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Methylation of exogenous promoters regulates soybean isoflavone synthase (GmIFS) transgene in T0 transgenic wheat (Triticum aestivum)
DNA methylation is one epigenetic strategy for gene regulation in living organisms. In this study, the expression of soybean isoflavone synthase (GmIFS) transgene in T0 transgenic wheat plants was investigated at the RNA and the final product genestin level. T0 plants showed variations in the GmIFS expression. Methylation status of the exogenous promoters (35S or Oleocin (OL)) proximal sequence was investigated in T0 plants using bisulphite sequencing to disclose their methylation in parallel with the GmIFS level of expression. Results concluded that the high GmIFS expressers of T0 plants exhibited high methylation of exogenous promoter proximal sequences as well as low expression of DNA methyltransferases (Mets). Variation in GmIFS was associated with the level of methylation in the 35S or OL promoters. High expression of GmIFS was negatively correlated with methylation level of 35S and OL promoter proximal regions. In 35S promoter, methylation level of the CpG sites –56 and –88 is strongly linked to GmIFS expression and is involved in the regulation of GmIFS gene. In OL promoter, the CpG site could be involved in the regulation of the GmIFS. Wheat Met3 expression varied among T0 transgenic plants. Its expression profile could explain the regulation of GmIFS transgene by methylation.
Key words: Transgenic, Wheat, Epigenetic, Methylation, Promoter, DNA methyltransferase
E-mail: elshehawi hotmail.com
1. Li, Y. and Tollefsbol, T.O., DNA methylation detection: bisulfite genomic sequencing analysis, Meth. Mol. Biol., 2011, vol. 791, pp. 11–21.
2. Känel, T. and Huber, A.R., DNA methylation analysis, Swiss. Med. Wkly., 2013, vol. 43, p. w13799.
3. Akimoto, K., Katakami, H., Kim, H., Ogawa, E., Sano, C.M., Wada, Y., and Sano, H., Epigenetic inheritance in rice plants, Ann. Bot., 2007, vol. 100, pp. 205–217.
4. Jones, L., Ratcliff, F., and Baulcombe, D.C., RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance, Curr. Biol., 2001, vol. 11, pp. 747–757.
5. Law, J.A. and Jacobsen, S.E., Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat. Rev. Genet., 2010, vol. 11, pp. 204–220.
6. Han, S. and Wagner, D., Role of chromatin in water stress responses in plants, J. Exp. Bot., 2014, vol. 65, no. 10, pp. 2785–2799.
7. Zilberman, D., An evolutionary case for functional gene body methylation in plants and animals, Genome Biol., 2017, vol. 18, p. 87.
8. Chan, S.W., Henderson, I.R., and Jacobsen, S.E., Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet., 2005, vol. 6, pp. 351–360.
9. Ikeuchi, M., Iwase, A., and Sugimoto, K., Control of plant cell differentiation by histone modification and DNA methylation. Curr. Opin. Plant Biol, 2015, vol. 28, pp. 60–67.
10. Fedoroff, N.V., Transposable elements, epigenetics, and genome evolution, Science, 2012, no. 338, no. 6108, pp. 758–767.
11. Demeulemeester, M., Van Stallen, N., and De Proft, M., Degree of DNA methylation in chicory (Cichorium intybus L.): influence of plant age and vernalization, Plant Sci., 1999, vol. 142, no. 1, pp. 101–108.
12. Yaish, M.W., Epigenetic modifications associated with abiotic and biotic stresses in plants: an implication for understanding plant evolution, Front. Plant. Sci., 2017, vol. 8, p. 1983.
13. Yaish, M.W., Al-Lawati, A., Al-Harrasi, I., and Patankar, H.V., Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula), BMC Genomics, 2018, vol. 19, no. 1, p. 78.
14. Yong-Villalobos, L., González-Morales, S.I., Wrobel, K., Gutiérrez-Alanis, D., Cervantes-Perćz, S.A., Hayano-Kanashiro, C., Oropeza-Aburto, A., Cruz-Ramírez, A., Martínez, O., and Herrera-Estrella, L., Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation, Proc. Natl. Acad. Sci. U. S. A., 2015, vol. 112, no. 52, pp. E7293–E7302.
15. Takatsuka, H. and Umeda, M., Epigenetic control of cell division and cell differentiation in the root apex, Front. Plant Sci., 2015, vol. 6, p. 1178.
16. Suzuki, M.M. and Bird, A., DNA methylationl and scapes: provocative insights from epigenomics, Nat. Rev. Genet., 2008, vol. 9, pp. 465–476.
17. Takuno, S. and Gaut, B.S., Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly, Mol. Biol. Evol., 2012, vol. 29, pp. 219–227.
18. Bird, A., DNA methylation patterns and epigenetic memory, Gen. Dev., 2002, vol. 16, pp. 6–21.
19. Saze, H., Tsugane, K., Kanno, T., and Nishimura, T., DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation, Plant Cell Physiol., 2012, vol. 53, pp. 766–784.
20. Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W., Chen, H., Henderson, I.R., Shinn, P., Ellegrini, M., Jacobsen, S.E., and Ecker, J.R., Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis,Cell, 2006, vol. 126, pp. 1189–1201.
21. Hauser, M., Aufsatz, W., Jonak, C., and Luschnig, C., Transgenerational epigenetic inheritance in plants, Biochim. Biophys. Acta, 2011, vol. 1809, no. 8, pp. 459–468.
22. Sahu, P.P., Pandey, G., Sharma, N., Puranik, S., Muthamilarasan, M., and Prasad, M., Epigenetic mechanisms of plant stress responses and adaptation, Plant Cell Rep., 2013, vol. 32, pp. 1151–1159.
23. Colaneri, A.C. and Jones, A.M., Genome-wide quantitative identification of DNA differentially methylated sites in Arabidopsis seedlings growing at different water potential, PLoS One, 2013, vol. 8, e59878.
24. Lira-Medeiros, C.F., Parisod, C., Fernandes, R.A., Mata, C.S., Cardoso, M.A., and Ferreira, PC, Epigenetic variation in mangrove plants occurring in contrasting natural environment, PLoS One, 2010, vol. 5, e10326.
25. Wang, W.S., Pan, Y.J., Zhao, X.Q., Dwivedi, D., Zhu, L.H., Ali, J., Fu, B.Y., and Li, Z.K., Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.), J. Exp. Bot., 2011, vol. 62, pp. 1951–1960.
26. Tricker, P.J., Gibbings, J.G., Rodriguez-Lopez, C.M., Hadley, P., and Wilkinson, M.J., Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development, J. Exp. Bot., 2012, vol. 63, pp. 3799–3713.
27. Tricker, P.J., Lopez, C.M., Gibbings, G., Hadley, P., and Wilkinson, M.J., Transgenerational, dynamic methylation of stomata genes in response to low relative humidity, Int. J. Mol. Set., 2013, vol. 14, pp. 6674–6689.
28. Berdasco, M., Alcázar, R., García-Ortiz, M.V., Ballestar, K., Fernández, A.F., et al., Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells, PLoS One, 2008, vol. 3, no. 10, e3306.
29. El-Shehawi, A.M., Fahmi, A.I., Elseehy, M.M., and Nagaty, H.H., Enhancement of nutritional quality of wheat (Triticum aestivum) by metabolic engineering of isoflavone pathway, Am. J. Biochem. Biotechnol., 2013, vol. 9, no. 4, vol. 407–417.
30. Kim, J.H., Park, F.J., Lee, T.K., and Lee, W.S., Genomic sequences of the soybean 24 kDa oleosin genes and initial analysis of their promoter sequences, Mol. Cells, 1996, vol. 6, no. 4, pp. 393–399.
31. Dai, Y., Ni1, Z., Dai, J., Zhao, T., and Sun, Q., Isolation and expression analysis of genes encoding DNA methyltransferase in wheat (Triticum aestivum L.), Biochim. Biophys. Acta, 2005, vol. 1729, pp. 118–125.
32. Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., and Allard, R.W., Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics, Proc. Natl. Acad. Sci. U. S. A., 1984, vol. 81, no. 24, pp. 8014–8018.
33. Ahmed, M.M., El-Shazly, A.S., El-Shehawi, A.M., and Alkafafy, M.E., Antiobesity effects of Taif and Egyptian pomegranates: molecular study, Biosci. Biotechnol. Biochem., 2015, vol. 79, no. 4, pp. 598–609.
34. Carr, I.M., Valleley, E.M.A., Cordery, S.F., Markham, A.F., and Bonthron, D.T., Sequence analysis and editing for bisulphite genomic sequencing projects, Nucleic Acids Res., 2007, vol. 35, e79.
35. Jorgensen, K., Rasmussen. A.V., Morant, M., Nielsen, A.H., and Bjarnholt, N., et al., Metabolon formation and metabolic channeling in the biosynthesis of plant natural products, Curr. Opin. Plant Biol., 2005, vol. 8, pp. 280–291.
36. Liu, R., Hu, Y., Li, J., and Lin, Z., Production of soybean isoflavone genistein in non-legume plants via genetically modified secondary metabolism pathway, Metab. Eng., 2007, vol. 9, pp. 1–7.
37. Bucherna, N., Szabo, E., Heszky, L.S., and Nagy, I., DNA methylation and gene expression differences during alternative in vitro morphogenic processes in eggplant (Solanum melongena L.), In Vitro Cell. Dev. Biol.—Plant, 2001, vol. 37, pp. 672–677.
38. Tolley, B.J., Woodfield, H., Wanchana, S., Bruskiewich, R., and Hibberd, J.M., Light-regulated and cell-specific methylation of the maize PEPC promoter, J. Exp. Bot., 2012, vol. 63, no. 3, pp. 1381–1390.
39. 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., Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2, Science, 2006, vol. 311, pp. 395–8.
40. Jeltscha, A., Ehrenhofer-Murray, A., Jurkowski, T.P., Lykoc, F., Reuterd, G., Ankri, S., Nellenf, W., Schaeferg, M., and Helmh, M., Mechanism and biological role of Dnmt2 in nucleic acid methylation, RNA Biol., 2017, vol. 14, no. 9, pp. 1108–1123.
41. Moritoh, S., Eun, C., Ono, E., Asao, H., Okano, Y., Yamaguchi, K., Shimatani, Z., Koizumi, A., and Terada, R., Targeted disruption of an orthologue of DOMAINS REARRANGED METHYLASE 2, OsDRM2, impairs the growth of rice plants by abnormal DNA methylation, Plant J., 2012, vol. 71, pp. 85–98.
42. Cao, X., Jacobsen, S.E., Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methytransferse genes, Proc. Natl. Acad. Sci. U. S. A., 2002, vol. 99, pp. 16491–16498.
43. Zhang, X., Yazaki, J., Sundaresan, A., et al., Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis,Cell, 2006, vol. 126, pp. 1189–1201.
44. Kurihara, Y., Matsui, A., Kawashima, M., et al., Identification of the candidate genes regulated by RNA-directed DNA methylation, Biochem. Biophys. Res. Commun., 2008, vol. 376, pp. 553–557.
45. Rodríguez Lopez, C.M. and Wilkinson, M.J., Epi-fingerprinting and epi-interventions for improved crop production and food quality, Front. Plant Sci., 2015, vol. 6, p. 397.
46. Wei, X., Song, X., Weim, L., Tang, S., Sun, J., Hu, P., and Cao, X., An epiallele of rice AK1 affects photosynthetic capacity, J. Integr. Plant Biol., 2017, vol. 59, no. 3, pp. 158–163.
47. Song, Q., Zhang, T., Stelly, D.M., and Chen, Z.J., Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons, Genome Biol., 2017, vol. 18, pp. 1, p. 99.
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