Genetics of DNA methylation patterning of arabidopsis.

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Cytosine DNA methylation is an epigenetic mark for gene silencing that is important in many gene regulatory systems including mammalian imprinting, X-chromosome inactivation, and the silencing of transposons and other DNA sequences containing either direct or inverted repeats. Methylation is important in cancer biology, as tumors often show both genome wide demethylation and hypermethylation of specific tumor suppressor genes. We are studying the mechanisms of DNA methylation control in the model plant Arabldopsis, which has methylation systems that have much in common with mammalian systems. In Arabldopsis, the initial establishment of methylation (de novo methylation) requires the activity of DRM2, a homolog of mammalian DnmtS, which is guided to appropriate targets, at least in part, by small interfering RNAs. Once established, DNA methylation is maintained by three different systems for methylation of cytosines in three different sequence contexts, CG, CHG and CHH (asymmetric). CG methylation is maintained by MET1, a homolog of mammalian Dnmtl CHG methylation is maintained by the CMT3 DNA methyltransferase, which is guided to appropriate targets by the methylation of histone H3. CHH methylation is maintained by the persistent activity of DRM2, which is targeted by small interfering RNAs. In this proposal, we plan to further study these DNA methylation control mechanisms. Genetic screens are being used to identify genes required for proper de novo DNA methylation, and we plan to perform a detailed molecular genetic characterization of these genes to understand more about the mechanism by which they contribute to de novo methylation. We have also begun using structural biology, in collaboration with Dinshaw Patel's laboratory, to help in our understanding of individual components of the de novo DNA methylation pathway. We are also applying genomics techniques the study of RNA-directed DNA methylation in order to assist in our understanding the genome wide functions of DNA methylation. These studies should shed new light on DNA methylation systems in Arabldopsis and have implications for related systems in mammals and other eukaryotes.