DNA methylation — an essential mechanism in plant molecular biology (original) (raw)

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.

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.

DNA METHYLATION IN PLANTS

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...

Evaluation of DNA methylation using methylation-sensitive amplification polymorphism in plant tissues grown in vivo and in vitro

Plant Growth Regulation, 2014

In present study, methylation-sensitive AFLP (MSAP) markers were employed to assess DNA methylation, degree of alterations in DNA methylation and methylation polymorphism in plant tissues growing in vivo and in vitro. The leaf tissues of six plants growing in vivo and in vitro were subjected to MSAP profiling. A total of 717 MSAP markers in Salvadora persica, 801 in Commiphora wightii, 874 in male (M) and 845 in female (F) genotype of Simmondsia chinensis, 719 in Jatropha curcas and 880 in Withania coagulans were obtained with seventeen MSAP primer combinations. Percentage methylation in genome obtained was higher in in vivo-grown tissues of S. persica (39.47 %), S. chinensis-M (61.71 %) and W. coagulans (71.59 %); and in in vitro-grown tissues of C. wightii (65.17 %), S. chinensis-F (60.83 %) and J. curcas (68.29 %). The percentage polymorphism in methylated DNA obtained was 8.71 % in S. persica, 9.81 % in J. curcas, 10.10 % in S. chinensis-F, 10.26 % in W. coagulans, 10.66 % in S. chinensis-M and 13.98 % in C. wightii. The difference in DNA methylation and polymorphism in genomes reflect the plasticity in genomes of the plants growing under two different environments. Different pattern of DNA methylation of the homologous nucleotide sequences and polymorphism in the methylated DNA in tissues under in vitro and in vivo conditions suggest possibility of involvement of these fragments in the dynamic processes regulating plant growth and development under prevailing growth conditions. Keywords Epigenetic Á In vitro Á In vivo Á Methylation Á MSAP Á Polymorphism Electronic supplementary material The online version of this article (

Recent Advances in DNA Methylation and Their Potential Breeding Applications in Plants

Horticulturae

Traditional plant breeding encompasses repetitive crossing and selection based on morphological traits, while phenotypic selection has been complemented by molecular methods in recent decades. Genome editing with techniques like the CRISPR-Cas9 system is still a novel approach that is being used to make direct modifications to nucleotide sequences of crops. In addition to these genetic alterations, an improved understanding of epigenetic variations such as DNA methylation on the phenotype of plants has led to increased opportunities to accelerate crop improvement. DNA methylation is the most widely studied epigenetic mark in plants and other eukaryotes. These epigenetic marks are highly conserved and involved in altering the activities and functions of developmental signals by catalyzing changes in the chromatin structure through methylation and demethylation. Cytosine methylation (5mC) is the most prevalent modification found in DNA. However, recent identification of N6-methyladeno...

Dynamic DNA Methylation in Plant Growth and Development

International journal of molecular sciences, 2018

DNA methylation is an epigenetic modification required for transposable element (TE) silencing, genome stability, and genomic imprinting. Although DNA methylation has been intensively studied, the dynamic nature of methylation among different species has just begun to be understood. Here we summarize the recent progress in research on the wide variation of DNA methylation in different plants, organs, tissues, and cells; dynamic changes of methylation are also reported during plant growth and development as well as changes in response to environmental stresses. Overall DNA methylation is quite diverse among species, and it occurs in CG, CHG, and CHH (H = A, C, or T) contexts of genes and TEs in angiosperms. Moderately expressed genes are most likely methylated in gene bodies. Methylation levels decrease significantly just upstream of the transcription start site and around transcription termination sites; its levels in the promoter are inversely correlated with the expression of some...

Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

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.

Determining the conservation of DNA methylation in Arabidopsis

Epigenetics, 2009

A high-resolution map of DNA methylation in Arabidopsis has recently been generated using high-throughput sequencing of bisulfite-converted DNA. This detailed profile measures the methylation state of most of the cytosines in the Arabidopsis genome, and allows us for the first time to address questions regarding the conservation of methylation across duplicated regions of the genome. To address these questions we measured the degree to which methylation is conserved in both duplicated genes and duplicated non-coding regions of the genome. Methylation is controlled by different mechanisms and methyltransferases depending on the genomic location. Methylation in genes occurs primarily at CG sites and is controlled by the maintenance methyltransferase MET1. In contrast, an RNAi mediated methylation pathway that leads to de novo methylation of asymmetric CHH sites along with CG and CHG sites by the methyltransferase DRM2, drives methylation at tandem and inverted repeats. We find that the cytosine methylation profile is strongly preserved between duplicated genes and repeat regions. The highest level of conservation can be found at CG sites in genes and CHH sites in repeat regions. By constructing substitution matrices between aligned genes we see that methylated cytosines often pair with thymines, which may be explained by the spontaneous deamination of methyl-cytosine to thymine. Despite this observation, we find that methylated cytosines are less often paired with other nucleotides than non-methylated cytosines within gene bodies indicating that they may play an important functional role.