel, M.W., Ramsey, DE., Stokes, T.L., Flowers, SK, Haag, J.R., Jeddeloh, J.A., Riddle, N.C., Verbsky, M.L., and Richards, E.J. (2003). Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163, 1109-1122
  23. Matzke, M.A., and Birchler, J.A. (2005). RNAi-mediated pathways in the nucleus. Nat. Rev. Genet. 6, 24-35 https://doi.org/10.1038/nrg1500
  24. Henderson, I.R., and Jacobsen, SE. (2007). Epigenetic inheritance in plants. Nature 447, 418-424 https://doi.org/10.1038/nature05917
  25. Choi, Y., Gehring, M., Johnson, L., Hannon, M., Harada, J.J., Goldberg, R.B., Jacobsen, S.E., and Fischer, R.L. (2002). DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110,33-42 https://doi.org/10.1016/S0092-8674(02)00807-3
  26. Finnegan, E.J., Peacock, w.J., and Dennis, E.S. (1996). Reduced DNA methylation in Arabidopsis results in abnormal plant development. Proc. Natl. Acad. Sci. USA 93, 8449-8454
  27. Rabinowicz, p.o., Palmer, L.E., May, B.P., Hemann, M.T., Lowe, SW., McCombie, W.R., and Martienssen, R.A. (2003). Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res. 13,2658-2664 https://doi.org/10.1101/gr.1784803
  28. Zhu, J.Q., Liu, J.H., Liang, X.w., Xu, B.Z., Hou, Y., Zhao, XX, and Sun, Q.Y. (2008). Heat stress causes aberrant DNA methylation of H19 and Igf-2r in mouse blastocysts. Mol. Cells 25, 211-215