DNA methylation through the years has become an evolutionary preserved mechanism that has contributed to the divergence of prokaryotes and eukaryotes, helping them adapt to different environmental conditions over the years (Bewick & Schmitz, 2017). Epigenetic modifications, including DNA methylation, histone modifications, and the expression of non-coding RNAs (ncRNA), influence the chromatin structure and alter the accessibility of genomic regions for interacting enzymes (H. Zhang, Lang, & Zhu, 2018). This means that DNA methylation is essential to many biological processes directly modifying the genome architecture, the definition of Euchromatin and Heterochromatin, and the control of gene expression (Bewick & Schmitz, 2017; H. Zhang et al., 2018). Dysfunctions of DNA methylation can lead to abnormalities in plants, such as failure in tomato and orange fruit ripening or vice versa promote early strawberry fruit ripening (Cheng et al., 2018; Huang et al., 2019; H. Zhang et al., 2018).
The genomic location of DNA methylation can display different roles in the maintenance of the structure and integrity of the genome and gene expression regulation (Bewick & Schmitz, 2017). In combination with histone modifications and other interacting proteins, DNA methylation defines the chromatin structure and, through this, the accessibility of the DNA. DNA methylation helps to regulate gene expression, transposon silencing, chromosome interactions (Fig. 1) (Zhang et al., 2018). To Illustrate, in plants, DNA methylation is distributed at the body of genes (where the function is often unclear) and at repetitive regions, where it restricts the expression of TEs, which represent in some plant species more than 80% of the genome, e.g., barley, sunflower, and maize. (Meyer, 2011; Vitte, Fustier, Alix, & Tenaillon, 2014). The function of the variability of DNA methylation in some genomic regions in some plant species remains a mystery (Zilberman, 2017). For example, five different apple cultivars showed differential methylation patterns in promoter regions of genes that regulate the anthocyanin pathway. Even though changes in the transcription of these genes generate different red-skin phenotypes, methylation was not the main factor to alter their expression (Jiang et al., 2019).
In plants, methylation can occur in distinct site classes based on the sequence context with which the methylated cytosine (mC) is accompanied. There are three sequence contexts, including the dinucleotide CpG or CG sites (mCG, the p marks the phosphate), and the trinucleotides CHG and CHH (mCHG and mCHH), where H can be adenine (A), cytosine (C), or thiamine (T) (Bewick & Schmitz, 2017). This contrasts with mammals, where methylation is primarily found in the CG context and, in specific cell types, also in the CH context (Chad E. & Schmitz, 2017).
The most common type of methylation across the different kingdoms, CG methylation, is also the most predominant in plants (Chad E. & Schmitz, 2017). One reason for this wide distribution is probably found in the relatively simple maintenance mechanism after DNA replication. Because CG and CHG contexts are symmetrical, due to the obligatory cytosine on the complementary strand (i.e., complementary to G), cytosine methylation can be copied from the old strand to the newly synthesized strand. In comparison, CHH sites are asymmetrical (i.e., the complementary strand does not contain C) and require special machinery to be maintained during DNA replication since no complementary methylated sequence is available to guide the re-methylation (Foyer & Noctor, 2013). In summary, cytosine methylation is the primary epigenetic mark, partly because it is technically easy to access (see Chapter 11). However, the consequences of cytosine methylation at a specific site depend on the position and the sequence context and are not easily interpreted.
Plant genomes are dynamic and differ strongly in size due to differences in gene content, the number of transposons, or other repetitive sequences, which influence the diversification of DNA methylation mechanisms (Chad E. & Schmitz, 2017; Pellicer, Hidalgo, Dodsworth, & Leitch, 2018). Several genome-wide methylome studies applying bisulfite sequencing (BiSeq) (see Chapter 11) demonstrated that plants have a higher epigenome diversity among species than animals (Fig. 6). This can be attributed to genetic variation, for example, large differences in the amount of heterochromatin and to the three different cytosine contexts in plants (Jones, 2012; Niederhuth et al., 2016; Pellicer et al., 2018; Yi, 2017).
Early papers reported cytosine methylation is mainly restricted to the nuclear DNA, suggesting DNA methylation in plastid genomes does not play a role in controlling gene activity (Ahlert, Stegemann, Kahlau, Ruf, & Bock, 2009; Finnegan, Genger, Peacock, & Dennis, 1998). However, high levels of N6-methyladenosine (m6A) methylation findings in the chloroplast and mitochondria propose the presence of methylation machinery inside these organelles. In addition, RNA methylation was identified, although its role in plant organelles is yet not fully understood (Manduzio & Kang, 2021).
The distribution of methylcytosines over the nuclear genome varies among species. Generally, it is concentrated in regions rich in repeated sequences, which include the centromere surrounding DNA and telomeres, or in genome regions containing many transposons (Finnegan, Genger, Peacock, & Dennis, 1998).
Such patterns of context-dependent accumulation of cytosine methylation can also be seen on a smaller scale. When we average methylation frequency across genes, transcription start sites, or transposons, as shown in the next infographic (Fig. 7).
The comparative epigenomic analysis identifies how dynamic the methylomes between flowering plant species can be. Families such as Brassicaceae and most Poaceae showed globally lower mCHG and mCHH methylation than other plants. One reason for these pronounced differences is that large genomes, like Zea mays, contain much higher numbers of repetitive sequences and transposons than smaller genomes, like strawberry. These sequences are commonly characterized by higher methylation levels. On the other hand, the gbM of ortholog genes showed a conserved pattern across species (Niederhuth et al., 2016). In conclusion, the variation in DNA methylation between plant species opens new areas of study to understand the role of DNA methylation and their correlation with evolutionary distance as well as biological diversity.
It is essential for plants to maintain the global DNA methylation patterns to keep transposons silenced, preserve cell type identity, or establish an epigenetic memory against environmental stresses (Law & Jacobsen, 2010). According to the sequence context of the cytosine sites (CG, CHG, and CHH), DNA methyltransferases control and regulate their methylation due to cooperative or competing interactions by different mechanisms (Meyer, 2011; H. Zhang et al., 2018). The efficiency of the different DNA methyltransferases is reflected in the methylation level at their preferred target sites. Symmetric methylation (CG and CHG) is most efficient, with most sites being 80–100% methylated, while methylation levels at nonsymmetric (CHH) target sites vary between 10% to 20% (Martínez-García et al., 2010; P. R. V. Satyaki & Gehring, 2017a).
The sequence context further influences DNA methylation in plants even beyond the mentioned dinucleotide and trinucleotide sites. For example, CG sites are undermethylated when the exact four-base context is ACGT. Also, CHG and CHH sites are less efficiently methylated when another cytosine follows the C, as in CCG instead of CAG or CTG. These more specific sequence contexts seem to reduce the efficiency of the methyltransferases. However, the reason is yet unknown. For example, in Arabidopsis thaliana, some methyltransferases share similar sequence specificities to probably provide a methylation backup system and avoid harmful alterations in the plant genome (Law & Jacobsen, 2010; Li et al., 2018; Meyer, 2011).
In plants, genetic analyses have demonstrated that CG methylation is regulated like in mammals through homolog proteins. CG cytosine methylation is maintained by the DNA METHYLTRANSFERASE 1 (MET1), which recognizes hemimethylated CG dinucleotides following DNA replication and methylates the unmodified cytosine in the new complementary strand (Fig. 2). To do this, MET1 probably is recruited to the replication complex by the VARIANT IN METHYLATION (VIM) protein family of SRA (SET- and RING-associated) domain proteins (Law & Jacobsen, 2010; Zhang et al., 2018). This interaction with VIM was proposed because VIM1 loss of function mutants of Arabidopsis thaliana lose the DNA methylation of their centromeres (J. Kim, Kim, Richards, Chung, & Woo, 2014).
Non-CG sites refer to symmetrical trinucleotide CHG sites and to asymmetrical CHH trinucleotide sites. Non-CG methylation is maintained by plant-specific enzymes such as the CHROMOMETHYLASE (CMT) family (Kenchanmane Raju, Ritter, & Niederhuth, 2019). CHG methylation is maintained via a reinforcing loop, which involves histone and DNA methylation (Fig. 3) (Law & Jacobsen, 2010). The DNA methyltransferases CHROMOMETHYLASE 3 (CMT3) and, to less extent, CMT2 catalyze the maintenance of CHG methylation in A. thaliana (Fig. 3A) (Zhang et al., 2018). However, they require a whole complex of other proteins. For example, the histone methyltransferases SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGs: SUVH4 (also known as KRYPTONITE (KYP)), SUVH5, and SUVH6 bind non-CG methylated regions and methylate H3K9 (Fig. 3B)(Kenchanmane Raju et al., 2019). SUVH4, primarily responsible for H3K9 demethylation, is an essential partner, as suggested by a dramatic decrease of DNA CHG methylation in loss of function mutants (Law & Jacobsen, 2010). Law & Jacobsen (2010) suggested that the reason for the interdependence of CMT3 and SUVH4 could be found in their multidomain structure. Because CMT3 can bind to the methylated histone H3 with a chromodomain, SUVH4 can bind to CHG methylated DNA with its SRA domain (Law & Jacobsen, 2010; Zhang et al., 2018). Interestingly, CMT3 appears to have a role also in gene-body methylation (gbM) in several plant species (Wendte et al., 2019). In Eutrema salsugineum, a plant that naturally lacks gbM, the gain of CMT3 triggered a new establishment of gbM in genes homolog to naturally methylated genes in A. thaliana. The gained gbM was maintained even in following generations (Wendte et al., 2019). However, this observation is still a very recent one.
CHH methylation cannot be copied from the old strand, and therefore is maintained by constant de novo methylation. De novo DNA methylation is a process that involves plant-specific pathways and enzymes. For instance, the methyltransferases DRM2 and CMT2 catalyze this reaction, depending on the broader sequence context (Henderson et al., 2010). DRM2 is part of the RNA-directed DNA methylation (RdDM) pathway (described in more detail in Chapter 3) that guides DRM2 to small-RNA target regions rich in transposons or other repeat sequences primarily located in the Euchromatin. On the contrary, CTM2 targets H1-containing Heterochromatin sites (Zhang et al., 2018). While the Euchromatine is the region containing most of the protein-coding genes, Heterochromatin contains most of the transposons and other repeat sequences. Other enzymes may affect the maintenance of asymmetric CHH methylation, like MET1, CMT3, SuvH2, and SuvH9, so there is also some cross-talk with H3K9 methylation. However, only CTM2 and DRM2 can catalyze this reaction. But in turn, these two enzymes can also de novo methylate cytosines in other sequence contexts (Zhang et al. 2018).
Notably, CMT2 maintained DNA methylation is reduced by mutations in DECRESED DNA METHYLATION 1 (DDM1), a chromatin-remodeling protein (Zhang et al., 2018). This association was used in a pivotal study to produce a population of Arabidopsis thaliana recombinant inbred lines with a nearly identical genomic sequence but different cytosine methylation patterns, called EpiRiLs (Johannes et al., 2009). The study demonstrated for the first time that differences only in DNA methylation produced phenotypic variation.
It is known that DNA methylation is a stable epigenetic mark across species; however, during different plant lifetime processes, a decrease in global methylation has been observed (Law & Jacobsen, 2010). A reduction of methyltransferases activity or low levels of methyl donors present may result in failure to conserve methylation during DNA replication , which is known as passive DNA demethylation. On the contrary, removing the methyl group by an enzymatic process is described as active DNA demethylation (Zhang et al., 2018).
Active demethylation implies a family of DNA demethylases, 5-mC DNA glycosylases–apurinic/apyrimidinic lyases, which drive the base excision repair (BER) pathway (Law & Jacobsen, 2010; Zhang et al., 2018). In A. thaliana, the group of glycosylases involves REPRESSOR OF SILENCING 1 (ROS1), TRANSCRIPTIONAL ACTIVATOR DEMETER (DME), DEMETER-LIKE PROTEIN 2 and 3 (DML2 and DML3), which are able to identify and extract 5-mC from all cytosines in a double-stranded DNA sequence (Law & Jacobsen, 2010; Zhang et al., 2018).
During DNA demethylation, DME/ROS1 behave as glycosylases hydrolyzing the glycosylic bond between the cytosine and the deoxyribose molecule, then apurinic or apyrimidinic lyases cut the DNA backbone and produce an excision of the methyl-cytosine base, which will be filled through a DNA polymerase and ligase enzymes with a non-methylated cytosine base (Figure 4). However, the exact process, how the reposition of the unmethylated cytosine occurs is still unidentified (Parrilla-Doblas, Roldán-Arjona, Ariza, & Córdoba-Cañero, 2019; H. Zhang et al., 2018).
The glycosylases ROS1, DML2, and DML3 are expressed preferably in vegetative tissues, possibly to counteract robust DNA methylation by the RdDM pathway. Law & Jacobsen (2010) suggest that the shared target sequences of these glycosylases with the RdDM pathway regulate gene expression activity by removing methylation cytosines in genes and preventing their silencing (Fig.5A). However, these enzymes also maintain an adaptable inactive state to keep silenced transposons. In addition, it has been shown that the activity of genes nearby transposons is negatively affected by the RdDM pathway, which maintains the methylation in Euchromatic regions (Fig. 5B) (M. Y. Kim & Zilberman, 2014; Law & Jacobsen, 2010; H. Zhang et al., 2018).
Unlike ROS1 and DML, DME has been observed preferentially expressed in plant gamete cells and being involved in imprinting, as will be further outlined in the section DNA methylation and imprinting (Wöhrmann et al., 2012).
Passive demethylation has been characterized in plant endosperm where MET1 activity decreases during female gametogenesis and results in a drop of the global methylation (Jullien et al., 2008). The reduction of MET1 expression levels activates demethylation pathways directed by DME. Together this activates genes that are expressed in a parent-of-origin-specific manner (Law & Jacobsen, 2010).
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
Imprinting is a preferential expression pattern of genes according to their maternal and paternal allele origin. When the preferential expression comes from the mother, the genes are called maternally expressed genes (MEG), when from the father, paternally expressed genes (PEG) (Batista & Köhler, 2020). Epigenetic modifications in DNA methylation, histone modifications, or chromatin composition might be directly favoring the activity of one allele over another (Dong et al., 2018; P. R. V. Satyaki & Gehring, 2017). This epigenetic phenomenon is exclusive for flowering plants, suggesting an independent evolution among plant species of different periods in time (Batista & Köhler, 2020).
Imprinting is detected mostly in the endosperm, an analog of the placenta of mammals. Even though the endosperm surrounds the embryo and supplies nutrients to it from the maternal parent, little is known of imprinted genes in the embryo (Fig. 8) (Batista & Köhler, 2020; Law & Jacobsen, 2010; P. R. V. Satyaki & Gehring, 2017). What we know is that a small number of genes are differentially methylated and silenced in male and female tissues. This is regulated by de novo methylation, maintenance methylation, and demethylation, with demethylation dominating the process (Batista & Köhler, 2020; P. R. V. Satyaki & Gehring, 2017). This is suggested by DME activity and the presence of DML2-3 and ROS1 in the central cell and the vegetative nucleus of the male and female gametophyte in Arabidopsis and rice (Batista & Köhler, 2020). The reason for this massive active demethylation in vegetative gametophyte tissue may be the protection through hypermethylation of the DNA in the haploid egg and sperm cells. In the germline, active transposons could produce much damage. The active demethylation of TEs leads to their transcription and the production of small interfering RNAs (siRNAs) in the tissue surrounding the egg and sperm cells. From their, siRNAs are thought to be transported into the egg and sperm cells, leading to hypermethylation of their homolog sequences throughout the RdDM pathway and thereby effectively hindering the activation of TEs in the germline (Fig. 8B) (Batista & Köhler, 2020; Law & Jacobsen, 2010). However, how the siRNAs are exported to adjacent compartments is yet unknown (Law & Jacobsen, 2010).
So, hypermethylation of the embryo DNA is most likely caused by the demethylation of the surrounding vegetative tissue. However, this is not yet imprinting because it does not yet include a preference of the maternal of the parental allele. What is needed here, ist that not only the egg but also the endosperm is fertilized, which is the case in flowering plants (Fig. 8). Now it is principally possible that only the male or the female allele is transcribed in the endosperm, leading to allele-specific gene expression in the endosperm. This is realized, for example, via the accumulation of the histone H3K27me3 on the maternal allele of the MADS-box transcription factor PHERES 1, after demethylation through DME in the central cell of the endosperm. The maternal allele is silenced through this accumulation. In the parental allele, a 3’ sequence is methylated, which is thought to prevent H3K27me3 accumulation. Consequently, only the parental allele of PHERES 1 can be expressed in the endosperm (Batista & Köhler, 2020).
In many plant species such as Arabidopsis thaliana, maize, rice, and sorghum between the 40 to 50% of maternal expressed imprinted genes (MEGs) and 60% of parental expressed imprinted genes (PEGs) are associated with epigenetic marks in gene bodies and flanking regions in the endosperm (Batista & Köhler, 2020; Satyaki & Gehring, 2017). There is little information about well-identified imprinted genes and their regulation mechanism in Plants. One of the most studiest genes is the FLOWERING WAGENINGEN (FWA) gene in Arabidopsis, which encodes a transcription factor related to delayed flowering. FWA is tissue-specific activated by DNA demethylation in the female gamete and endosperm (Fujimoto et al., 2008; Meyer, 2011). The FWA gene is rich in tandem repeats and a SINE-related sequence which are direct targets for the methylation machinery, and it is sufficient for imprinting and vegetative silencing (Fujimoto et al., 2008; Meyer, 2011).
To summarize, a combination of epigenetic mechanisms is responsible for parent-of-origin expressed genes. However, it seems so far that plant species contain differ in their regulating systems hampering the general understanding of this phenomenon. Therefore, the development of new molecular tools probably is needed.
María Estefanía López
DNA methylation plays a crucial role in the regulation of gene expression, in the activity of transposable elements, in the defense against foreign DNA, and even in the inheritance of specific gene expression patterns (Xu, Tanino, & Robinson, 2016; Finnegan, Genger, Peacock, & Dennis, 1998; Xu, Tanino, Horner, & Robinson, 2016). DNA methylation refers to the cytosine methylation process through the covalent enzyme-catalyzed transfer of a methyl group from S-adenosylmethionine to the 5’ position of cytosine, thus converting cytosine to 5-methylcytosine (5mC) (Pikaard et al., 2014; Sahu et al., 2013). DNA methylation in plants is species-, tissue-, organelle-, and age-specific. It is controlled by phytohormones, changes during plant development, and biotic and abiotic stress conditions (Finnegan et al., 1998). This epigenetic mark can be accumulated during plant vegetative phases and, principally, be passed on to the next generations. DNA cytosine methylation appears in three contexts, CG, CHG, and CHH, where H can be A, C, or T (Sahu et al., 2013). It predominantly occurs on transposons and other repetitive DNA elements in the genome. DNA methylation patterns must be stably maintained to ensure that transposons remain silenced and preserve cell-type identity. Three different pathways maintain DNA methylation differing in their central enzyme: the DNA METHYLTRANSFERASE 1 (MET1) maintains CG methylation, the CHROMOMETHYLASE (CMT3), a plant-specific DNA methyltransferase, maintains CHG methylation, and the DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) maintains the asymmetric CHH methylation through de novo methylation (Law & Jacobsen, 2011). Although DNA methylation is a stable epigenetic mark in most cases, reduced levels of methylation are observed during plant development. Methylation loss can either occur passively via replication without functional maintenance methylation pathways or actively by removing methylated cytosines with DNA glycosylase activity. The symmetrical CG or CHG methylation is inherited during the DNA replication in the form of hemimethylated sequences. It provides the memory of the methylation imprint present in the parental DNA, suggesting a role in stress protection memory (Suzuki & Bird, 2008). On the contrary, the asymmetrical cytosine methylation must be reestablished de novo after each replication cycle. DNA methylation in plants is closely associated with histone modifications, and it affects the binding of specific proteins to DNA and the formation of respective transcription complexes in the chromatin (Pikaard et al., 2014; Zamir, 2001). Those epigenetic marks trigger chromatin remodeling, which plays a crucial role not only in transcriptional regulation but also in DNA repair and replication (Kim et al., 2019). It has been proposed that MET1 and DDM1 could be involved in the DNA damage response reducing chromatin density (Kim et al., 2019; Shaked, Avivi-ragolsky, & Levy, 2006). DDM1 mutations generate a strong alteration in the nuclear organization and chromatin structure, particularly in the centromeric and pericentromeric regions, resulting in the impediment of the DNA repair machinery that loses its access to the damaged sequences. This emphasizes the broad involvement of recombination and DNA repair proteins in plant genome maintenance and the link between epigenetic and genetic processes.
Kim, J. H. (2019). Chromatin remodeling and epigenetic regulation in plant DNA damage repair. International Journal of Molecular Sciences, 20(17). https://doi.org/10.3390/ijms20174093
Finnegan, E. J., Genger, R. K., Peacock, W. J., & Dennis, E. S. (1998). DNA METHYLATION IN PLANTS.
Law, J. A., & Jacobsen, S. E. (2011). patterns in plants and animals, 11(3), 204–220. https://doi.org/10.1038/nrg2719.Establishing
Pikaard, C. S., Scheid, O. M., Kingston, R. E., Tamkun, J. W., Baulcombe, D. C., & Dean, C. (2014). Epigenetic Regulation in Plants Epigenetic Regulation in Plants, 1–31. https://doi.org/10.1101/cshperspect.a019315
Sahu, P. P., Pandey, G., Sharma, N., Puranik, S., Muthamilarasan, M., & Prasad, M. (2013). Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Reports, 32(8), 1151–1159. https://doi.org/10.1007/s00299-013-1462-x
Shaked, H., Avivi-ragolsky, N., & Levy, A. A. (2006). Involvement of the Arabidopsis SWI2/SNF2 Chromatin Remodeling Gene Family in DNA Damage Response and Recombination, 2(June), 985–994. https://doi.org/10.1534/genetics.105.051664
Suzuki, M. M., & Bird, A. (2008). DNA methylation landscapes: provocative insights from epigenomics, 9(June), 465–476. https://doi.org/10.1038/nrg2341
Xu, J., Tanino, K. K., Horner, K. N., & Robinson, S. J. (2016). Quantitative trait variation is revealed in a novel hypomethylated population of woodland strawberry (Fragaria vesca). BMC Plant Biology, 16(1), 1–17. https://doi.org/10.1186/s12870-016-0936-8
Xu, J., Tanino, K. K., & Robinson, S. J. (2016). Stable Epigenetic Variants Selected from an Induced Hypomethylated Fragaria vesca Population. Frontiers in Plant Science, 7(November), 1–14. https://doi.org/10.3389/fpls.2016.01768
Zamir, D. (2001). Improving plant breeding with exotic genetic libraries. Nature Reviews Genetics, 2(12), 983–989. https://doi.org/10.1038/35103590