Active DNA Demethylation in Plants

Abstract

Methylation of cytosine (5-meC) is a critical epigenetic modification in many eukaryotes, and genomic DNA methylation landscapes are dynamically regulated by opposed methylation and demethylation processes. Plants are unique in possessing a mechanism for active DNA demethylation involving DNA glycosylases that excise 5-meC and initiate its replacement with unmodified C through a base excision repair (BER) pathway. Plant BER-mediated DNA demethylation is a complex process involving numerous proteins, as well as additional regulatory factors that avoid accumulation of potentially harmful intermediates and coordinate demethylation and methylation to maintain balanced yet flexible DNA methylation patterns. Active DNA demethylation counteracts excessive methylation at transposable elements (TEs), mainly in euchromatic regions, and one of its major functions is to avoid methylation spreading to nearby genes. It is also involved in transcriptional activation of TEs and TE-derived sequences in companion cells of male and female gametophytes, which reinforces transposon silencing in gametes and also contributes to gene imprinting in the endosperm. Plant 5-meC DNA glycosylases are additionally involved in many other physiological processes, including seed development and germination, fruit ripening, and plant responses to a variety of biotic and abiotic environmental stimuli.

1. Introduction

DNA methylation at carbon 5 of cytosine (5-methylcytosine, 5-meC) is a stable but reversible modification, usually associated with gene silencing, that functions as an epigenetic mark in embryonic development, X-chromosome inactivation, imprinting, and control of transposon activity [1]. DNA methylation is established and maintained by DNA methyltransferases, which transfer a methyl group from S-adenosyl-L-methionine to carbon 5 of cytosine to generate 5-meC [2]. Mammalian methylation primarily occurs at symmetric CG contexts in patterns that are established by the DNA methyltransferase 3 (DNMT3) family of de novo methyltransferases and copied in post-replicative hemimethylated DNA by the maintenance methyltransferase DNMT1 [2]. Plant DNA methylation can occur at any cytosine sequence context: CG, CHG, or CHH (H = A, T, C). In plants, de novo methylation is usually mediated by the RNA-directed DNA methylation (RdDM) pathway and catalyzed by the DNMT3-like enzymes DRM1 and DRM2 [3]. However, at some genomic regions DNA methylation is established in a RdDM-independent manner by two members of the plant-specific chromomethylase family (CMT2 and CMT3) [4,5]. Plant DNA methylation is maintained by different pathways depending on the sequence context. At CG sites it is maintained by the DNMT1 ortholog MET1, at CHG sites by CMT2 and CMT3 [3], and at CHH sequences by persistent RdDM-dependent de novo methylation catalyzed by DRM2 [3] or RdDM-independent methylation carried out by CMT2 [4].

DNA methylation patterns, which change during normal development, are the dynamic outcome of antagonistic methylation and demethylation processes. DNA demethylation may be either the passive result of consecutive DNA replication cycles in the absence of maintenance methylation or an active mechanism involving enzymes that remove 5-meC [6]. Despite intense research efforts, the nature of DNA demethylation mechanisms in animals has been largely elusive [7]. However, accumulating evidence suggests that a family of dioxygenases (Ten-Eleven Translocation, TET proteins) convert 5-meC into derivatives that inhibit maintenance methylation, thus promoting passive demethylation, and/or are actively removed through DNA repair [8].

In contrast to animals, plants have evolved a specific active DNA demethylation mechanism involving 5-meC DNA glycosylases that directly excise 5-meC and initiate its replacement with unmethylated C through a base excision repair (BER) pathway [9,10]. Plant 5-meC DNA glycosylases are typified by Arabidopsis ROS1 (REPRESSOR OF SILENCING 1) [11,12,13] and its paralogs DME (DEMETER) [12,14], DML2, and DML3 (DEMETER-LIKE proteins 2 and 3) [12,15,16]. ROS1, DML2, and DML3 counteract excessive methylation at several hundred loci across the genome in vegetative tissues [15,16,17]. DME demethylates the maternal allele of imprinted genes in the endosperm [18], but its basal function appears to be the reactivation of transposons in companion cells of male and female gametophytes to generate siRNAs that would reinforce transposon silencing in male and female gametes [19,20]. In addition to gametogenesis and seed development, active DNA demethylation serves important functions during various stages of the plant life cycle, including seed germination, fruit ripening, and responses to a variety of stress conditions [21,22,23,24,25].

BER-mediated DNA demethylation in plants is a complex process comprising three major steps: (i) excision of 5-meC coupled to strand incision, which generates a gapped DNA intermediate with a 3′-blocked end; (ii) cleaning-up of the 3’-terminus to generate a 3´-OH group; (iii) gap DNA repair synthesis inserting an unmethylated C and sealing of the DNA strand by DNA ligation. In addition to 5-meC DNA glycosylases, the plant DNA demethylation pathway involves a variety of enzymes processing the successive DNA demethylation intermediates, as well as other proteins performing regulatory roles.

In this review we summarize the key molecular features of the enzymes responsible for 5-meC removal, describe the roles of additional proteins implicated in the various stages of the plant DNA demethylation pathway and its regulation, and outline the main physiological processes in which active DNA demethylation has been implicated.

2. The DML Family: Plant-Specific DNA Glycosylases That Excise 5-meC

Plant 5-meC DNA glycosylases are grouped in the DEMETER-LIKE (DML) family, which belongs to the HhH-GPD superfamily, the largest and most functionally diverse group of DNA glycosylases [26]. DML proteins are unusually large DNA glycosylases, ranging from 1100 to over 2000 residues and so far they have been only detected in plants, including mosses (e.g., Phycomitrella patens) and unicellular green algae (e.g., Ostreococcus), suggesting that active demethylation through 5-meC excision arose early during plant evolution [9]. DML proteins are bifunctional enzymes with both DNA glycosylase and apurinic/apyrimidinic (AP) lyase activities [12,13,15,16,18].

Sequence alignment with other members of the HhH-GPD superfamily revealed that DML proteins possess a discontinuous DNA glycosylase domain comprising two segments connected by a predicted disordered region of variable sequence and length [27] (Figure 1). The function of this region is unknown, although it has been speculated that it might facilitate target localization and undergo folding upon DNA binding [27]. Replacement of this linker region in DME with a short peptide sequence does not abrogate 5-meC excision, indicating that is dispensable for enzymatic activity [28].

Figure 1.

Bipartite DNA glycosylase domain in members of the DEMETER-LIKE (DML) family. (a) Schematic representation of ROS1 domains conserved among DML proteins. (b) Multiple sequence alignment of DML and HhH-GPD representative proteins. Critical residues for catalysis or DNA binding in ROS1 (REPRESSOR OF SILENCING 1) are indicated by asterisks (see text for more details). Names of organisms are abbreviated as follows: Ath, Arabidopsis thaliana; Nta, Nicotiana tabacum; Ta, Triticum aestivum; Osa, Oryza sativa; Zma, Zea mays; Bst, Bacillus stearothermophilus; Eco, Escherichia coli; Mth, Methanobacterium thermoautotrophicum; Mmu, Mus musculus; Hsa, Homo sapiens. Genbank accession numbers are: Ath ROS1: AAP37178; Ath DME: ABC61677; Nta ROS1: BAF52855; Tae DME: AEF38424; Osa DNG701: B8YIE8; Osa ROS1a: XP_015650531; Zma DME1: AQK70999; Bst EndoIII: 1P59; Eco EndoIII: P20625; Mth Mig: NP_039762; Eco MutY: NP_417436; Mmu MBD4: 1NGN; Hsa OGG1: O15527; Eco AlkA: P04395.

DML proteins show in their catalytic domain a characteristic helix–hairpin–helix motif and a Gly/Pro rich loop (HhH-GPD, amino acids from 941 to 969 in ROS1), followed by a conserved catalytic aspartate (amino acid 971 in ROS1) [26]. In addition, they share a lysine residue specifically conserved in bifunctional DNA glycosylases (amino acid 953 in ROS1) and a [4Fe-4S] cluster with four cysteine residues (Cys-X₆-Cys-X₂-Cys-X₅-Cys) conserved in a subset of HhH-GPD proteins (amino acids from 1309 to 1055 in ROS1) [29] (Figure 1). It has been demonstrated that the invariant aspartate of the HhH-GPD motif is essential for catalytic activity [12,16,18]. Using Bacillus stearothermophilus Endo III as a template for a 3D model structure, additional residues specifically involved in 5-meC recognition and catalysis have been identified in ROS1 [27]. Residues T606 and D611, located in the first segment of ROS1 catalytic domain and predicted to be positioned between the base stack and the recognition pocket, were found to be essential for DNA glycosylase activity. On the other hand, mutational changes in two aromatic residues presumably located in the substrate-binding pocket (F589 and Y1028) altered the base specificity of the enzyme. Additionally, amino acid Q607, which is essential for both catalytic activity and stable DNA binding, has been proposed as a base flipper, replacing 5-meC in the base stack when it is extruded from the helix and inserted in the substrate-binding pocket [27]. Interestingly, Q607 is necessary for efficient extrusion of both methylated and unmethylated bases, which suggests that the enzyme uses helix-invading residues to actively interrogate DNA in search of 5-meC [30]. Furthermore, Q607 and two residues positioned close to the G opposite 5-meC (R903 and M905) are specifically required for efficient excision of 5-meC opposite G, but not for mismatched 5-meC [30]. On other hand, point mutations at each cysteine residue of the [4Fe-4S] cluster motif of DME resulted in abrogation of DNA glycosylase activity, suggesting that this motif is also necessary for catalytic activity and/or protein stability [28]. It has been proposed that the oxidation state of the [4Fe-4S] cluster mediates binding and dissociation of DML proteins from DNA [31].

In addition to their bipartite DNA glycosylase domain, DML proteins are characterized by a large C-terminal domain exclusively conserved among DML family members and a short N-terminal domain significantly rich in lysine [27,32]. The N-terminal basic domain is not essential for catalytic activity [28,32], but in ROS1 mediates methylation-independent binding to DNA and endows the protein with the capacity to slide along DNA substrates in search of 5-meC [32,33]. The C-terminal domain is highly conserved among DML family members, but no sequence similarity has been detected with any known protein in either plants or other taxa. Point mutations or deletions in the C-terminal domain of DME and ROS1 result in abrogation of the 5-meC excision activity [13,28,32]. The C-terminal domain of ROS1 lacks detectable enzymatic activity and binds DNA with very low affinity [32], whereas its isolated DNA glycosylase domain is inactive for 5-meC excision but retains partial AP lyase activity [34]. Interestingly, when the C-terminal domain is added in trans to the DNA glycosylase domain, the base excision activity is restored, suggesting that the C-terminal region is essential for the 5-meC DNA glycosylase activity, perhaps by stabilizing the DNA glycosylase domain and/or stimulating its enzymatic activity [34].

3. The Plant DNA Demethylation Pathway

3.1. Base Excision and Strand Incision

Plant 5-meC DNA glycosylases initiate BER-mediated DNA demethylation by hydrolyzing the glycosylic bond between 5-meC and the deoxyribose moiety. Upon catalyzing 5-meC excision, they cleave the phosphodiester backbone 3′ to the generated AP site by β- or β, δ-elimination. The result is a single-nucleotide gap flanked by 3′-PUA or 3′-P ends, respectively, and a 5′-P terminus (Figure 2) [12,13,15,16,18]. It has been reported that in ROS1 5-meC excision is coupled to the AP lyase step [35], in agreement with a unified mechanism of DNA glycosylases/AP lyases postulating coordinated base excision and strand incision as a result of Schiff base formation [36]. In fact, excision of 5-meC catalyzed by ROS1 and DME proceeds via a Schiff base intermediate [12].

Figure 2.

Schematic representation of the active DNA demethylation pathway in Arabidopsis. Different 3’ blocked ends are indicated in red. Stimulatory or inhibitory effect of DDB2 over different proteins of active DNA demethylation pathway are indicated with green or red arrows, respectively. See text for details.

ROS1, DME, and DML3 target 5-meC in any sequence context, although they display a preference for CG sequences [12,15,16]. Mutational analysis of ROS1 supports a mechanism in which the enzyme detects 5-meC by extrahelical interrogation [30] (see Section 2 above). Importantly, ROS1 excises 5-meC less efficiently when correctly paired with G than when mispaired with A, C, or T [35], which suggests that extrusion of the target base from the DNA helix is a limiting step in 5-meC excision. After performing 5-meC excision and strand incision in a CG context, ROS1 tightly binds its reaction product, thus inhibiting processing of the 5-meC in the opposite strand [32,35]. It has also been shown that the presence of an abasic site instead of 5-meC at a CG site strongly inhibits DME activity on the 5-meC located in the complementary strand [18]. It is likely that strong product binding and the requirement for two intact DNA strands for 5-meC excision contribute to avoiding deleterious double strand breaks in symmetric DNA methylation contexts (CG and CHG).

Interestingly, in addition to 5-meC, DML proteins also efficiently excise T (=5-meU) but only when mispaired with G [12,16,35]. This strongly suggests that DML proteins additionally perform a DNA repair function, preventing the mutagenic consequences of spontaneous deamination of 5-mC:G pairs to T:G mispairs.

3.2. Gap Tailoring by 3´-End Cleaning

The product generated after 5-meC excision and strand incision catalyzed by DML proteins is a single nucleotide gap with either 3´-PUA or 3´-P ends (Figure 2). These non-canonical 3´ termini must be converted to 3´-OH ends before DNA polymerase and ligase activities complete the DNA demethylation process.

In Arabidopsis, strong biochemical and genetic evidence indicates that 3′-P processing is mainly performed by the DNA phosphatase ZDP, both in active DNA demethylation [37] and during BER of different DNA lesions [38,39]. ZDP accounts for all DNA phosphatase activity detected in Arabidopsis cells in vitro and cell-free extracts from zdp mutant plants are unable to complete DNA demethylation [37]. Mutations in ZDP cause hypermethylation at hundreds of genome loci and, importantly, ZDP and ROS1 interact in vitro and colocalize in vivo [37]. On other hand, the Arabidopsis AP endonuclease APE2 possesses limited 3´-phosphatase activity and may function redundantly with ZDP during active DNA demethylation [40].

Blocked 3′-PUA termini generated by β-elimination need to be processed by a 3′-phosphodiesterase activity. Like human APE1 [41], two Arabidopsis AP endonucleases, APE1L and ARP, possess 3´-phosphodiesterase activity and are able to convert 3´-PUA into 3´-OH ends [42,43]. However, APE1L displays a much more potent activity than ARP against 3´-PUA termini and in vitro and in vivo interactions have only been reported between APE1L and ROS1 [42]. Although both ape1l and arp mutant plants display an altered methylome, the number of differentially methylated regions in ape1L mutants is about 10-fold higher than in arp mutants [42]. Therefore, it has been suggested that the majority of 3´-PUA intermediates generated during active DNA demethylation are processed by APE1L [42]. Importantly, whereas single zdp and ape1l mutants exhibit a normal phenotype, double zdp ape1l mutants are maternally lethal, indicating that ZDP and APE1L function downstream of 5-meC DNA glycosylases/lyases in independent branches of the active DNA demethylation pathway [42] (Figure 2).

3.3. Gap Filling and DNA Ligation

Once noncanonical 3´ termini have been converted to 3´-OH ends, DNA polymerase and DNA ligase activities must complete the DNA demethylation process. In mammals, gap filling during BER occurs either by insertion of one nucleotide (short-patch, SP-BER) or by incorporation of two or more nucleotides and simultaneous strand displacement (long-patch, LP-BER) [44]. Although both SP- and LP-BER subpathways have been detected in repair reactions catalyzed by Arabidopsis cell-free extracts [45], the DNA polymerase(s) responsible for repair synthesis remain(s) unknown. In mammals, single-nucleotide insertion during SP-BER is catalyzed by the X-family DNA polymerase β (Pol β) [46], which also incorporates the first nucleotide during LP-BER, while subsequent elongation is carried out by replicative DNA polymerases (DNA Pol δ and Pol ε) [47]. No homologs of DNA Pol β have been detected in plants, where the only X-family member is DNA polymerase λ (Pol λ). Although Pol λ has been partially characterized in rice and Arabidopsis and reported to be implicated in oxidative lesion bypass and repair of UV-induced DNA damage [48,49,50], its role in BER, and specifically in active DNA demethylation, remains to be determined.

Strand displacement during LP-BER generates a 5´-flap structure that in mammalian cells is removed by FEN1, a structure-specific DNA endonuclease that also performs an essential role processing Okazaki fragments during DNA replication [51]. Mutation of the Arabidopsis FEN1 homolog causes hypersensitivity to DNA-damaging agents and telomere shortening [52], but its role in plant BER and/or DNA demethylation has not yet been established.

Both the SP- and LP-BER DNA demethylation subpathways generate a single DNA strand break (SSB) that needs to be sealed by a DNA ligase activity (Figure 2). In mammals, a complex of Lig III and the scaffold protein XRCC1 catalyzes DNA ligation in SP-BER [53], whereas LP-BER ligation is performed by Lig I [54]. The Arabidopsis genome encodes three DNA ligases (LIG1, LIG4, and the plant-specific LIG6) but lacks a Lig III homologue [55]. Plant DNA ligases have been implicated in different processes [56,57,58], but only Arabidopsis LIG1 has been demonstrated to participate in BER, performing the ligation step in both SP- and LP-BER subpathways [59]. Arabidopsis LIG1 colocalizes with ROS1, ZDP, and APE1L in vivo and is essential for DNA demethylation and activation of maternally imprinted genes FWA and MEDEA in the endosperm [60]. Moreover, gene interaction analyses indicate that LIG1 participates in DME-mediated demethylation [61]. Although Arabidopsis XRCC1 lacks the BRCT2 domain that in mammals is implicated in the interaction with DNA ligase III, for which there is no homolog in plants, it stimulates the ligation step during ROS1-initiated DNA demethylation, probably through interaction with LIG1 [62]. In addition, XRCC1 interacts in vitro with both ROS1 and ZDP and stimulates their respective activities [62]. Therefore, XRCC1 functions at different stages during active DNA demethylation in plants (Figure 2).

3.4. Regulation of Active DNA Demethylation

It is still poorly understood how plant 5-meC DNA glycosylases are directed to specific genomic regions, but the process likely involves the presence of particular chromatin modifications at target loci and/or the activity of recruiting factors. It has been reported that loci targeted by ROS1 are enriched for H3K18Ac and H3K27me3 and depleted of H3K27me and H3K9me2 [63]. On other hand, a genetic screen for DNA hypermethylation mutants identified IDM1 (INCREASED DNA METHYLATION 1) as a histone acetyltransferase acting on H3K18 and required for demethylation at a subset of ROS1-targeted loci [64]. Furthermore, it has been shown that IDM1 forms a complex with additional proteins, including IDM2, IDM3, the METHYL-CPG-BINDING DOMAIN-CONTAINING PROTEIN 7 (MBD7), and the HARBINGER TRANSPOSON-DERIVED PROTEINS HDP1 and HDP2 [65,66,67]. It has been proposed that such an IDM complex facilitates ROS1 recruitment by IDM1-catalyzed histone acetylation [67], but the specific mechanism involved remains unknown. On other hand, the RNA-binding protein ROS3 is required for ROS1-dependent demethylation at several genomic regions [68], suggesting that small RNAs similar to those targeting RdDM may be involved in recruiting ROS1 to specific loci. However, the role of ROS3 in targeting DNA demethylation, if any, remains undetermined.

Plant DNA methylation and demethylation mechanisms need to be balanced in order to maintain stable genome-wide methylation patterns. Arabidopsis ROS1, DML2, and DML3 antagonize RdDM targeted to transposable elements (TE) and TE-derived sequences and prevent methylation spreading to nearby genes [15,16,17,69] (see Section 4.1 below). Interestingly, ROS1 expression is repressed in mutants defective in RdDM or MET1 [70,71,72,73,74], which suggests that DNA methylation and demethylation are coordinated processes. In fact, methylation of a short sequence targeted by RdDM in the ROS1 promoter is required for ROS1 expression [75,76]. This sequence, which has been defined as a “methylstat” that senses DNA methylation levels, is conserved in other plant species [76], suggesting that it has evolved as a mechanism to balance methylation and demethylation processes. An additional factor implicated in such DNA demethylation control is DDB2 (DNA damage-binding protein 2). DDB2 was initially identified in human cells as a DNA repair factor in complex with DDB1 and is involved in recognition of DNA lesions, probably acting as a sensor for conformational changes in DNA [77]. Arabidopsis ddb2 mutant plants show genome-wide methylation alterations [78] and it has been shown that DDB2 forms a complex in vivo with ROS1 and AGO4, controlling RdDM at the ROS1 locus and influencing its expression [79]. Moreover, biochemical evidence suggests that DDB2 plays an additional role in regulating various steps of ROS1-initiated DNA demethylation. Thus, it interacts in vitro with ROS1, inhibiting its 5-meC excision activity, but also with ZDP and APE1L, stimulating their enzymatic (3´-end cleaning) activities, thus avoiding accumulation of toxic SSB intermediates with blocked 3′-ends [79]. Altogether, these findings suggest that the coordinated control of DNA demethylation involves complex mechanisms at both the transcriptional and posttranscriptional levels.

There are also indications that active DNA demethylation may be further integrated with important aspects of the cell metabolism through the conserved [4Fe-4S] cluster conserved in DML proteins (see Section 2 above). Thus, genetic screens aimed at finding new factors involved in DME- or ROS1-initiated DNA demethylation have identified at least four proteins (AE7, NAR1, DRE2, and MET18/MMS19) functioning in the cytosolic iron–sulfur assembly (CIA) pathway, which is responsible for the maturation of cytosolic and nuclear Fe-S proteins [80,81,82,83,84]. Therefore, controlled assembly of [4Fe-4S] clusters in 5-meC DNA glycosylases may represent an important link connecting plant metabolism and nutrition states with DNA methylation patterns.

4. Biological Roles of DNA Demethylation

Plant DNA methylation is targeted to TEs and other repetitive sequences. Long TEs are primarily located in heterochromatin and methylated by CMT2 and CMT3, but gene-rich euchromatic regions contain a significant portion of shorter TEs or TE-derived sequences that are targeted by RdDM [4,85,86]. A primary function of plant DNA demethylation is to maintain genome stability by counteracting RdDM, thus preventing methylation spreading to neighboring genes. Active DNA demethylation is also implicated in genome-wide methylation changes during reproductive development that occur in both the female and male gametophytes. Demethylation in gametophytes, which takes places in companion cells and is also mostly directed to euchromatic TE sequences, may be important for reinforcing methylation patterns in gametes and one of its consequences is gene imprinting in the endosperm [19,20]. Additional demethylation associated to reproductive development takes place during seed development and germination, as well as during fruit ripening. A third major role of DNA demethylation in plants is to activate genes in response to biotic or abiotic stimuli, in many cases by targeting TE sequences located at their 5´ regions.

4.1. Maintenance of Genome Stability by Preventing Hypermethylation

Arabidopsis ROS1, DML2, and DML3 are expressed in a wide range of plant vegetative tissues and they seem to contribute to the stability and plasticity of plant epigenome and protect the genome from excessive methylation [11,15,16,17,63]. Arabidopsis ROS1, which is the major 5-meC DNA glycosylase in vegetative tissues, was identified in a screen for mutants with deregulated expression of the repetitive RD29A-LUC transgene [11]. Whereas in wild-type plants the transgene and the homologous endogenous gene are expressed, ros1 mutant plants display transcriptional silencing and hypermethylation of both loci [11], showing that active DNA demethylation can protect genes from being incorrectly silenced. Nearly 5000 regions are hypermethylated in the ros1 mutant when compared to the wild-type, mainly located at TEs and intergenic regions [63,64]. Transposons targeted by ROS1 are usually close to protein-coding genes, and hypermethylation in ros1 mutants spreads from TE edges to neighboring sequences [17,63]. These findings indicate that DNA demethylation by ROS1 aids in delimiting transposons and genes, preventing DNA methylation spreads from TEs, and, therefore, protecting nearby genes from transcriptional repression [63]. Analysis of hypermethylated regions in ros1 mutants led to the identification of thousands of RdDM targets, and ROS1 expression was reduced in all known RdDM mutants, suggesting that ROS1 counteracts DNA methylation established by the RdDM pathway, although it has been reported that it also antagonizes RdDM-independent DNA methylation at some loci [63]. The role of ROS1 in counteracting RdDM seems to be evolutionary conserved, since rice mutants deficient in the ROS1 homolog DNG701 also show hypermethylation at TEs [87]. ROS1 activity may be also important for reactivating expression of TEs that perform regulatory functions during vegetative development. For example, ros1 mutant plants show a defect in the pattern of leaf epidermal cells characterized by a higher number of stomate lineage cells due to hypermethylation of a TE located at the promoter of EPF2 (EPIDERMAL PATTERNING FACTOR 2) [88].

ROS1 might also contribute to genome stability by controlling telomere length. A study that characterized a mutation in the gene encoding the largest subunit of replication factor C (RFC1) as a ros1 suppressor reported that telomere length was longer in ros1 mutants compared to wild-type, whereas telomeres were shorter in the rfc1 mutant [89]. These results suggest that ROS1 may play a role as a negative regulator of Arabidopsis telomere length, probably via regulation of TERT (telomerase reverse transcriptase) or other telomere-related proteins (POT1a, BT2), since expression levels of these proteins were slightly higher in ros1 mutants and much lower in rfc1 or rfc1 ros1 mutants than in wild-type plants [89].

Similarly to ROS1, Arabidopsis DML2 and DML3 are expressed in a variety of plant organs and tissues and were found to be required for removing DNA methylation marks from improperly methylated cytosines [15,16]. Although dml2 and/or dml3 mutants do not show any obvious phenotypes, they display hypermethylation of cytosine residues that are either unmethylated or weakly methylated in wild-type plants. However, sites that are strongly methylated in wild-type plants are hypomethylated in dml2 and/or dml3 mutants [16]. Therefore, in addition to counteracting hypermethylation at erroneously methylated sites, DML2 and DML3 are required to maintain high methylation levels at properly methylated sites.

4.2. Methylome Reprogramming During Reproductive Development

The plant embryo is generated by fertilization of an egg cell by a sperm cell. In angiosperms, an additional fertilization event involving a second sperm cell and the central cell, a companion cell of the egg in the female gametophyte, generates an extraembryonic tissue, termed endosperm, that nourishes the embryo. The male gametophyte also has a companion cell, the vegetative cell, that forms a tube that transports the two sperm cells to the female gametophyte [90]. In Arabidopsis, active DNA demethylation initiated by DME in both types of companion cells, the vegetative, and central cells is important for successful reproduction and seed development.

Arabidopsis DME was identified in a search for mutations causing parent-of-origin effects on seed viability [14]. It was found to be necessary to establish imprinting of specific genes in the endosperm and its loss of function causes endosperm damage, alterations in embryonic development. and, therefore, abortive seeds [14]. DME-dependent DNA demethylation is initiated in the central cell of the female gametophyte [91], where the expression of the maternal alleles of MEA, FWA, and FIS2 genes, among others, are activated prior to fertilization [14,18,92,93,94,95]. The presence of a wild-type maternal DME allele is essential for seed development and viability, since a maternally inherited dme mutation did not express MEA::GFP or FWA::GFP transgenes in the endosperm after fertilization, causing embryo and endosperm abortion even if the paternal DME allele is not mutated [14]. Analysis of the methylation levels of Arabidopsis wild-type endosperm showed hypomethylation of the maternal MEA or FWA alleles, in comparison with the paternal alleles, whereas in dme endosperm, maternal and paternal MEA alleles are highly methylated [18,92]. Altogether, these observations indicate that, in the central cell of Arabidopsis, DME DNA glycosylase is responsible for 5-meC removal to activate expression of maternally imprinted genes in the endosperm that are necessary for proper seed development.

Genome-wide DNA methylation profiles have revealed that DME-dependent demethylation in the endosperm is large-scale and causes extensive hypomethylation of TEs [94,96], thus suggesting that its basal function may not be gene imprinting. In fact, DME is also expressed in the companion cell of the male gametophyte, the vegetative cell, after separation of the sperm cells lineage and is required for pollen germination in some ecotypes [97,98]. In the vegetative cell, DME demethylates DNA to activate the expression of MEA and FWA genes and the Mu1a repetitive element, thus suggesting a function similar to that observed in the central cell [97]. A genome-wide comparison of hypomethylated regions in the vegetative cell and the maternal endosperm genome revealed a large overlap between sites demethylated in the male and female companion cells [20,94,96]. DME-dependent demethylation in companion cells affects preferentially small, AT-rich, euchromatic TEs [20]. Available evidence suggests that the basal function of DME appears to be the reactivation of TEs in companion cells to generate short interfering RNAs (siRNAs) that would reinforce transposon methylation in male and female gametes, thus promoting stable silencing of TEs in the embryo genome [19,20,99,100]. ROS1, DML2, and DML3 are expressed in the vegetative cell and may also contribute to such functions in male gametes [19].

Dynamic methylation reprogramming also takes place during subsequent seed development and germination. Comparison of time-series methylomes from dry and germinating Arabidopsis seeds revealed extensive gain of methylation in TEs at CHH sequences during seed development, followed by DML-independent, passive global CHH demethylation during germination [21]. During the late embryogenesis stage, ROS1 is implicated in active DNA demethylation at CG sequences, antagonizing RdDM in the embryo, and establishing specific DNA methylation in the endosperm [21].

Although mainly inferred through studies with Arabidopsis, the function of active DNA demethylation during plant reproductive development seems to be evolutionarily conserved. In rice (Oryza sativa), active DNA demethylation in the female gametophyte is also initiated in the central cell [91]. Rice lacks DME orthologues [101] but one of its four ROS1 orthologues, named ROS1a, seems to have similar functions to Arabidopsis DME in both male and female gametophytes, as observed in genetic and genome-wide DNA methylation studies. Thus, mutation in rice ROS1a causes loss of hypomethylation of the vegetative cell compared to the sperm, endosperm defects, and seed abortion [102,103]. In addition to ROS1a, rice DNG701, which is closely related to Arabidopsis DML2 and ROS1, seems to play a role in seed development, as dng701 mutants show a high proportion of wrinkled seeds [87]. On other hand, maize (Zea mays) contains a DME homologous gene, termed DME-like, which is expressed at higher levels in the endosperm than in the embryo. Such differential expression correlates with lower DNA methylation levels in the endosperm at numerous genes implicated in seed development, including imprinted genes [104]. In wheat (Triticum aestivum) endosperm, the DME homolog TaDME demethylates the promoters of seed storage proteins, including immunogenic prolamins such as gliadins and low-molecular-weight glutenins (LMWgs), inducing their expression [105]. TaDME transcript suppression by RNAi entailed reduced accumulation of gliadins and LMWgs in the endosperm, suggesting a potential approach to generate celiac-suitable wheat cultivars [105].

Another stage of reproductive development in which active DNA demethylation performs important functions is fruit ripening. A global loss of DNA methylation takes place during tomato (Solanum lycopersicum) fruit ripening and has been recently attributed to active DNA demethylation mediated by SlDML2, one of the four putative DML genes encoding 5-meC DNA glycosylases in tomato (SlDML1, SlDML2, SlDML3, SlDML4) [22,23]. SlDML2 is an Arabidopsis ROS1 orthologue that is highly expressed during fruit ripening and that preferentially targets TEs in euchromatic regions. Tomato fruits in which SlDML2 is silenced by RNAi [23] or mutated by using the CRISPR/Cas system [22] showed dramatic ripening inhibition due to an increase of DNA methylation of thousands of genes involved in fruit ripening. Interestingly, these genes included both ripening-induced genes (e.g., RIN, NOR, PSY1), which were repressed in sldml2 mutants, and ripening-repressed genes (e.g., CAP10B, RBCS-2A), which were activated in sldml2 mutants [22]. These observations suggest that SlDML2 DNA demethylase activity is necessary for both the activation of ripening-induced genes and the inhibition of ripening-repressed genes in order to promote tomato fruit ripening.

DNA methylation changes have been described in the ripening of other fruits by comparing the methylomes of immature and ripe fruits. Strawberry (Fragaria vesca) contains four Arabidopsis ROS1 homologs (FvDME1, FvROS1.1, FvROS1.2, FvROS1.3) and, like tomato, showed decreased DNA demethylation during fruit ripening [106]. However, DNA hypomethylation during strawberry ripening was associated with downregulation of the RdDM pathway, as no upregulation of the DNA demethylases expression was observed [106]. By contrast, orange (Citrus sinensis), which also harbors four Arabidopsis ROS1 orthologs (CsDME, CsDML1, CsDML4, CsDML3), showed a gradual global increase in DNA methylation levels during ripening correlated with a gradual decrease in DNA demethylases expression, since DNA methyltransferases transcripts were relatively less abundant and were not upregulated [107]. Interestingly, this DNA hypermethylation was associated with both repression and activation of several hundred genes.

4.3. Gene Regulation in Response to Biotic Stimuli

In the past few years, several studies have reported alterations in plant DNA methylation levels and the role of plant 5-meC DNA glycosylases in response to several biotic stimuli, such as association with symbiotic microorganisms and attack by diverse pathogens. For example, a recent report found that the symbiotic relationship of legumes with nitrogen-fixing soil bacteria is partially controlled by active DNA demethylation [108]. The legume Medicago truncatula possesses four putative members of the DML family (MtDME, MtDML1, MtROS, and MtROSL1). Only MtMDE is robustly upregulated in the differentiation zone of mature Rhizobium-induced nodules compared with roots [108]. MtDME expression is associated with upregulation of TEs close to nodule-specific cysteine-rich (NCR) genes. Nodules in wild-type plants displayed DNA hypomethylation in CG and CHG contexts compared to roots, mostly associated to NCR genes. Plants in which MtDME is silenced by RNAi exhibited smaller nodules incapable to fix nitrogen and showed hypermethylation and downregulation of 400 genes, including NCR genes, suggesting that MtDME is critical for nodule development [108].

There is also evidence that active DNA demethylation plays a role in antibacterial defense. Thus, Arabidopsis ros1 mutants (but not dml2 or dml3 mutants) exhibited increased bacterial multiplication and propagation when infected with the pathogen Pseudomonas syringae [25]. Furthermore, they showed hypermethylation of an AtREP4 helitron-related repeat located at the promoter of the RGM1 disease resistance gene, concomitant with RGM1 downregulation [25]. Several studies have also implicated DNA demethylation in responses to viral infections. For example, transcription levels of two ROS1 homologs in Nicotiana benthamiana (NbROS1 and NbROS2) decreased after local and/or global infection of the plant with different geminiviruses [109].

Several studies have reported that active DNA demethylation is also essential for defense against infection by pathogenic fungi. Arabidopsis triple ros1 dml2 dml3 (rdd) mutant plants show enhanced susceptibility to the hemibiotrophic fungal pathogen Fusarium oxysporum and exhibit downregulation of many plant response stress genes containing TE sequences in their promoters, a subset of which display hypermethylation [110]. A subsequent study reported that ROS1 is the main enzyme responsible for demethylation of promoter-associated TEs and for the induction of defense-related genes in response to F. oxysporum infection [111]. Interestingly, the consequences of active DNA demethylation upon infection seem to depend on the fungal lifestyle. Thus, Arabidopsis ros1 mutants exhibit increased susceptibility to the biotrophic fungus Hyaloperonospora arabidopsidis, but increased resistance to the necrotrophic fungi Plectosphaerella cucumerina and Alternaria brassicicola [112]. These contrasting outcomes are partially linked to differential effects of ros1 deficiency on salicylic acid- and jasmonic acid-dependent signaling pathways, implicated in plant resistance to biotrophs and necrotrophs, respectively [112].

4.4. Gene Regulation in Response to Abiotic Stress

Many studies have reported changes in DNA methylation levels in response to a variety of abiotic stresses that correlate with transcriptional regulation of genes implicated in plant stress responses [24]. However, the role of the enzymes involved in active DNA demethylation on these alterations has been incompletely addressed and remains poorly understood. Reports in this field have been mostly limited to analyzing changes in DNA demethylases gene expression during different abiotic stress conditions and few studies have performed more comprehensive analyses involving, for example, loss-of-function mutants.

One area that has received particular attention is the role of methylation/demethylation processes in nutritional stress. In Arabidopsis, zinc (Zn) starvation causes moderate changes in total methylation, leading to hypo- and hyper-methylation predominantly in TEs, promoters, and genes in CG and CHG contexts, preferentially in the proximity of transcriptionally responsive genes [113]. Mutant ros1 plants are impaired in Zn uptake under Zn deficiency, suggesting that DNA demethylation is important for Zn starvation tolerance [113]. In maize roots, Zn deficiency produced a massive loss of DNA methylation, mostly in TEs associated with up- and downregulated genes. Among these genes, several maintenance DNA methylation enzymes were downregulated, and a ROS1 homolog was upregulated [114]. Arabidopsis wild-type seedlings grown under low phosphate (Pi) levels showed increases in DNA methylation levels concomitant with upregulation of transcript levels of all DNA methyltransferases (except for CMT3) and, to a lesser extent, ROS1 and DML2 transcripts, but exhibited downregulation of DML3, compared with high Pi conditions [115]. An rdd mutant showed a small increase in 5-meC, both in low and high Pi conditions, when compared to wild-type plants [115].

Active DNA demethylation is also involved in salt tolerance and responses to salt stress. The salt-tolerant rice variety Pokkali, but not the salt-sensitive variety IR29, showed decreased DNA methylation levels after salt stress, accompanied by induction in expression of DNG701 and DNG710 genes, encoding 5-meC DNA glycosylases, as well as demethylation of transposon Ty3-gypsy and a telomeric repetitive sequence [116]. Furthermore, recent evidence suggests that active DNA demethylation is involved in intergenerational transmission of a “stress memory” that facilitates rapid adaptation to short-term environmental fluctuations, a phenomenon known as ’priming’. Thus, hyperosmotic stress memory in Arabidopsis plants exposed to salt stress during their vegetative development is transiently transmitted to subsequent generations and is associated with changes in DNA methylation, primarily at non-CG sites located in intergenic TE-related sequences, and transcription levels of genes associated with environmental stress [117]. Salt stress tolerance and DNA methylation changes were preferentially transmitted through the female germline, but paternal memory transmission was restored in dme mutants, suggesting that active DNA demethylation in male gametes is essential to inhibit paternal inheritance of hyperosmotic priming responses [117].

Several studies have reported changes in DNA methylation levels and/or expression of DML homologs in different species subject to additional types of abiotic stresses such as drought [118,119,120], high or low temperatures [121,122], continuous cropping [123], and exposure to heavy metals [124] or ionizing radiation [125]. Active DNA demethylation has also been involved in the plant response to abscisic acid (ABA), a phytohormone that plays a crucial role in coordinating various signal transduction pathways during abiotic stresses. Thus, Arabidopsis ros1 mutants are hypersensitive to ABA during early seedling development and ROS1 is required to demethylate and activate a subset of ABA-inducible genes [126]. Factors involved in regulation of active DNA demethylation during responses to abiotic stress are poorly understood, although microRNAs (miRNAs) might play a role. Thus, Arabidopsis plants overexpressing miR402, a regulatory miRNA induced under different stress conditions, exhibited downregulation of DML3 expression and displayed earlier seed germination than wild-type plants under salt and cold stress, a phenotype that was also observed in dml3 mutant plants [127].

5. Future Perspectives

Recent years have witnessed significant advances in our understanding of the molecular mechanisms and biological roles of active DNA demethylation in plants. However, there are still many open questions and important aspects that remain to be elucidated. For example, additional players in the demethylation pathway initiated by DML proteins, such as the DNA polymerase(s) involved in gap-filling, are yet to be identified. On the other hand, recent discoveries suggest that a complex web of regulatory mechanisms is required to balance methylation and demethylation processes, likely involving still unknown components. In this regard, the identification of the DNA repair factor DDB2 as a player in regulating DNA demethylation raises the question of how this process is coordinated with DNA repair pathways, particularly since potentially toxic DNA intermediates are generated during demethylation. Furthermore, the likely, but often overlooked, role of DML proteins in repairing T:G mispairs arising from 5-meC spontaneous deamination remains virtually unexplored. An additional area that needs to be further studied is the role that chromatin modifications and/or recruiting factors play in targeting 5-meC DNA glycosylases to specific genome regions. It is still unknown whether DML proteins are able to recognize specific histone modifications, either directly or through their interaction with recruiting factors. Furthermore, the possible role of small RNAs in targeting DNA demethylation is still an open question.

Advances in the study of basic molecular mechanisms of DNA demethylation will have to be complemented with additional studies to establish its specific roles in plant physiology. As efficient epigenetic erasers, it is likely that plant 5-meC DNA glycosylases play still unidentified functions in plant development and responses to environmental signals, including stress. In this area, studies in non-model plants will be increasingly important, particularly when addressing issues such as transgenerational transmission of stress memory or the generation and maintenance of epiallelic variation, which may have major impacts in crop productivity.

Finally, our increasing knowledge about 5-meC DNA glycosylases may have also a significant impact in the emerging field of epigenetic editing, with potential applications not necessarily restricted to plants. Since no direct mechanism to excise 5-meC has apparently evolved in animals, it may be possible to use plant DML proteins to modify DNA methylation in human cells. Unlike TET-mediated oxidation, such direct excision would avoid generation of 5-meC derivatives that may have epigenetic roles on their own. Some recent results support the feasibility of using plant 5-meC DNA glycosylases as molecular tools to modify cell methylomes. Thus, overexpression of Arabidopsis DME in human cells causes genome-wide DNA methylation changes and significant alterations in the cellular phenotype, both in noncancerous [128] and cancer cells [129]. Furthermore, it has been reported that a fusion protein containing the catalytic domain of Arabidopsis ROS1 and the DNA-binding domain of yeast GAL4 can be targeted for specific demethylation and reactivation of a methylation-silenced reporter gene in human cells [130]. In summary, it is most likely that future research will generate new and exciting results on the molecular biology of plant active DNA demethylation and its physiological roles, as well as promising applications in emerging epigenetic technologies.

Author Contributions

J.T.P.-D., T.R.-A., R.R.A., and D.C.-C. jointly wrote the manuscript.

Funding

Funding was provided by the Spanish Ministry of Science, Innovation and Universities, as well as the European Regional Development Fund, under Grant BFU2016-80728-P.

Conflicts of Interest

The authors declare no conflict of interest.