Control of DNA and histone methylation in Arabidopsis thaliana

Epigenetics is the mechanism by which specific states of gene expression are controlled and maintained throughout multiple generations. The study of epigenetics is important for a better understanding of development, fertility, cancer, and aging. Ultimately, our understanding of epigenetics will impact our views of heredity and evolution.; Here, we use two epigenetically modified genes of the flowering plant Arabidopsis thaliana to study patterns of DNA methylation and to identify enzymes that are important in the control of these patterns. The homeotic gene FWA and the floral development gene SUPERMAN are discussed. By studying these genes, we have identified two components of the epigenetic pathways that control them: the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and the histone methyltransferase KRYPTONITE (KYP).; CMT3 is specifically responsible for maintenance of non-canonical methyl cytosines found in the CpNpG and asymmetric context. It is required for the silencing of hypermethylated alleles of SUPERMAN as well as a subset of retrotransposons.; KYP, a member of the Su(var)3–9 family of histone methyltransferases, is specific for methylation of lysine 9 of histone H3 (H3K9). Like CMT3, KYP is required for the silencing of the hypermethylated SUPERMAN alleles and the same set of retrotransposons. kyp mutations result in decreased DNA methylation at CpNpG sites. This evidence suggests a link between chromatin modifications and DNA methylation.; We identify a plant homologue of KYP that is active in vitro , SUVH6. Using mass spectrometry we show that both enzymes preferentially add a single methyl group to H3K9 in vitro. Additional results indicate that the majority of H3K9 sites in Arabidopsis thaliana that are methylated have only one or two groups added.; This work identifies and characterizes a subset of components that are necessary for proper maintenance of epigenetic marks. Additional studies will build upon these findings, ultimately leading to a better understanding of eukaryotic inheritance.