About this Research Topic
Methylation of DNA is an evolutionarily conserved modification. It is associated with heterochromatic structures. Together with histone modifications, DNA methylation generates unique patterns that support gene regulation, chromatin structuring, and repression of repetitive elements. This modification provides a heritable mark that can be propagated through mitosis and meiosis. The methylated region of DNA is recognized and interpreted by the epigenetic toolkit: the readers, writers, and erasers.
In most higher organisms, DNA methylation is restricted to symmetric cytosines. Due to the symmetry, the pattern can easily be propagated from one cell generation to the next after replication. Plants are the only organisms that display methylation of asymmetric cytosines, which represents a novel feature of regulation. This mechanism, defined as RNA-directed DNA methylation (RdDM), involves the presence of small regulatory RNAs as triggering molecules.
As several of the identified regulatory components of DNA methylation respond to the environmental conditions, the pattern of methylation in the genome can also change. Some of the environmental changes can occur from minutes to hours, others can affect longer periods like days, weeks, or even years for perennial plants. These changes can result in differential methylated regions in the genome (DMRs). If the DMR is located in the regulatory region of a gene, it might influence the transcriptional activity. In several cases, methylation of a promoter element leads to suppression of transcriptional activity, described as transcriptional gene silencing. In other cases, such as gene body methylation, the regulatory effect is not completely understood. It is generated as a footprint of post-transcriptional gene silencing. During the silencing process not only are 21mer siRNA generated but 24mer heterochromatic (hc)-siRNAs can also be generated. These hc-siRNAs lead via the RdDM process to methylate the region homologous to the silencing trigger. The question of whether methylation inside the coding sequence affects the rate of transcription requires further analysis. Meanwhile, transcription factors are described that require cis-element methylation for transcriptional activation. This finding contradicts the hypothesis of transcriptional gene silencing.
As the origin of most small RNAs is from repetitive DNA elements and retrotransposons, it is obvious that any environmental change that might lead to transcriptional reactivation of these elements has the potential to change the DNA methylation pattern. Therefore, for many environmental changes, differentially methylated genomic areas or sites are described. In some cases, these changes are affecting nearby genes and can cause changes in the phenotype. Although many factors involved in the molecular mechanism of DNA methylation pattern formation are identified, the complex interplay of environmentally induced DNA methylation change and phenotypic change is not always easy to address.
This Research Topic should collect examples of changes in DNA methylation caused by changes in the environment. This will shed light on the dynamics of pattern formation, the persistence of these patterns through the generations, and gene regulatory aspects.
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