Heterochromatin in both mammals and plants is associated with methylation of cytosines within the DNA sequence. While DNA methylation is widespread in plants, fungi, and animals, it has been curiously lost in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, and Drosophila. However, the methylation system in Arabidopsis is very similar to that in mammals, showing that DNA methylation is highly conserved, and that Arabidopsis is an excellent model system to study it. DNA methylation is controlled by two different but equally important processes: establishment and maintenance. Two classes of DNA methyltransferases, DNMT3 and DNMT1, respectively, are responsible for them, and are conserved between mammals and plants. Maintenance DNA methyltransferases methylate hemi-methylated sites upon DNA replication, so that the methylated or unmethylated status is inherited on both of the two newly synthesized DNA molecules. Therefore, DNA methylation serves as a marker on genomic DNA that can persist over cell generations. Evidence suggests that methylation DNA is linked to the methylation status of the surrounding histones, a self-reinforcing feedback loop for the maintenance of DNA and histone methylation that may help to explain the remarkable stability of epigenetic silent states. A group of proteins with a methylated DNA-binding domain, the SRA domain, from both Arabidopsis and humans has been recently discovered with a potential role in recognizing hemymethylated DNA and interacting with chromatin remodeling factors. In this proposal, I plan to characterize the role of the Arabidopsis SRA-domain containing proteins family (VIM family) in DNA methylation control, and how this is related with histone acetylation and methylation in a way to regulate gene transcription and the epigenetic code.
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