References

Ahlert, D., Stegemann, S., Kahlau, S., Ruf, S., & Bock, R. (2009). Insensitivity of chloroplast gene expression to DNA methylation. Molecular Genetics and Genomics, 282(1), 17–24. https://doi.org/10.1007/s00438-009-0440-z

Batista, R. A., & Köhler, C. (2020). Genomic imprinting in plants-revisiting existing models. Genes & Development, 34(1–2), 24–36. https://doi.org/10.1101/gad.332924.119

Bewick, A. J., & Schmitz, R. J. (2017). Gene body DNA methylation in plants. Current Opinion in Plant Biology, 36, 103–110. https://doi.org/10.1016/j.pbi.2016.12.007

Chad E., N., & Schmitz, R. J. (2017). Putting DNA methylation in context: from genomes to gene expression in plants, 4(11), 149–156. https://doi.org/10.1016/S2214-109X(16)30265-0.Cost-effectiveness

Cheng, J., Niu, Q., Zhang, B., Chen, K., Yang, R., Zhu, J. K., … Lang, Z. (2018). Downregulation of RdDM during strawberry fruit ripening. Genome Biology, 19(1), 1–14. https://doi.org/10.1186/s13059-018-1587-x

Dong, X., Chen, J., Li, T., Li, E., Zhang, X., Zhang, M., … Lai, J. (2018). Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize. Genome Research, 28(7), 1020–1028. https://doi.org/10.1101/gr.230201.117

Finnegan, E. J., Genger, R. K., Peacock, W. J., & Dennis, E. S. (1998). DNA methylation in plants. Annual Review of Plant Biology, 49(1), 223–247. https://doi.org/10.1146/annurev.arplant.49.1.223

Foyer, C. H., & Noctor, G. (2013). Redox Signaling in Plants. Antioxidants & Redox Signaling, 18(16), 2087–2090. https://doi.org/10.1089/ars.2013.5278

Fujimoto, R., Kinoshita, Y., Kawabe, A., Kinoshita, T., Takashima, K., Nordborg, M., … Kakutani, T. (2008). Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genetics, 4(4). https://doi.org/10.1371/journal.pgen.1000048

Henderson, I. R., Deleris, A., Wong, W., Zhong, X., Chin, H. G., Horwitz, G. A., … 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 Genetics, 6(10), 1–11. https://doi.org/10.1371/journal.pgen.1001182

Huang, H., Liu, R., Niu, Q., Tang, K., Zhang, B., Zhang, H., … Lang, Z. (2019). Global increase in DNA methylation during orange fruit development and ripening. Proceedings of the National Academy of Sciences, 116(4), 1430 LP – 1436. https://doi.org/10.1073/pnas.1815441116

Jiang, S. H., Sun, Q. G., Chen, M., Wang, N., Xu, H. F., Fang, H. C., … Chen, X. Sen. (2019). Methylome and transcriptome analyses of apple fruit somatic mutations reveal the difference of red phenotype. BMC Genomics, 20(1), 1–13. https://doi.org/10.1186/s12864-019-5499-2

Johannes, F., Porcher, E., Teixeira, F. K., Saliba-Colombani, V., Simon, M., Agier, N., … Colot, V. (2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genetics, 5(6). https://doi.org/10.1371/journal.pgen.1000530

Jones, P. A. (2012). Functions of DNA methylation: Islands, start sites, gene bodies and beyond. Nature Reviews Genetics, 13(7), 484–492. https://doi.org/10.1038/nrg3230

Jullien, P. E., Mosquna, A., Ingouff, M., Sakata, T., Ohad, N., & Berger, F. (2008). Retinoblastoma and Its Binding Partner MSI1 Control Imprinting in Arabidopsis. PLoS Biology, 6(8), e194. https://doi.org/10.1371/journal.pbio.0060194

Kenchanmane Raju, S. K., Ritter, E. J., & Niederhuth, C. E. (2019). Establishment, maintenance, and biological roles of non-CG methylation in plants. Essays in Biochemistry, 63(6), 743–755. https://doi.org/10.1042/EBC20190032

Kim, J., Kim, J. H., Richards, E. J., Chung, K. M., & Woo, H. R. (2014). Arabidopsis VIM proteins regulate epigenetic silencing by modulating DNA methylation and histone modification in cooperation with MET1. Molecular Plant, 7(9), 1470–1485. https://doi.org/10.1093/mp/ssu079

Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. Trends in Plant Science, 19(5), 320–326. https://doi.org/10.1016/j.tplants.2014.01.014

Law, J. A., & Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics, 11(3), 204–220. https://doi.org/10.1038/nrg2719

Li, X., Jake Harris, C., Zhong, Z., Chen, W., Liu, R., Jia, B., … Du, J. (2018). Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Proceedings of the National Academy of Sciences of the United States of America, 115(37), E8793–E8802. https://doi.org/10.1073/pnas.1809841115

Manduzio, S., & Kang, H. (2021). RNA methylation in chloroplasts or mitochondria in plants. RNA Biology, 160. https://doi.org/10.1080/15476286.2021.1909321

Martínez-García, J. F., Galstyan, A., Salla-Martret, M., Cifuentes-Esquivel, N., Gallemí, M., & Bou-Torrent, J. (2010). Regulatory Components of Shade Avoidance Syndrome. Advances in Botanical Research, 53(November 2015), 65–116. https://doi.org/10.1016/S0065-2296(10)53003-9

Meyer, P. (2011). DNA methylation systems and targets in plants. FEBS Letters, 585(13), 2008–2015. https://doi.org/10.1016/j.febslet.2010.08.017

Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M. S., Kim, K. Do, Li, Q., … Schmitz, R. J. (2016). Widespread natural variation of DNA methylation within angiosperms. Genome Biology, 17(1), 1–19. https://doi.org/10.1186/s13059-016-1059-0

Parrilla-Doblas, J. T., Roldán-Arjona, T., Ariza, R. R., & Córdoba-Cañero, D. (2019). Active DNA Demethylation in Plants. International Journal of Molecular Sciences, 20(19), 1–19. https://doi.org/10.3390/ijms20194683

Pellicer, J., Hidalgo, O., Dodsworth, S., & Leitch, I. J. (2018). Genome size diversity and its impact on the evolution of land plants. Genes, 9(2). https://doi.org/10.3390/genes9020088

Satyaki, P. R. V., & Gehring, M. (2017). DNA methylation and imprinting in plants: machinery and mechanisms. Critical Reviews in Biochemistry and Molecular Biology, 52(2), 163–175. https://doi.org/10.1080/10409238.2017.1279119

Schmitz, R. J., Schultz, M. D., Urich, M. A., Nery, J. R., Pelizzola, M., Libiger, O., … Ecker, J. R. (2013). Patterns of population epigenomic diversity. Nature, 495(7440), 193–198. https://doi.org/10.1038/nature11968

Vitte, C., Fustier, M. A., Alix, K., & Tenaillon, M. I. (2014). The bright side of transposons in crop evolution. Briefings in Functional Genomics and Proteomics, 13(4), 276–295. https://doi.org/10.1093/bfgp/elu002

Wendte, J. M., Zhang, Y., Ji, L., Shi, X., Hazarika, R. R., Shahryary, Y., … Schmitz, R. J. (2019). Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. ELife, 8, 1–27. https://doi.org/10.7554/eLife.47891

Wöhrmann, H. J. P., Gagliardini, V., Raissig, M. T., Wehrle, W., Arand, J., Schmidt, A., … Grossniklaus, U. (2012). Identification of a DNA methylationindependent imprinting control region at the Arabidopsis MEDEA locus. Genes and Development, 26(16), 1837–1850. https://doi.org/10.1101/gad.195123.112

Yi, S. V. (2017). Insights into epigenome evolution from animal and plant methylomes. Genome Biology and Evolution, 9(11), 3189–3201. https://doi.org/10.1093/gbe/evx203

Zhang, H., Lang, Z., & Zhu, J.-K. (2018). Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology, 19(8), 489–506. https://doi.org/10.1038/s41580-018-0016-z

Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S. W. L., Chen, H., … Ecker, J. R. R. (2006). Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis. Cell, 126(6), 1189–1201. https://doi.org/10.1016/j.cell.2006.08.003 Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology, 18(1), 17–19. https://doi.org/10.1186/s13059-017-1230-2

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