Epigenetic Regulatory Mechanisms in Plants

Genomes are defined by their primary sequence, which provides the genetic blueprint of a species. Eukaryotic DNA functions within the context of chromatin, which provides additional layers of gene regulation referred to as “epigenetic.” The commonly found definition of epigenetics is that of a “study of heritable changes in genome function that occur without a change in DNA sequence.” However, evidence that neuronal gene-expression states are also regulated by epigenetic mechanisms, despite evidence that neuronal cells do not divide, has opened space for a broader unifying definition that keeps “the sense of prevailing usage but avoids constraints imposed by stringently required heritability.” Epigenetic mechanisms regulate developmental programs, stress responses and adaptation, senescence, disease, and various patterns of non-Mendelian inheritance. The totipotency of plant cells, in addition to the ability of plants to withstand biotic, abiotic, and genome stresses, such as changes in chromosome number and massive presence of transposable elements, reflects the plasticity of plant genomes and makes them an excellent system to study epigenetic phenomena. Genome plasticity is determined by the EPIGENOME. DNA methylation and histone modification profiles define epigenomes of animals and plants. The main molecular mechanisms operating in epigenetic phenomena are DNA methylation, histone modifications, and RNA-based mechanisms, often referred to as “the three pillars of epigenetics.” Recent advances in genome research technologies, deep sequencing analysis in particular, have led to an explosion of studies and novel results that are reshaping our views. Noncoding RNAs (ncRNAs) are emerging as central players responsible for the establishment, maintenance, and regulation of plant genome epigenetic structure

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status.

DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing

Epigenetic memory in plants.

Epigenetics refers to heritable changes in patterns of gene expression that occur without alterations in DNA sequence. The epigenetic mechanisms involve covalent modifications of DNA and histones, which affect transcriptional activity of chromatin. Since chromatin states can be propagated through mitotic and meiotic divisions, epigenetic mechanisms are thought to provide heritable 'cellular memory'. Here, we review selected examples of epigenetic memory in plants and briefly discuss underlying mechanisms.This work was supported by the Gatsby Charitable Foundation and the European Research Council.This is the author accepted manuscript. The final version is available from EMBO Press via http://dx.doi.org/10.15252/embj.20148888