Date of this Version
Chapter 16 in Handbook of Epigenetics: The New Molecular and Medical Genetics (Trygve Tollefsbol, editor), pp. 251–278. Amsterdam: Academic Press/Elsevier.
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.