Study on Plant DNA Methylation through RdDM Pathway and DRM2 (original) (raw)
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DNA Methylation: A Stabilizing and Regulatory Mechanism of Plant Genome
2020
The immobile lifestyle of plants requires responses to adapt the environmental stress. Flexible epigenetic regulations are essential for reprogramming of plant gene expression. The overall phenotype and gene expression profile of an organism is controlled by mechanisms other than the normal mechanism of expression. DNA methylation is one of them which control many important cellular functions, such as transposon silencing, genome stability, cell identity maintenance and defense against exogenous DNAs. DNA methylation maintained by a set of enzymes named DNA (cytosine-5-)-methyltransferases (DCMTases). In this paper, types, importance, mechanism, maintenance, and impact of DNA methylation on plant genome expression and transposition have been discussed. Methods to detect DNA methylation and CpG islands in plants genome has also been explored.
DNA Methylation-Associated Epigenetic Changes in Stress Tolerance of Plants
Plants require optimum environmental conditions to grow, develop, and reproduce. Abiotic and biotic stresses have direct, negative effects on the biochemical and physiological processes which is associated with plant growth and development. These processes, under stress conditions, are significantly modified to increase a plant’s tolerance and to allow it to reproduce in the shortest possible time leads to escape or to minimize its exposure to unfavorable environmental conditions. As a consequence of these changes on its life cycle, a significant reduction in plant yield is expected. Plants have evolved several strategies to cope with environmental stresses which include expression level alteration of some genes through the introduction of epigenetic modifications, such as DNA methylation. DNA methylation plays a key role in gene expression by enhancing RNA-directed DNA methylation (RdDM) of genes and by inducing some histone modifications. Plants sometimes inherit their tolerance to stresses through the transmission of methylated genes from the parents. They may also produce new alleles by favoring homologous recombination at less methylated loci. However, sometimes this type of inheritance is not stable. DNA methylation may be significantly affected by the environment and cannot be experimentally manipulated or maintained. Therefore, extra care should be taken when designing strategies intended on producing plants with novel traits based on variations in DNA methylation. This chapter dealt with a brief account on epigenetic changes due to DNA methylation, histone modifications, and small RNA interference to modify gene expression pattern throughout the growth and developmental stages of plants to adjust different biotic and abiotic plants responses. The chapter will discuss also the possible use of genetic modifications to induce epigenetic changes that may improve plant traits, especially a plant’s ability to grow under abiotic and biotic stresses, and will try to answer fundamental questions on how DNA methylation, chromatin alteration, and small RNA molecules control gene expression.
DNA Methylation and Plants Response to Biotic and Abiotic Stress
Trends in Sciences
DNA methylation is a conserved epigenetic modification that regulates, stabilizes, and maintains genomic integrity. Loss of DNA methylation or aberrant patterns of DNA methylation causes abnormalities in the gene regulation of plants. DNA methylation in plants is regulated by the combined action of de novo methylation, maintenance of methylation, and demethylation. The enzymes that regulate DNA methylation in plants are different but have some homology to that of mammalian DNA methylation enzymes. DNA methylation helps to develop adaptation mechanisms towards various biotic and abiotic stresses. This paper provides a comprehensive review of the DNA methylation pathway and its role in biotic and abiotic stress tolerances in plants. HIGHLIGHTS Plants responds to the changing climatic condition via epigenetic changes - changing the gene expression patterns, without changing the DNA sequences Abiotic and biotic stress leads to the differential expression of genes; furthermore, plants ha...
RNA-directed DNA methylation and demethylation in plants
Science China-life Sciences, 2009
RNA-directed DNA methylation (RdDM) is a nuclear process in which small interfering RNAs (siRNAs) direct the cytosine methylation of DNA sequences that are complementary to the siRNAs. In plants, double stranded-RNAs (dsRNAs) generated by RNA-dependent RNA polymerase 2 (RDR2) serve as precursors for Dicer-like 3 dependent biogenesis of 24-nt siRNAs. Plant specific RNA polymerase IV (Pol IV) is presumed to generate the initial RNA transcripts that are substrates for RDR2. siRNAs are loaded onto an argonaute4-containing RISC (RNA-induced silencing complex) that targets the de novo DNA methyltransferase DRM2 to RdDM target loci. Nascent RNA transcripts from the target loci are generated by another plant-specific RNA polymerase, Pol V, and these transcripts help recruit complementary siRNAs and the associated RdDM effector complex to the target loci in a transcription-coupled DNA methylation process. Small RNA binding proteins such as ROS3 may direct target-specific DNA demethylation by the ROS1 family of DNA demethylases. Chromatin remodeling enzymes and histone modifying enzymes also participate in DNA methylation and possibly demethylation. One of the well studied functions of RdDM is transposon silencing and genome stability. In addition, RdDM is important for paramutation, imprinting, gene regulation, and plant development. Locus-specific DNA methylation and demethylation, and transposon activation under abiotic stresses suggest that RdDM is also important in stress responses of plants. Further studies will help illuminate the functions of RdDM in the dynamic control of epigenomes during development and environmental stress responses. abiotic stress, plant development, siRNAs, DNA methylation, demethylation, RdDM
Journal of Global Innovations in Agriculture Sciences, 2021
Common DNA methylation controls gene expression and preserves genomic integrity. Mal methylation can cause developmental abnormalities in the plants. Multiple enzymes carrying out de novo methylation, methylation maintenance, and active demethylation culminate in a particular DNA methylation state. Next-generation sequencing advances and computational methods to analyze the data. The model plant Arabidopsis thaliana was used to study DNA methylation patterns, epigenetic inheritance, and plant methylation. Plant DNA methylation research reveals methylation patterns and describing variations in plant tissues. Determining the kinetics of DNA methylation in diverse plant tissues is also a new field. However, it is vital to understand regulatory and developmental decisions and use plant model species to develop new commercial crops; that are more resistant to stress and yield more. There are several methods available for assessing DNA methylation data. The performance of several techniqu...
DNA methylation — an essential mechanism in plant molecular biology
Acta Physiologiae Plantarum, 2001
DNA methylation is a common phenomenon in plants. In plant genomes, its level is comparatively lower than that of animal genomes. It is involved in gene regulation and controls many development pathways. Methylation status of particular DNA sequence controls the potential for transition from vegetative to reproductive growth. It is believed that fully methylated elements are genetically and transcriptionally silent, however, some methylated genes may also be expressed. While hypomethylated elements are active and partially methylated elements, designated programmable, exhibit a variety of development expression programmes during plant development. DNA methylation plays an important role in the evolution of plant species through alloploidy or polyploidy. The methylation pattern in parental plants is highly heritable which is of great interest for plant breeders: DNA methylation also plays an important role in genome defense system by inactivating and methylating the invasive DNA sequences. A methylated sequence may suppress gene expression in other sequences. The generation and breeding of transgenic plants becomes complex due to inactivation of transgenes and instability of their expression. The pattern of methylation is maintained by methyltransferase through DNA replication. Several methods are in use to detect methylated nucleotides motifs that may help in identification of some essential genes.
4 Inheritance of DNA Methylation in Plant Genome
2012
Genomic DNA contains not only information of DNA sequence, but also epigenetic information that is the direct DNA modification by methylation (the addition of methyl group to the 5th carbon of pyrimidine ring of cytosine) and histone modifications (acetylation, methylation, etc). Epigenetic information is closely related to regulation of gene expression. If a methyl group is dislocated to position 5 of the pyrimidine ring of cytosine, the hydrogen bond between complementary GC bases will not be inhibited, but this methyl group is positioned so as to be exposed in the major groove of the double-helix structure of DNA, and according to the genome region/sequence undergoing modification of methylation, gene expression is inhibited by the interaction between the genome and DNAbinding molecules.
Journal of Genetics, 2013
Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants.
In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants
Plants, 2021
Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their gro...
Phytopathogen-induced changes to plant methylomes
Plant Cell Reports, 2017
DNA methylation is a dynamic and reversible type of epigenetic mark that contributes to cellular physiology by affecting transcription activity, transposon mobility and genome stability. When plants are infected with pathogens, plant DNA methylation patterns can change, indicating an epigenetic interplay between plant host and pathogen. In most cases methylation can change susceptibility. While DNA hypomethylation appears to be a common phenomenon during the susceptible interaction, the levels and patterns of hypomethylation in transposable elements and genic regions may mediate distinct responses against various plant pathogens. The effect of DNA methylation on the plant immune response and other cellular activities and molecular functions is established by localized differential DNA methylation via cis-regulatory mechanisms as well as through transacting mechanisms. Understanding the epigenetic differences that control the phenotypic variations between susceptible and resistant interactions should facilitate the identification of new sources of resistance mediated by epigenetic mechanisms, which can be exploited to endow pathogen resistance to crops.