Epigenetic Variation in the Arabidopsis Genome

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Epigenetic information, in the form of differential cytosine methylation and alternative chromatin structures, plays a central role in the modulation of eukaryotic gene expression. In some cases, alternative epigenetic modifications can be inherited through meiosis, opening up the possibility that epigenetic variation plays a role in generating phenotypic and genomic diversity. This project is an investigation of two examples of epigenetic variation in the flowering plant Arabidopsis thaliana. The first epigenetic system to be investigated involves the complex BAL genomic locus, which contains paralogous pathogen defense genes and interspersed transposable elements. The defective bal epigenetic allele leads to overexpression of several genes from the locus and confers both developmental and pathogen defense phenotypes. The research will probe the molecular changes at the locus that cause this mis-regulation of gene expression, as well as the unusual metastable behavior of the bal allele. The second objective of the project is to characterize a newly discovered class of non-LTR retrotransposons, comprised of members that are epigenetically silenced in some strains of Arabidopsis but not others. The mechanistic basis and significance of this natural epigenetic variation will be investigated.The slightly different forms of individual organisms in a population result from the interaction between the genetic potential of those individuals and the environment. Also important are epigenetic changes, which do not involve alterations in DNA sequence but rather the packaging of this genetic information. This project takes advantage of the experimental tools available in the small flowering plant Arabidopsis to study the role of epigenetic changes in inheritance and the control of morphological diversity among individuals and strains.