Plants as leading systems for epigenetics and epigenomics research

Epigenetic phenomena involve mitotically or meiotically heritable alternative gene expression states that are not due to DNA sequence differences. These phenomena have long fascinated geneticists and molecular biologists because they do not conform to the rules of Mendelian genetics nor can they be understood simply by determining the DNA sequences of genes or entire genomes. As such, an understanding of epigenetic phenomena has become a major focus of research activity in the current post-genomics era - a period in which the complete genome sequences of multiple model organisms is known yet we still do not understand how the information encoded in their genomes is regulated or interpreted.

A number of epigenetic phenomena were discovered in plants, but are not limited to plants. For instance, paramutation describes the heritable change in expression status of an allele upon its exposure to an allele that has the same sequence but displays a different expression status . Nucleolar dominance describes the selective silencing of the ribosomal RNA genes inherited from one progenitor of a genetic hybrid, regardless of whether that progenitor served as the male or the female parent. The selective expression of genes inherited from only the maternal or the paternal parent is known as imprinting and is an essential aspect of both plant and animal development. Other epigenetic phenomena are plant-specific and are agriculturally important. For instance, the induction of flowering in plants in response to the experience of winter (prolonged cold) is a physiological phenomenon known as vernalization, which is now known to have an epigenetic basis. Another epigenetic phenomenon with implications for applied science is the sporadic silencing of transgenes via RNA-mediated homology-dependent mechanisms - a phenomenon that has important ramifications for plant genetic engineering as well as for medical gene therapy. RNA-mediated DNA methylation, leading to transcriptional gene silencing, and RNA-mediated post-transcriptional silencing, involving mRNA degradation or inactivation, are principal RNA silencing mechanisms.

In addition to the rich contributions plant biology has made to the discovery and study of epigenetic phenomena, plants provide ideal systems for epigenomics research. Like humans, plants make extensive use of DNA methylation as an epigenetic mark, which is not the case in yeast, nematodes or fruit flies. Plants modify their histones and execute transcriptional as well as post-transcriptional gene silencing programs as a defense against transposable elements and viruses. Like animals, plants make use of miRNAs and siRNAs; in the case of Arabidopsis, these small RNAs are generated via pathways that have been, and continue to be, genetically defined. Importantly, plants tolerate null mutations in many chromatin regulators that are lethal in animals, despite undergoing similarly complex developmental transitions. Genome sequences for Arabidopsis, rice, poplar, maize and moss are available, facilitating genome-wide analyses of DNA methylation, histone modifications, and their relationships to coding as well as noncoding RNAs.  These positive attributes of plants as model systems have helped keep plants at the forefront of discoveries in the fields of epigenetics and epigenomics.

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The Epigenomics of Plants
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