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Epigenetic changes in plants

 

Principal Investigator: Ortrun Mittelsten Scheid

Epigenetic changes contribute significantly to diversity in gene expression and, thereby, to adaptation potential. Using the model plant Arabidopsis, we investigate chromatin, gene expression, recombination, inheritance and natural variation in diploids, upon genome duplication in polyploids and after stress treatments.

Epigenetic regulation controls a broad range of heritable, yet reversible, changes in gene expression. It generates an additional level of transmitted information and gene expression diversity in many eukaryotes. It is involved in defence against intruding DNA and RNA molecules, in genome stabilisation, and in the regulation of development and morphology. Our group is interested in the interplay between genetic and epigenetic changes, in epigenetic diversity in polyploid plants, in different ecotypes and after exposure to abiotic stress. We study these aspects in Arabidopsis thaliana with well-established genetic, cytological and molecular methods, using mutants, reporter genes, chromatin analysis, flow sorting, fluorescence in situ hybridisation, defined stress treatments, specific and genome-wide expression assays and bioinformatic approaches.

Genetic and epigenetic aspects of abiotic stress effects
While there are many examples for genome instability after exposure to stress treatments, evidence for epigenetic destabilization by external factors is only recently documented. Arabidopsis thaliana has several repetitive elements that are under epigenetic regulation by transcriptional gene silencing and are not expressed at ambient temperatures or upon short term heat exposure. However, these normally heterochromatic repeats become activated by prolonged heat stress. The activation occurs in spite of remaining heterochromatin marks, but is accompanied by loss of nucleosomes and by heterochromatin decondensation. Nucleosome association and transcriptional silencing are restored upon recovery from heat stress but are delayed in mutants with impaired chromatin assembly functions. We are currently studying Arabidopsis accessions from different habitats and geographic origin to determine genetic factors responsible for substantial differences in heat-induced transcriptional activation and subsequent restoration of chromatin features.
DNA damage after stress treatments or triggered by endogenous stimuli induces transient chromatin marks at the site of damage. These sites need to be accessed by the repair enzymes, and this is expected to require chromatin remodelling activity. We have evidence from several assays for a role of a putative remodelling complex during DNA repair and recombination. On the other hand, we demonstrated that deletions of DNA sequences can trigger also lasting chromatin changes in the proximity. Therefore, genetic and epigenetic events can be tightly interconnected. We (in collaboration with the Nordborg group) are also analyzing this in genome-wide approaches, linking epigenetic diversity in DNA methylation and histone modifications with genetic variation between different Arabidopsis accessions. Together with the group of Arndt von Haeseler (CIBIV), we are developing improved methods for the analysis of genome-wide DNA methylation data. In an international collaboration, we are studying the effects of different environmental factors on phenotype and (epi-)genotype and asking if they can be transmitted to non-exposed progeny.

Genetic and epigenetic aspects of polyploidy
Polyploidy is the result of multiplication of the complete chromosome complement and is frequent among higher plants. Polyploidy affects genetic features, like multivalent formation and double reduction in meiosis, segregation ratios, and degree of heterozygosity but is can also cause sequence rearrangements and/or change gene expression patterns without genetic changes. Based on the recent finding that the frequency of meiotic recombination between two marker genes is significantly increased in auto- and allotetraploid Arabidopsis, compared to that in diploid plants, we are investigating the molecular basis for this difference and determining the role of cis- and trans-acting genetic factors in meiotic recombination. Since polyploidy occurs after endoreplication also in somatic cells of otherwise diploid plants, we are investigating the differences of gene expression in cells with increased DNA content and the factors that determine the degree of endoreplication.

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