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Epigenetic mechanism: silent nucleosomal structures and non‐coding RNAs.

A paradigm for epigenetic regulation is the stable silencing of genes that are involved in cell fate decisions. This maintained silencing is essential for regulation of genes such as HOX genes in flies and mammals and mating type genes in yeast. Nucleosomes are known to be involved in these silencing mechanisms, both by forming compacted structures and by virtue of their covalent modification. We are studying how nucleosomes might contribute to silenced structures by examining nucleosome occupancy in cells, by using functional biochemical assays, by using electron microscopy, and by using X‐ray crystallography. I will discuss the proteins that can lead to compacted structures, how those structures might function, and our work toward understanding the biological relevance of compacted structures to gene expression. Covalent modification of histones can help to either promote or inhibit formation of these structures and our data address how modifications interact with silencing proteins. Silencing proteins must be targeted in order to function appropriately, and one proposed mechanism for targeting involves non‐coding RNAs. To understand these mechanisms, we have developed a method to map binding sites for ncRNAs in the genome. We are applying these methods to ncRNAs that are involved in epigenetic processes.