DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis

Le, Tuan-Ngoc; Schümann, Ulrike; Smith, Nerida Ann; Tiwari, Sameer K.; Au, Phil Chi Khang; Zhu, Qian; Taylor, Jennifer; Kazan, Kemal; Llewellyn, Danny; Zhang, Ren; Dennis, Elizabeth S.; Wang, Ming-Bo

doi:10.1186/s13059-014-0458-3

Cited by 236 publications

(91 citation statements)

References 40 publications

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“…Although usually suppressed by DNA methylation, TEs contributed to the activation of the plant responses to abiotic stress33. In A.thaliana , DNA demethylases played significant roles in regulating the expression of stress-responsive genes through targeting TEs in their promoter regions34. Therefore, DNA methylation variation in promoter TEs could be considered another type of epimutation.…”

Section: Discussionmentioning

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

145

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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Section: Discussionmentioning

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

145

118

View full text Add to dashboard Cite

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“…An increased activity of TE (Transposable Elements) was observed under unfavorable environmental conditions (McCue et al, 2012; Le et al, 2014; Makarevitch et al, 2015). Recently, the mechanism of the modulation of ABI5 expression via TE has been described.…”

Section: Epigenetic Regulation Of the Abi5 Genementioning

confidence: 99%

The Role and Regulation of ABI5 (ABA-Insensitive 5) in Plant Development, Abiotic Stress Responses and Phytohormone Crosstalk

2016

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ABA Insensitive 5 (ABI5) is a basic leucine zipper transcription factor that plays a key role in the regulation of seed germination and early seedling growth in the presence of ABA and abiotic stresses. ABI5 functions in the core ABA signaling, which is composed of PYR/PYL/RCAR receptors, PP2C phosphatases and SnRK2 kinases, through the regulation of the expression of genes that contain the ABSCISIC ACID RESPONSE ELEMENT (ABRE) motif within their promoter region. The regulated targets include stress adaptation genes, e.g., LEA proteins. However, the expression and activation of ABI5 is not only dependent on the core ABA signaling. Many transcription factors such as ABI3, ABI4, MYB7 and WRKYs play either a positive or a negative role in the regulation of ABI5 expression. Additionally, the stability and activity of ABI5 are also regulated by other proteins through post-translational modifications such as phosphorylation, ubiquitination, sumoylation and S-nitrosylation. Moreover, ABI5 also acts as an ABA and other phytohormone signaling integrator. Components of auxin, cytokinin, gibberellic acid, jasmonate and brassinosteroid signaling and metabolism pathways were shown to take part in ABI5 regulation and/or to be regulated by ABI5. Monocot orthologs of AtABI5 have been identified. Although their roles in the molecular and physiological adaptations during abiotic stress have been elucidated, knowledge about their detailed action still remains elusive. Here, we describe the recent advances in understanding the action of ABI5 in early developmental processes and the adaptation of plants to unfavorable environmental conditions. We also focus on ABI5 relation to other phytohormones in the abiotic stress response of plants.

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“…RdDM (RNA-directed DNA methylation), the most important and well-characterized DNA methylation pathway, is guided by 24-nt siRNAs, induces de novo cytosine methylation, and regulates gene expression (Le et al, 2014). RdDM occurs only in plants performing transcriptional gene silencing (TGS) involving the Pol IV–RDR2–DCL3 complex.…”

Section: Introductionmentioning

confidence: 99%

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

Shi

Quan

et al. 2017

Front. Plant Sci.

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Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0.62), suggesting that the interaction of NERDL with its putative target might be involved in wood formation. We conducted association mapping in a natural population of P. tomentosa (435 unrelated individuals) to evaluate genetic variation and the interaction of the lncRNA NERDL with PtoNERD. Using additive and dominant models, we identified 30 SNPs (P < 0.01) associated with five tree growth and wood property traits. Each SNP explained 3.90–8.57% of phenotypic variance, suggesting that NERDL and its putative target play a common role in wood formation. Epistasis analysis uncovered nine SNP-SNP association pairs between NERDL and PtoNERD, with an information gain of -7.55 to 2.16%, reflecting the strong interactions between NERDL and its putative target. This analysis provides a powerful method for deciphering the genetic interactions of lncRNAs with mRNA and dissecting the complex genetic network of quantitative traits in trees.

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DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis

Cited by 236 publications

References 40 publications

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

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

The Role and Regulation of ABI5 (ABA-Insensitive 5) in Plant Development, Abiotic Stress Responses and Phytohormone Crosstalk

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

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