Epigenetic regulatory mechanisms in plants

This chapter discusses the epigenetic regulatory mechanisms in plants. 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. 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 re-shaping our views. Non-coding RNAs (ncRNAs) are emerging as central players responsible for the establishment, maintenance, and regulation of plant genome epigenetic structure. At the molecular level, a unifying view of epigenetics postulates that DNA methylation and histone modification patterns provide "information" instructing genome function. Following this information, the chromatin remodelers (the ATPase-containing machines) re-position the nucleosomes thus modulating the access of Polymerase II (Pol II) to genes. NcRNAs (small silencing RNAs, in particular) are the molecular mechanism integrating numerous seemingly disparate cellular events.