Epigenetic responses to environmental stress in plants
Environmental signals can directly influence gene expression through epigenetic\ud mechanisms, causing phenotypic changes that can be transmitted to progeny. In plants, this\ud is in part achieved by short interfering RNA (siRNA) which guide covalent modification of\ud DNA, such as cytosine methylation, to specific targets including repetitive sequences and\ud transposable elements. Environmental stress also leads to genome-wide DNA\ud hypomethylation, misregulation of transposable elements and ultimately ‘genomic shock’.\ud Although most stress-induced epigenetic modifications are not thought to be heritable, there\ud is increasing evidence for the inheritance of novel environmentally-induced epigenetic states\ud or ‘environmental epialleles’. The formation of environmental epialleles represents an\ud important source of variation and a powerful driving force of adaptive evolution but the\ud precise mechanism remains unclear.\ud The aim of this thesis is to identify environmental epialleles through computational methods.\ud Analysis of Illumina sequencing data from environmentally stressed maize plants sampled\ud during stress and after a recovery period has so far revealed that a significant proportion of\ud the maize genome is misregulated at both the genetic and epigenetic level. These findings\ud indicate that plants continue to respond after exposure to stress and that this response is\ud likely mediated by at least one epigenetic mechanism, including siRNA-directed DNA\ud modifications.
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