Plant DNA methyltransferase genes: Multiplicity, expression, methylation patterns

Biochemistry (Moscow)

Volumn 81, Issue 2, 2016, Pages 141-151

  Ashapkin, V V ^a   Kutueva, L I ^a   Vanyushin, B F ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Arabidopsis thaliana; bisulfite sequencing; DNA methylation; DNA methyltransferase; gene expression; quantitative PCR

Indexed keywords

ARABIDOPSIS PROTEIN; DNA (CYTOSINE 5) METHYLTRANSFERASE; MET1 PROTEIN, ARABIDOPSIS; TRANSCRIPTOME;

ARABIDOPSIS; DNA METHYLATION; GENETICS; METABOLISM; PLANT SEED;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; SEEDS; TRANSCRIPTOME;

EID: 84958982381     PISSN: 00062979     EISSN: 16083040     Source Type: Journal    
DOI: 10.1134/S0006297916020085     Document Type: Article

References (34)

1. Feng, S., and Jacobsen, S. E. (2011) Epigenetic modifications in plants: an evolutionary perspective, Curr. Opin. Plant Biol., 14, 179-186.
2. Vanyushin, B. F., and Ashapkin, V. V. (2011) DNA methylation in higher plants: past, present and future, Biochim. Biophys. Acta, 1809, 360-368.
3. 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 bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature, 452, 215-219.
4. 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.
5. Vanyushin, B. F., and Ashapkin, V. V. (2009) DNA Methylation in Plants, Nova Science Publishers Inc., N. Y.
6. Buryanov, Ya. I., and Shevchuk, T. V. (2005) DNA methyltransferases and structural-functional specificity of eukaryotic DNA modification, Biochemistry (Moscow), 70, 730-742.
7. Goll, M. G., and Bestor, T. H. (2005) Eukaryotic cytosine methyltransferases, Annu. Rev. Biochem., 74, 481-514.
8. Pavlopoulou, A., and Kossida, S. (2007) Plant cytosine-5 DNA methyltransferases: structure, function, and molecular evolution, Genomics, 90, 530-541.
9. Woo, H. R., Dittmer, T. A., and Richards, E. J. (2008) Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis, PLoS Genet., 4, e1000156.
10. Du, J., Zhong, X., Bernatavichute, Y. V., Stroud, H., Feng, S., Caro, E., Vashisht, A. A., Terragni, J., Chin, H. G., Tu, A., Hetzel, J., Wohlschlegel, J. A., Pradhan, S., Patel, D. J., and Jacobsen, S. E. (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants, Cell, 151, 167-180.
11. Johnson, L. M., Bostick, M., Zhang, X., Kraft, E., Henderson, I., Callis, J., and Jacobsen, S. E. (2007) The SRA methylcytosine-binding domain links DNA and histone methylation, Curr. Biol., 17, 379-384.
12. 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.
13. Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M., and Jacobsen, S. E. (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation, Curr. Biol., 13, 2212-2217.
14. Johnson, L. M., Law, J. A., Khattar, A., Henderson, I. R., and Jacobsen, S. E. (2008) SRA-domain proteins required for DRM2-mediated de novo DNA methylation, PLoS Genet., 4, e1000280.
15. Zhang, X., and Jacobsen, S. E. (2006) Genetic analyses of DNA methyltransferases in Arabidopsis thaliana, Cold Spring Harb. Symp. Quant. Biol., 71, 439-447.
16. Ashapkin, V. V., Kutueva, L. I., and Vanyushin, B. F. (2002) The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues, FEBS Lett., 532, 367-372.
17. Perry, S. E., and Wang, H. (2003) Rapid isolation of Arabidopsis thaliana developing embryos, BioTechniques, 35, 278-282.
18. Ashapkin, V. V., Linkova, N. S., Khavinson, V. Kh., and Vanyushin, B. F. (2015) Epigenetic mechanisms of peptidergic regulation of gene expression during aging of human cells, Biochemistry (Moscow), 80, 310-322.
19. Suzuki, Y., Kawazu, T., and Koyama, H. (2004) RNA isolation from siliques, dry seeds, and other tissues of Arabidopsis thaliana, BioTechniques, 37, 542-544.
20. Ashapkin, V. V., Kutueva, L. I., and Vanyushin, B. F. (2011) Is the cytosine DNA methyltransferase gene MET1 regulated by DNA methylation in Arabidopsis thaliana plants? Russ. J. Genet., 47, 279-288.
21. Pagnussat, G. C., Yu, H.-J., Ngo, Q. A., Rajani, S., Mayalagu, S., Johnson, C. S., Capron, A., Xie, L.-F., Ye, D., and Sundaresan, V. (2005) Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis, Development, 132, 603-614.
22. Makarevich, G., Villar, C. B. R., Erilova, A., and Koehler, C. (2008) Mechanism of PHERES1 imprinting in Arabidopsis, J. Cell Sci., 121, 906-912.
23. Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., Hashimoto, M., Kirkbride, R. C., Harada, J. J., Zilberman, D., and Fischer, R. L. (2011) Regulation of imprinted gene expression in Arabidopsis endosperm, Proc. Natl. Acad. Sci. USA, 108, 1755-1762.
24. Jullien, P. E., Susaki, D., Yelagandula, R., Higashiyama, T., and Berger, F. (2012) DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana, Curr. Biol., 22, 1825-1830.
25. Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., Harmer, S. L., and Zilberman, D. (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1containing heterochromatin, Cell, 153, 193-205.
26. Stroud, H., Do, T., Du, J., Zhong, X., Feng, S., Johnson, L., Patel, D. J., and Jacobsen, S. E. (2014) Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis, Nat. Struct. Mol. Biol., 21, 64-72.
27. Henderson, I. R., Deleris, A., Wong, W., Zhong, X., Chin, H. G., Horwitz, G. A., Kelly, K. A., Pradhan, S., and Jacobsen, S. E. (2010) The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana, PLoS Genet., 6, e1001182.
28. Costa-Nunes, P., Kim, J. Y., Hong, E., and Pontes, O. (2014) The cytological and molecular role of domains rearranged methyltransferase3 in RNA-dependent DNA methylation of Arabidopsis thaliana, BMC Res. Notes, 7, 721.
29. Zhong, X., Hale, C. J., Nguyen, M., Ausin, I., Groth, M., Hetzel, J., Vashisht, A. A., Henderson, I. R., Wohlschlegel, J. A., and Jacobsen, S. E. (2015) Domains rearranged methyltransferase3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis, Proc. Natl. Acad. Sci. USA, 112, 911-916.
30. Goll, M. G., Kirpekar, F., Maggert, K. A., Yoder, J. A., Hsieh, C. L., Zhang, X., Golic, K. G., Jacobsen, S. E., and Bestor, T. H. (2006) Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2, Science, 311, 395-398.
31. Song, Y., Wu, K., Dhaubhadel, S., An, L., and Tian, L. (2010) Arabidopsis DNA methyltransferase AtDNMT2 associates with histone deacetylase AtHD2s activity, Biochem. Biophys. Res. Commun., 396, 187-192.
32. Shorning, B. Yu., and Vanyushin, B. F. (2001) Putative DNA-(amino)methyltransferases in eukaryotes, Biochemistry (Moscow), 66, 753-762.
33. Chen, P., Jager, G., and Zheng, B. (2010) Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana, BMC Plant Biol., 10, 201.
34. Greer, E. L., Blanco, M. A., Gu, L., Sendinc, E., Liu, J., Aristizabal-Corrales, D., Hsu, C.-H., Aravind, L., He, C., and Shi, Y. (2015) DNA methylation on N6-adenine in C. elegans, Cell, 161, 868-878.