We are interested in how the eukaryotic genome is structured, how it functions, and how it changes. Our current research concentrates on gene silencing in eukaryotes. We are particularly interested in mechanisms involving special states of chromatin (e.g. heterochromatin) and DNA methylation. Methylation alters properties of DNA, affects DNA-protein interactions, represses genes in animals, plants, and fungi and is essential for normal development in plants and mammals. Remarkably little is understood, however, about what determines which chromosomal regions are methylated. We are using genetic and biochemical approaches, primarily with the filamentous fungus Neurospora crassa (Fig. 1) as a model, to elucidate the mechanism, regulation and function of DNA methylation. In addition, we are using these approaches to explore silencing associated with chromosome ends, centromeres and other specialized regions of the genome.
DNA methylation is essential for normal development in a wide range of organisms including mammals and plants but is absent in some organisms including many popular model eukaryotes (e.g., yeasts, Drosophila, C. elegans). We showed that ~2% of cytosines in Neurospora DNA are methylated and that DNA methylation is not essential for development or viability in this organism. This set the stage for us to exploit this model eukaryote to elucidate the control and function of DNA methylation.
We found that most methylated regions of Neurospora are relics of transposons inactivated by RIP (repeat-induced point mutation), a premeiotic homology-based genome defense system that litters duplicated sequences with C:G to T:A mutations (Figs. 2 & 3).
Our genetic and biochemical studies on the control of DNA methylation revealed clear ties between DNA methylation and chromatin modifications. The DIM-2 DNA methyltransferase is directed by heterochromatin protein 1 (HP1), which in turn recognizes trimethyl-lysine 9 on histone H3, placed by the DIM-5 histone H3 methyltransferase (Fig. 4).
DNA methylation is modulated by a variety of additional factors. For example, in dmm-1 (DNA methylation modulator-1) mutants, methylation spreads from inactivated transposable elements, which can silence adjacent genes and lead to poor growth. Additional studies in the laboratory are providing other insights into the workings of DNA methylation and other silencing processes.
(pulled from pubmed)