During development and differentiation, genes become competent to be expressed or are stably silenced in an epigenetically heritable manner. This selective activation/repression of genes leads to the differentiation of tissue types. Our group is interested in the molecular mechanisms that lead to the heritable transmission of the silenced state. To address this problem, we are studying the mechanism of gene silencing by the Polycomb group genes (PcG) in Drosophila. The PcG genes encode a diverse group of proteins known to be important for silencing of homeotic and segmentation genes during development. Many PcG genes encode chromatin-associated proteins and it has been proposed that they silence transcription by forming protein complexes that inactivate chromatin. PcG proteins act through poorly defined cis-acting DNA sequences called Polycomb group Response Elements (PREs). PREs are thought to recruit PcG protein complexes to the DNA. We have completed a detailed study of one PRE from the segmentation gene engrailed. Our data suggest that the combination of sites for 5 DNA binding proteins are required for the function of this PRE. We identified one of the proteins that binds to this PRE as the product of the pleiohomeotic (pho) gene, a known PcG gene. pleiohomeotic encodes a Drosophila homolog of the mammalian zinc-finger transcription factor Yin Yang 1 (YY1). We call the Drosophila protein PHO. PHO and YY1 are 96% identical in sequence over 4 zinc fingers and share the same DNA binding specificity. Mutation of YY1/PHO binding sites within the engrailed PRE leads to a loss of PRE activity. We have also shown that YY1/PHO binding sites are required for the activity of another PRE, one from the homeotic gene Ultrabithorax. YY1/PHO binding sites have also been identified in many other PREs. These data suggest that PHO binding sites may be required for the function of many different PREs and we propose that PHO recruits or anchors PcG protein complexes to the DNA. If this were the case, then the phenotype of pho mutants should be severe derepression of homeotic and segmentation genes. However, the phenotype of pho mutants is only mild derepression. With the sequence of the Drosophila genome, a possible explanation to this apparent paradox was found. Another YY1 homolog exists in Drosophila. We are currently investigating whether this homolog functions in a manner similar to PHO during Drosophila development. To date, PcG proteins have been found in at least three distinct protein complexes. One question our laboratory is beginning to address is whether these different protein complexes act through different PREs. Although there are some sequence similarities between PREs, there are many differences, and one possibility is that these different elements recruit different PcG protein complexes using different DNA binding proteins. Our laboratory is therefore beginning a detailed analysis of another PRE to begin to understand the diversity of this important class of regulatory elements.
