Plants’ Epigenetic Mechanisms and Abiotic Stress

Miryeganeh, Matin

doi:10.3390/genes12081106

Cited by 92 publications

(68 citation statements)

References 128 publications

(176 reference statements)

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“…Throughout their evolutionary history, plants have adapted to widely varied and sometimes very stressful environments. The efficiency of their adaptation to environmental stresses (such as extreme temperature, high salinity, and hypoxia), not only depends on the presence of stress response genes, but it also relies on how the expression of those genes is controlled [1]. When plants encounter environmental pressure, the expression of related genes will change accordingly, in order to help plants to overcome and survive the stress, which can especially be important for long living plants that have to cope with different kind of undesirable conditions during their long lifespan [2][3][4].…”

Section: Introductionmentioning

confidence: 99%

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Miryeganeh

Saze

2021

IJMS

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Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

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Section: Introductionmentioning

confidence: 99%

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Miryeganeh

Saze

2021

IJMS

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“…This supports the hypothesis that DNA methylation regulates abiotic gene expression. Drought in several plant species leads to substantial remodelling of DNA methylation, which allows plants to respond more effectively to recurring stress and prepares offspring for future stress responses [272]. However, in this case, modifying DNA methylation still seems to be essential to regulate neighbouring gene expression [273].…”

Section: Abiotic Stressmentioning

confidence: 99%

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Ramakrishnan

Satish

Kalendar

et al. 2021

IJMS

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Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

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“…In addition to histone modifications and DNA methylation, ATP-dependent chromatin reorganization modulates the DNA accessibility for transcription factors and RNA polymerase II, and therefore regulates the transcription of the genes within the chromatin structure [ 61 , 62 , 63 ]. This dynamic change of DNA accessibility influences many processes in plants, including developmental events, such as flowering time and senescence, as well as the response to stresses and environmental changes [ 64 , 65 ]. Studies have shown that changes in the chromatin structure during senescence by chromatin-remodeler enzymes play an important role in controlling leaf senescence [ 17 ].…”

Section: Atp-dependent Chromatin Remodeling and Senescencementioning

confidence: 99%

Epigenetic Mechanisms of Senescence in Plants

Miryeganeh

2022

Cells

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Senescence is a major developmental transition in plants that requires a massive reprogramming of gene expression and includes various layers of regulations. Senescence is either an age-dependent or a stress-induced process, and is under the control of complex regulatory networks that interact with each other. It has been shown that besides genetic reprogramming, which is an important aspect of plant senescence, transcription factors and higher-level mechanisms, such as epigenetic and small RNA-mediated regulators, are also key factors of senescence-related genes. Epigenetic mechanisms are an important layer of this multilevel regulatory system that change the activity of transcription factors (TFs) and play an important role in modulating the expression of senescence-related gene. They include chromatin remodeling, DNA methylation, histone modification, and the RNA-mediated control of transcription factors and genes. This review provides an overview of the known epigenetic regulation of plant senescence, which has mostly been studied in the form of leaf senescence, and it also covers what has been reported about whole-plant senescence.

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Plants’ Epigenetic Mechanisms and Abiotic Stress

Cited by 92 publications

References 128 publications

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Epigenetic Mechanisms of Senescence in Plants

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