<scp>DNA</scp> methylation maintenance consolidates <scp>RNA</scp>‐directed <scp>DNA</scp> methylation and transcriptional gene silencing over generations in <i>Arabidopsis thaliana</i>

Kuhlmann, Markus; Finke, Andreas; Mascher, Martin; Mette, Michael Florian

doi:10.1111/tpj.12630

Cited by 16 publications

(13 citation statements)

References 76 publications

(123 reference statements)

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“…The results of analysis of the DNA methylation of specific genes showed that the degree of DNA methylation of the promoter −109 to −279 bp region in the flanking region of the phenylalanine ammonia-lyase2 gene of L. maackii was higher than that of L. maackii, and the degree of DNA methylation of the CG site was significantly different between the two [28]. In the present study, we conducted DNA methylation analysis of the key enzymes [29,30], so were regarded as DNA methylation nonspecific sites of gene promoters. The SS cytosine at −558 and cytosines at positions −684 and −847 of the SE gene were specific sites involved in the regulation of gene expression that need further research.…”

Section: Discussionmentioning

confidence: 72%

DNA Methylation of Farnesyl Pyrophosphate Synthase, Squalene Synthase, and Squalene Epoxidase Gene Promoters and Effect on the Saponin Content of Eleutherococcus Senticosus

Wang

Guo

Zhang

et al. 2019

Forests

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Eleutherococcus senticosus (Ruper. et Maxim.) Maxim is a traditional Chinese medicine. The saponin components of E. senticosus have several biological effects, including reduction of blood lipids; protection against liver, heart, and vascular disease; and antitumor activity. The DNA methylation of E. senticosus farnesyl pyrophosphate synthase (FPS), squalene synthase (SS), and squalene epoxidase (SE) gene promoters and the mechanism of the influence of these enzymes on saponin synthesis and accumulation in E. senticosus were explored using bisulfite sequencing technology, real-time PCR, the vanillin-concentrated sulfuric acid chromogenic method, and LC-MS. There are 19 DNA methylation sites and 8 methylation types in the FPS gene. The SS gene has nine DNA methylation sites and two DNA methylation types. The SE gene has 16 DNA methylation sites and 7 methylation types. The total saponin content in the high and low DNA methylation groups were 1.07 ± 0.12 and 2.92 ± 0.32 mg/g, respectively. Statistical analysis indicated that the gene expression of the FPS, SS, and SE genes was significantly positively correlated with the saponin content (p < 0.05), and that the methylation ratio was significantly negatively correlated with the saponin content (p < 0.01), while the expression of the SS and SE genes was significantly positively correlated (p < 0.01). A total of 488 metabolites were detected from E. senticosus and 100 different metabolites were screened out by extensive targeted metabolomics. The amount of most metabolites related to the mevalonate pathway was higher in the low DNA methylation group than in the high DNA methylation group. It was demonstrated that there are DNA methylation sites in the promoter regions of the FPS, SS, and SE genes of E. senticosus, and DNA methylation in this region could significantly inhibit synthesis in the mevalonate pathway, thus reducing the content of the final product E. senticosus saponin.

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Section: Discussionmentioning

confidence: 72%

DNA Methylation of Farnesyl Pyrophosphate Synthase, Squalene Synthase, and Squalene Epoxidase Gene Promoters and Effect on the Saponin Content of Eleutherococcus Senticosus

Wang

Guo

Zhang

et al. 2019

Forests

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“…The inheritance of accumulated epimutations showed epigenetic inheritance, which was not due to underlying genetic variation (genetic inheritance)27, as all analyses were based on samples from a common ancestor and genetic variation was almost completely absent. In a similar study in A. thaliana , RNA-directed de novo DNA methylation in CG dinucleotides was stably transmitted to offspring for at least three generations8.…”

Section: Discussionmentioning

confidence: 92%

“…Previous studies have revealed that heritable epimutations play important roles in plant growth and development7. In Arabidopsis thaliana , RNA-directed de novo DNA methylation of CG dinucleotides is stably inherited, and in offspring, this methylation affects the transcription of the target gene8. Moreover, transgenerational epimutations have critical functions in the adaptations of plants to their changing environments because epimutation states can be modified by environmental factors and are reversible910.…”

mentioning

confidence: 99%

Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant’s adaptation to drought condition

Zheng

Chen

Xia

et al. 2017

Sci Rep

146

118

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Epigenetic mechanisms are crucial mediators of appropriate plant reactions to adverse environments, but their involvement in long-term adaptation is less clear. Here, we established two rice epimutation accumulation lines by applying drought conditions to 11 successive generations of two rice varieties. We took advantage of recent technical advances to examine the role of DNA methylation variations on rice adaptation to drought stress. We found that multi-generational drought improved the drought adaptability of offspring in upland fields. At single-base resolution, we discovered non-random appearance of drought-induced epimutations. Moreover, we found that a high proportion of drought-induced epimutations maintained their altered DNA methylation status in advanced generations. In addition, genes related to transgenerational epimutations directly participated in stress-responsive pathways. Analysis based on a cluster of drought-responsive genes revealed that their DNA methylation patterns were affected by multi-generational drought. These results suggested that epigenetic mechanisms play important roles in rice adaptations to upland growth conditions. Epigenetic variations have morphological, physiological and ecological consequences and are heritable across generations, suggesting that epigenetics can be considered an important regulatory mechanism in plant long-term adaptation and evolution under adverse environments.

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“…Intriguingly, the transcription and transposition of a substantial proportion of TEs are extensively controlled by endogenous or exogenous siRNAs through an RNA‐directed DNA methylation (RdDM) pathway (Xie et al ., ; Kuhlmann et al ., ; Marré et al ., ; Houri‐Zeevi and Rechavi, ). Furthermore, double‐stranded RNA (dsRNA), the precursor of siRNA, can be derived from the complementary inverted terminal repeats in DNA transposons (Levin and Moran, ).…”

Section: Introductionmentioning

confidence: 99%

Maintenance of grafting‐induced epigenetic variations in the asexual progeny of Brassica oleracea and B. juncea chimera

Cao

et al. 2018

The Plant Journal

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Grafting-induced variations have been observed in many plant species, but the heritability of variation in progeny is not well understood. In our study, adventitious shoots from the C cell lineage of shoot apical meristem (SAM) grafting chimera TCC (where the origin of the outmost, middle and innermost cell layers, respectively, of SAM is designated by 'T' for tuber mustard and 'C' for red cabbage) were induced and identified as r-CCC (r = regenerated). To investigate the maintenance of grafting variations during cell propagation and regeneration, different generations of asexual progeny (r-CCCn, n = generation) were established through successive regeneration of axillary shoots from r-CCC. The fourth generation of r-CCC (r-CCC4) was selected to perform whole genome bisulfite sequencing for comparative analysis of hetero-grafting-induced global methylation changes relative to r-s-CCC4 (s = self-grafting). Increased CHH methylation levels and proportions were observed in r-CCC4, with substantial changes occurring in the repeat elements. Small RNA sequencing revealed 1135 specific small interfering RNA (siRNA) tags that were typically expressed in r-CCC, r-CCC2 and r-CCC4. Notably, 65% of these specific siRNAs were associated with repeat elements, termed RE siRNAs. Subsequent analysis revealed that the CHH methylation of RE siRNA-overlapping regions was mainly hypermethylation in r-CCC4, indicating that they were responsible for directing and maintaining grafting-induced CHH methylation. Moreover, the expression of 13 differentially methylated genes (DMGs) correlated with the phenotypic variation, showing differential expression levels between r-CCC4 and r-s-CCC4. These DMGs were predominantly CG hypermethylated, their methylation modifications corresponded to the transcription of relative methyltransferase.

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DNA methylation maintenance consolidates RNA‐directed DNA methylation and transcriptional gene silencing over generations in Arabidopsis thaliana

Cited by 16 publications

References 76 publications

DNA Methylation of Farnesyl Pyrophosphate Synthase, Squalene Synthase, and Squalene Epoxidase Gene Promoters and Effect on the Saponin Content of Eleutherococcus Senticosus

DNA Methylation of Farnesyl Pyrophosphate Synthase, Squalene Synthase, and Squalene Epoxidase Gene Promoters and Effect on the Saponin Content of Eleutherococcus Senticosus

Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant’s adaptation to drought condition

Maintenance of grafting‐induced epigenetic variations in the asexual progeny of Brassica oleracea and B. juncea chimera

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