Non-coding RNAs and DNA methylation in plants

Zhao, Yuanyuan; Chen, Xuemei

doi:10.1093/nsr/nwu003

Cited by 25 publications

(17 citation statements)

References 96 publications

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“…Accordingly, 5mC has long been considered the ‘fifth base’ in eukaryotic genomes, providing another layer of genome regulation 10 . DNA methylation fine-tunes gene expression and transposon silencing, playing important roles in maintenance of the structure and function of heterochromatin, genome stability, genomic imprinting, transgene silencing, and gene evolution 11–13 . In animals, almost all methylated cytosines occur in the CG context 10 .…”

Section: Introductionmentioning

confidence: 99%

DNA methylation repels targeting of Arabidopsis REF6

et al. 2019

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RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bind motifs located in active chromatin states that are depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, we show that REF6 preferentially bind to hypo-methylated CTCTGYTY motifs in vivo, and that CHG methylation decreases REF6 DNA binding affinity in vitro. In addition, crystal structures of ZnF-clusters in complex with DNA oligonucleotides reveal that 5-methylcytosine is unfavorable for REF6 binding. In drm1 drm2 cmt2 cmt3 ( ddcc ) quadruple mutants, in which non-CG methylation is significantly reduced, REF6 can ectopically bind a small number of new target loci, most of which are located in or neighbored with short TEs in euchromatic regions. Collectively, our findings reveal that DNA methylation, likely acting in combination with other epigenetic modifications, may partially explain why REF6 binding is depleted in heterochromatic loci.

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Section: Introductionmentioning

confidence: 99%

DNA methylation repels targeting of Arabidopsis REF6

et al. 2019

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“…According to current models, chromatin remodelers, histone modifiers and DNA methylating/demethylating activities interact and influence each other's performance, and their interactions are often mediated by both short and long non‐coding RNAs (NcRNAs). These topics are actively researched and extensively reviewed (Castel and Martienssen, ; Baulcombe and Dean, ; Deinlein et al ., ; Han and Wagner, ; Zhao and Chen, ; Vriet et al ., ), and are not discussed in detail here. A comprehensive list of chromatin activities and the marks they establish at stress‐response genes has been published (Van Oosten et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional ‘memory’ of a stress: transient chromatin and memory (epigenetic) marks at stress‐response genes

2015

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SUMMARYDrought, salinity, extreme temperature variations, pathogen and herbivory attacks are recurring environmental stresses experienced by plants throughout their life. To survive repeated stresses, plants provide responses that may be different from their response during the first encounter with the stress. A different response to a similar stress represents the concept of 'stress memory'. A coordinated reaction at the organismal, cellular and gene/genome levels is thought to increase survival chances by improving the plant's tolerance/avoidance abilities. Ultimately, stress memory may provide a mechanism for acclimation and adaptation. At the molecular level, the concept of stress memory indicates that the mechanisms responsible for memory-type transcription during repeated stresses are not based on repetitive activation of the same response pathways activated by the first stress. Some recent advances in the search for transcription 'memory factors' are discussed with an emphasis on super-induced dehydration stress memory response genes in Arabidopsis.

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“…LncRNAs are poorly conserved and display diverse synthesis, processing and regulatory functions. In plants, lncRNAs can function as gene [80][81][82] , transcription [83][84][85] , or epigenetic regulators 86 . Moreover, they are known to participate in basal defense against stresses, including response to pathogenic fungi, where they act as precursors of sRNAs, microRNAs (miRNAs) and/or small interfering RNAs (siRNAs) [87][88][89][90][91] .…”

Section: Discussionmentioning

confidence: 99%

Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis

Fass

Rivarola

Ehrenbolger

et al. 2020

Sci Rep

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Sclerotinia head rot (SHR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating sunflower crop diseases. Despite its worldwide occurrence, the genetic determinants of plant resistance are still largely unknown. Here, we investigated the Sclerotiniasunflower pathosystem by analysing temporal changes in gene expression in one susceptible and two tolerant inbred lines (IL) inoculated with the pathogen under field conditions. Differential expression analysis showed little overlapping among ILs, suggesting genotype-specific control of cell defense responses possibly related to differences in disease resistance strategies. Functional enrichment assessments yielded a similar pattern. However, all three ILs altered the expression of genes involved in the cellular redox state and cell wall remodeling, in agreement with current knowledge about the initiation of plant immune responses. Remarkably, the over-representation of long non-coding RNAs (lncRNA) was another common feature among ILs. Our findings highlight the diversity of transcriptional responses to SHR within sunflower breeding lines and provide evidence of lncRNAs playing a significant role at early stages of defense. Sunflower is one of the most important crops for the production of high-quality oil and seeds consumed by both humans and livestock. In recent years, sunflower production showed a steady increase driven by a boost in sunflower oil consumption (FAO, 2017). However, the projected expansion of the sunflower oil market requires appropriate agronomic management and improved genetic resources to cope with abiotic and biotic stresses. Among the latter, special attention should be paid to fungal diseases, as they have the greatest impact on yield and seed quality 1. The necrotrophic fungus Sclerotinia sclerotiorum is the causal agent of Sclerotinia head (SHR) and stalk (SSR) rots in sunflower. In particular, SHR is a recurrent disease in sunflower-growing areas worldwide. It affects oil quality and, under favourable conditions, may lead to total production loss 1,2. Chemical fungicides proved to be ineffective and breeding of resistant genotypes has emerged as the most promising control strategy 3. So far, there is no evidence of any major gene controlling the resistance to SHR in sunflower. Instead, inbred lines (ILs) show a broad range of responses in accordance with quantitative disease resistance (QDR) patterns depending on the genotype 4-8. During the last 20 years, QTL mapping techniques have been used to unravel the complexity of the defense response to both SHR and SSR in sunflower. Biparental mapping has led to the discovery of several main effect loci and epistatic interactions 9-11 , whereas association mapping has served to identify candidate genes

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Non-coding RNAs and DNA methylation in plants

Cited by 25 publications

References 96 publications

DNA methylation repels targeting of Arabidopsis REF6

DNA methylation repels targeting of Arabidopsis REF6

Transcriptional ‘memory’ of a stress: transient chromatin and memory (epigenetic) marks at stress‐response genes

Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis

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