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DNA methylation sequence contexts and related DNA methyltransferases. DNA methylation at cytosines followed by guanines (CG methylation) is maintained by MET1, while CHG and CHH methylation are maintained by CMT3 and CMT2, respectively. The methyltransferase involved in RdDM, DRM2, can add DNA methylation regardless of sequence context. https://doi.org/10.1371/journal.pgen.1009034.g002
Source publication
RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, although other mechanisms of RNA-directed chromatin modification have also been described in fungi and animals. To date, the RdDM pathway is best charac...
Contexts in source publication
Context 1
... is the only mechanism in plants that can add DNA methylation to cytosines regardless of sequence context [55]. DNA methylation in plants is typically divided into three categories based on the sequence context of the methylated cytosine: CG, CHG, and CHH, where H is any nucleotide except G (Fig 2). These reflect the different sequence contexts targeted by several DNA methylation pathways in plants. ...
Context 2
... methylation at these same heterochromatic loci is also recognized by the histone methyltransferases SUVH4/KYP, SUVH5, and SUVH6, which bind to non-CG methylation and add H3K9me2 to nearby histones [123,124], closing the positive feedback loop. Similarly, CMT3 and CMT2, the two DNA methyltransferases involved in the maintenance of CHG and CHH methylation respectively (Fig 2) [75], both bind and add DNA methylation to H3K9me2-marked heterochromatin, forming their own feedback loop with SUVH4/5/6 [123,125]. These interactions help strongly reinforce silencing at TEs and other heterochromatic regions. ...
Context 3
... contrast, CMT2 and CMT3 preferentially function in constitutive heterochromatin and depend strongly on DDM1 to maintain silencing over these regions [3,5,131]. Similarly, MET1, which maintains DNA methylation at CG sites after replication (Fig 2), requires DDM1 to access heterochromatin and maintain CG methylation in those regions [132]. Thus, DDM1 is a key regulator of DNA methylation in dense heterochromatin, but regulates sites mostly independently from RdDM [5,99]. ...
Context 4
... between RdDM and the other three maintenance DNA methylation pathways (Fig 2) are limited and predominantly indirect. The DNA methyltransferase MET1 robustly maintains CG methylation genome-wide (Fig 2), including at RdDM target sites. ...
Context 5
... between RdDM and the other three maintenance DNA methylation pathways (Fig 2) are limited and predominantly indirect. The DNA methyltransferase MET1 robustly maintains CG methylation genome-wide (Fig 2), including at RdDM target sites. In RdDM mutants, non-CG methylation at RdDM target sites is lost, but CG methylation is still maintained, suggesting that MET1 activity is independent of RdDM [99]. ...
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Background
The antisense noncoding mitochondrial RNAs (ASncmtRNAs) derive from the mitochondrial 16S gene. Knockdown of these transcripts with chemically-modified antisense oligonucleotides induces proliferative arrest, apoptosis and invasiveness reduction in tumor but not normal cells. One of these transcripts, ASncmtRNA-2, contains the complete a...
Citations
... The numbers of m CG-DMCs with increased methylation levels in ungraft TK vs PT were higher than in ungraft TK vs TT (Table 4). This indicated that grafting affected methylation levels by influencing probably the activities of domains rearranged methyltransferase 1 (DRM1) and (DRM2) and directed by small interfering RNAs (siRNAs) (Erdmann and Picard 2020;Agius et al. 2023). Differences in the numbers of m CG + m CHG-DMCs among three gene elements were studied, and results revealed that among the gene elements, UPS regions contained the highest numbers of m CG + m CHG-DMCs, followed by DWN regions but the lowest numbers were observed in GB regions (Table 4). ...
... In tomato and Arabidopsis, the vigorous phenotype induced by a mutation in MSH1 passed through grafting via siRNAs and inherited in the offspring of wild-type scions (Kundariya et al. 2020). Transgenerational transmissions of methylation changes into the progeny were also reported in other studies (Erdmann and Picard 2020;Boquete et al. 2021). However, there were limited studies on the methylation status of snoRNA genes in grafting. ...
The effects of grafting in response to various biotic and abiotic stressors have been studied, however, the methylation status of small nucleolar RNA (snoRNA) genes in heterograft and homograft cotton needs investigation. This study was undertaken to determine grafting effects on DNA methylation of snoRNA genes in Upland cotton. Rootstocks used were Pima 3-79 (Gossypium barbadense acc. Pima 3-79) and Texas Marker-1 (G. hirsutum acc. TM-1), representing two different species with different fiber properties, adaptations, and morphologies. The methylation ratio and differently methylated cytosines (DMCs) of 10935 snoRNA genes in mature seeds of heterograft and homograft cotton samples were studied using the whole genome bisulfite sequencing method. Seedling vigor and seed weight were studied to investigate phenotype alterations that might be associated with altered methylation levels among grafts. Statistically significant DMC differences among gene elements of snoRNA genes and between homograft and heterograft cotton samples were identified in the absence of DNA sequence alterations. DNA methylation alterations of snoRNA genes associated with seedling vigor and 100 seed weight. The majority of snoRNA genes showed higher numbers of m CG + m CHG-DMCs with increased methylation levels in heterograft, while there were higher numbers of m CG + m CHG-DMCs with decreased methylation levels in homograft. Since snoRNAs regulate essential genes for plant growth and development and plant adaptation to different habitats or extreme environments, their altered methylation levels should be related with plant physiology.
... In plants, euchromatic repetitive regions are targeted by the RNA-directed DNA methylation pathway (RdDM) (Erdmann and Picard, 2020), in which the concerted action of non-coding RNA polymerases and small RNAs direct the DNA methyltransferase, DRM2, to specific sites of the genome. Newly invading genetic elements are targeted by the 'non-canonical' RdDM pathway, and involve the action of Pol II derived small RNAs (Cuerda-Gil and Slotkin, 2016). ...
Silencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT DNA methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localized to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localization in an h1 mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase, Pol V. Loss of H1 resulted in NRPE1 enrichment predominantly in heterochromatic TEs. Increased NRPE1 binding was associated with increased chromatin accessibility in h1 , suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating an h1/nrpe1 double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions in h1 corresponded to the loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposition correlated with increased methylation specifically in the CHH context. Additionally, we found that H1 similarly restricts the occupancy of the methylation reader, SUVH1, and polycomb-mediated H3K27me3. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.
... In the RdDM pathway, Pol V and its transcripts provide a docking platform for downstream components 40 . The mutation of SPT5L dramatically reduced the intergenic enrichment of SPT6L (Fig. 5b) and compromised the association between SPT6L and NRPE1 (Fig. 5e), suggesting that Pol V downstream events rather than Pol V itself determines the intergenic recruitment of SPT6L. ...
In plants, the plant-specific RNA polymerase V (Pol V) transcripts non-coding RNAs and provides a docking platform for the association of accessory proteins in the RNA-directed DNA methylation (RdDM) pathway. Various components have been uncovered that are involved in the process of DNA methylation, but it is still not clear how the transcription of Pol V is regulated. Here, we report that the conserved RNA polymerase II (Pol II) elongator, SPT6L, binds to thousands of intergenic regions in a Pol II-independent manner. The intergenic enrichment of SPT6L, interestingly, co-occupies with the largest subunit of Pol V (NRPE1) and mutation of SPT6L leads to the reduction of DNA methylation but not Pol V enrichment. Furthermore, the association of SPT6L at Pol V loci is dependent on the Pol V associated factor, SPT5L, rather than the presence of Pol V, and the interaction between SPT6L and NRPE1 is compromised in spt5l. Finally, Pol V RIP-seq reveals that SPT6L is required to maintain the amount and length of Pol V transcripts. Our findings thus uncover the critical role of a Pol II conserved elongator in Pol V mediated DNA methylation and transcription, and shed light on the mutual regulation between Pol V and II in plants.
... (De Oliveira Urquiaga et al. 2021;Erdmann & Picard 2020;Yong-Villalobos et al. 2015). ...
... However, recent research (Jagić et al. 2022) proposed an additional role for the BPM1 protein as part of the RNA-directed DNA methylation (RdDM) mechanism. As an epigenetic process, RdDM contributes to the regulation of gene expression and suppression of transposable element activity (Erdmann and Picard 2020). Moreover, it has been linked to abiotic stress response in plants. ...
... Interestingly, we found that the seeds of primed oeBPM1 plants did not show significant differences in germination rate compared to the corresponding control. The opposite result was observed for seeds of control and primed wild-type plants supporting the theory that BPM1, as part of RdDM, regulates HSinducible genes and mitigates the negative consequences of transposable elements on genome stability (Erdmann and Picard 2020), thus promoting improved tolerance to HS, but also increasing the viability of heat-treated progeny. However, it should be noted that heat-stressed oeBPM1 seedlings did not show increased thermotolerance compared to wild type, suggesting that BPM1 is important for acquired thermotolerance but not for basal thermotolerance. ...
Rising temperatures due to global warming pose a growing threat to plant metabolism. Priming plants with moderately elevated temperatures prior to severe heat stress (HS) has been shown to increase tolerance to HS. In Arabidopsis thaliana (L.) Heynh. MATH-BTB (BPM) proteins, as part of the proteasomal degradation pathway, modulate plant response to abiotic stress, but there are no data on their role in HS tolerance. Therefore, we investigated the response of BPM1-overexpressing (oeBPM1) and wild-type A. thaliana seedlings exposed to severe HS of 42 °C with or without priming at 37 °C. This study included the analysis of certain physiological and biochemical parameters, the expression of several heat-inducible genes and the expression of the ONSEN retrotransposon. In both non-primed oeBPM1 and wild-type seedlings, HS led to severe damage despite induced expression of HS-responsive genes, including DREB2A, HSFA3 and HSP90. Priming resulted in up-regulation of HSFA2 stress memory gene, activation of the ONSEN retrotransposon, and preserved photosynthetic performance, followed by long-term survival of both oeBPM1 and wild-type seedlings. However, PCA analysis revealed separation of primed oeBPM1 seedlings from primed wild type due to lower induction of HSFA2 and ONSEN transcript. Moreover, the germination rate of seeds collected from primed oeBPM1 plants was higher than that of wild-type seeds. These results suggest that overexpression of BPM1 contributes to acquired thermotolerance by adjusting responses to adverse temperature conditions. Our research sheds new light on BPM-mediated thermotolerance and highlights the importance of BPM1 overexpression for acquired thermotolerance.
... Activation of TEs leads to an initial response of post-transcriptional gene silencing involving siRNA, which is followed by establishment and maintenance of silencing with DNA and histone methylation in RNA-directed DNA methylation (RdDM) pathways. RdDM methylation leads to chromatin modification making the TE inaccessible to transcriptional machinery(Erdmann & Picard, 2020). The intersection of methylation and ...
DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long‐read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long‐reads. Hybrid and reference‐guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re‐basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.
... Notably, easiRNAs which are derived from TEs also use the RNA-dependent RNA (RDR) polymerase-mediated silencing pathway to maintain many TEs in a silenced state although they direct their silencing function at the post-transcriptional level (Ariel and Manavella 2021). Both het-siRNAs and easiRNAs orchestrate the maintenance and de novo methylation states, respectively, at various features throughout the plant genome (Erdmann and Picard 2020). ...
... The higher proportion in the 21 to 22-nt sRNAs aligning with the two categories of TEs detected in the 4xAL2 allotetraploid may potentially guide the initiation of DNA methylation in a non-traditional manner, influencing regulatory responses to genomic stress. Non-canonical RdDM pathways involve 21 to 22-nt sRNAs from a variety of sources, allowing de novo DNA methylation to be initiated at many different types of loci (Erdmann and Picard 2020). However, not all 21-22 nt sRNAs are related to non-canonical RdDM. ...
Key message
The shock produced by the allopolyploidization process on a potato interspecific diploid hybrid displays a non-random remobilization of the small RNAs profile on a variety of genomic features.
Abstract
Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic “shock” that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
... RdDM is accomplished through the coordinated action of two plant-specific versions of RNA polymerase II. Guided by TE-derived small RNAs (sRNAs), a variety of epigenetic factors such as DNA and histone methyltransferases are recruited [11]. RdDM typically acts on the edges of TEs located in genic-rich regions of the genome, thereby creating and reinforcing a heterochromatin environment within euchromatin [12]. ...
Background
Plant responses to a wide range of stresses are known to be regulated by epigenetic mechanisms. Pathogen-related investigations, particularly against RNA viruses, are however scarce. It has been demonstrated that Arabidopsis thaliana plants defective in some members of the RNA-directed DNA methylation (RdDM) or histone modification pathways presented differential susceptibility to the turnip mosaic virus. In order to identify genes directly targeted by the RdDM-related RNA Polymerase V (POLV) complex and the histone demethylase protein JUMONJI14 (JMJ14) during infection, the transcriptomes of infected mutant and control plants were obtained and integrated with available chromatin occupancy data for various epigenetic proteins and marks.
Results
A comprehensive list of virus-responsive gene candidates to be regulated by the two proteins was obtained. Twelve genes were selected for further characterization, confirming their dynamic regulation during the course of infection. Several epigenetic marks on their promoter sequences were found using in silico data, raising confidence that the identified genes are actually regulated by epigenetic mechanisms. The altered expression of six of these genes in mutants of the methyltransferase gene CURLY LEAF and the histone deacetylase gene HISTONE DEACETYLASE 19 suggests that some virus-responsive genes may be regulated by multiple coordinated epigenetic complexes. A temporally separated multiple plant virus infection experiment in which plants were transiently infected with one virus and then infected by a second one was designed to investigate the possible roles of the identified POLV- and JMJ14-regulated genes in wild-type (WT) plants. Plants that had previously been stimulated with viruses were found to be more resistant to subsequent virus challenge than control plants. Several POLV- and JMJ14-regulated genes were found to be regulated in virus induced resistance in WT plants, with some of them poisoned to be expressed in early infection stages.
Conclusions
A set of confident candidate genes directly regulated by the POLV and JMJ14 proteins during virus infection was identified, with indications that some of them may be regulated by multiple epigenetic modules. A subset of these genes may also play a role in the tolerance of WT plants to repeated, intermittent virus infections.
... These pathways are functionally similar but not identical. During the first stage of the canonical RdDM pathway, the plant specific RNA polymerase IV (Pol IV) complex is recruited to chromatin regions through its interaction with Sawadee homeodomain homolog1 (SHH1) and CLASSY family proteins (CLSYs) [30]. Next, Pol IV transcribes these regions producing short singlestranded RNAs (ssRNAs), which are then converted into double-stranded RNAs (dsR-NAs) by the RNA-directed RNA polymerase 2 (RDR2) [31]. ...
... The formation of this complex triggers the recruitment of the DNA methyltransferase domains rearranged methyltransferase 2 (DRM2), which is responsible for targeting the de novo methylation of nearby DNA at all sequence contexts resulting in transcriptional gene silence ( Figure 2). The non-canonical RdDM pathway is generally involved in the initial establishment of DNA methylation at new target loci, such as new transposable element insertions, rather than maintaining the existing silent heterochromatin state [30]. In fact, the non-canonical RdDM pathway often acts as a link between the initial post-transcriptional silencing (PTGS) and the long-term transcriptional silencing (TGS) through the canonical RdDM pathway [35]. ...
... The main difference between the two pathways lies in the origin and the production of small RNAs (sRNAs), either siRNAs or miRNAs, involved. Specifically, in contrast to the canonical RdDM pathway that involves 24 nt siRNAs originating solely from Pol IV transcripts, the non-canonical RdDM pathway involves 21-22 nt sRNAs originating from a variety of sources [30]. These 21-22 nt sRNAs are involved not only in the non-canonical RdDM but also participate in other PTGS pathways. ...
Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype–environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.
... RdDM is essential for plant resistance to biotic and abiotic stresses (Erdmann and Picard, 2020). Downstream of the RdDM pathway, SUVH2 and SUVH9 are significant for the association of Pol V with chromatin (Johnson et al., 2014). ...
New transposon insertions are deleterious to genome stability. The RNA-directed DNA methylation (RdDM) pathway evolved to regulate transposon activity via DNA methylation. However, current studies have not yet clearly described the transposition regulation. ONSEN is a heat-activated retrotransposon that is activated at 37°C. The plant-specific SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG (SUVH) family proteins function downstream of the RdDM pathway. The SUVH protein families are linked to TE silencing by two pathways, one through DNA methylation and the other through chromatin remodeling. In this study, we analyzed the regulation of ONSEN activity by SUVH2. We observed that ONSEN transcripts were increased; however, there was no transpositional activity in Arabidopsis suvh2 mutant. The suvh2 mutant produced siRNAs from the ONSEN locus under heat stress, suggesting that siRNAs are involved in suppressing transposition. These results provide new insights into the regulatory mechanisms of retrotransposons that involve siRNA in the RdDM pathway.
