The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

Yang, Rong; Zheng, Zhimin; Chen, Qing; Yang, Lan; Huang, Huan; Miki, Daisuke; Wu, Wenwu; Zeng, Liang; Li, Jun; Zhou, Jin‐Xing; Ogas, Joe; Zhu, Jian‐Kang; He, Xin‐Jian; Zhang, Heng

doi:10.1186/s13059-017-1226-y

Cited by 43 publications

(37 citation statements)

References 81 publications

(144 reference statements)

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“…It is also possible that mobile maternal p4-siRNAs are required for correct expression of specific transposon-associated genes, such as AGAMOUS-like transcription factors, which are upregulated in Arabidopsis seeds lacking maternal NRPD1 (Lu et al, 2012). Finally, mobile maternal p4-siRNAs might function across the genome to maintain the effective parental dosage in endosperm and their loss could unbalance parental contributions and lead to endosperm failure (Gehring, 2013;Yang et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa

et al. 2018

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Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA methylation (RdDM). The molecular mechanism of RdDM is well characterized in Arabidopsis, yet the biological function remains unclear, as loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. It is known that 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction. Here we show that, unlike Arabidopsis, mutations in the Pol IV-dependent small RNA pathway cause severe and specific reproductive defects in Brassica rapa. High rates of abortion occur when seeds have RdDM mutant mothers, but not when they have mutant fathers. Although abortion occurs after fertilization, RdDM function is required in maternal somatic tissue, not in the female gametophyte or the developing zygote, suggesting that siRNAs from the maternal soma might function in filial tissues. We propose that recently outbreeding species such as B. rapa are key to understanding the role of RdDM during plant reproduction.

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Section: Resultsmentioning

confidence: 99%

Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa

et al. 2018

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“…However, the silencing of FWA in the vegetative tissue by DNA methylation suggests a minimal role of FWA in flowering time regulation [ 70 ]. Interestingly, PICKLE (PKL), a chromatin remodeling factor, plays a role in non-coding RNA-directed DNA methylation by maintaining the levels of CG, CHG, and CHH methylation [ 71 ]. pkl-1 mutants exhibit late flowering and reduced the hypocotyl elongation at a warm temperature [ 72 , 73 ].…”

Section: Histone Variants Histone Modification and Dna Methylatimentioning

confidence: 99%

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

Susila

Nasim

Ahn

2018

IJMS

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In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.

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“…More than 600 genes were differentially expressed between the wild-type and pkl mutant plants after cold treatment, including the downregulation of CBF3 and multiple CBF target genes, such as RD29A , COR15A , and COR15B . Since PKL is known to be involved in the RdDM [ 32 ] and H3K27me3 deposition [ 33 ] pathways, both H3K27me3 and DNA methylation could serve as memory marks for cold-induced freeze tolerance.…”

Section: Epigenetic Responses To Stressful Factorsmentioning

confidence: 99%

“…In evolution, they elaborate specific adaptive mechanisms to overcome various kinds of environmental stress and retain the stress response information for some time after the stress encounters are over. It was shown that stress factors induce alterations in the epigenetic status of stress-response genes that could still be present for some time after recovery or even in the progeny [ 32 , 42 , 45 , 47 , 83 ]. This kind of information used by plants to respond faster or stronger at repeated exposure to the same stress was named stress priming or stress memory [ 45 , 84 ].…”

Section: Short-term Epigenetic Memory (Priming) Of Stressmentioning

confidence: 99%

Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses

Ashapkin

Kutueva

Aleksandrushkina

et al. 2020

IJMS

122

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Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.

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The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

Cited by 43 publications

References 81 publications

Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa

Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses

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