Epigenetics

Epigenetic phenomenon can be defined as phenotypic alteration that is heritable but does not involve DNA mutation. In molecular (mechanistical) terms, epigenetics is defined as the sum of alterations to the chromatin template that collectively establish and propagate different patterns of gene expression and silencing from the same genome. Therefore, while genome is invariant DNA sequence of an individual, the epigenome is overall chromatin composition, which indexes the entire genome in any given cell. It varies according to cell type and response to internal and external signals it receives.  

Changes in transcriptional activity of a gene are realized through six epigenetic mechanisms that include: modifications of DNA by cytosine methylation, modifications to histone proteins (such as phosphorylation, acetylation, methylation, ubiquitylation, etc.), histone variants and chromatin remodeling, higher-order chromatin structures, action of small non-coding RNA molecules, and positional information (i.e. organization and position of nucleotide sequence within the interphase nucleus). Chromatin changes are transmitted through mitotic division on new cells (so called cellular memory), that may extend the heritable information potential of the genetic (DNA) code. Some chromatin marks (i.e. cytosine metylation and histone modifications) can be transmitted, in spite of the two waves of epigenetic resetting, through gametes on new generations (transgenerational epigenetic inheritance).  

Epigenetics can impact evolution when epigenetic changes are heritable across generations. Epigenetic transgenerational inheritance is more common in plants and microbes, since these organisms have more plastic genomes than animal ones. A number of recent studies indicate that epigenetic variation in natural populations can be independent from genetic variation, and that in some cases environmentally induced epigenetic changes may be inherited by future generations (Bossdorf et al., 2008; Herrera and Bazaga, 2008; Richards et al., 2010; Lira-Medeiros et al., 2010). So far, the potential ecological and evolutionary implications of epigenetic processes have mostly been studied on model species and agricultural crops, frequently under artificial conditions. How important is epigenetic inheritance in the real-world context, when compared to genetic inheritance is a matter of debate at the international level.  

Two important ways in which epigenetic inheritance can be different from traditional genetic inheritance, with important consequences for evolution, are that rates of epimutation (achieved by change in DNA methylation or histone modification marks) can be much faster than rates of mutation (Rando & Verstrepen, 2007) and the epimutations are more easily reversible (Lancaster & Masel, 2009). An epigenetically inherited element can act as a "stop-gap", well enough for short-term adaptation that allows the lineage to survive for long enough for mutation and/or recombination to genetically assimilate the adaptive phenotypic change (Griswold & Masel, 2009). The existence of this possibility increases the evolvability of a species.  

In contrast to the classical genetic view of the bottleneck, which winnows genotypes and corresponding phenotypes according to the requirements of genetic drift and natural selection, in an epigenetic view of a bottleneck this winnowing process is ameliorated at the phenotypic level by novel, epigenetically mediated, phenotypes (Rapp and Wendel, 2005). In this view, the bottleneck itself would provide the stimulus for evolutionary novelty, mediated by epigenetic response to genomic stresses, as well as population genetic context in which novel variation might rapidly be fixed. On the other side, the epigenetic variation would have the evolutionary relevance only if it is independent of genetic variation (Rapp and Wendel, 2005; Richards, 2006). The combination of heritability and phenotypic consequences (Kalisz and Purugganan, 2004; Richards, 2006) of epialleles suggests that epigenetic change could play an important role in natural selection, adaptation and plant evolution (Boyko and Kovalchuk, 2008; Jablonka and Raz, 2009) in currently insufficiently comprehensible way.

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