Practical Computer Science - Bielefeld University

Until recently, identification of Drosophila PRE/TREs has relied upon functional assays such as transgene analysis or chromatin immunoprecipitation. The PRE/TREs thus identified all show similar properties when taken out of their endogenous context and inserted elsewhere in the genome. These properties include pairing-sensitive repression of adjacent reporter genes in a manner that is genetically dependent on the PcG and trxG, and recruitment of PcG/trxG proteins to the site of transgene insertion. These functional similarities indicate that PRE/TREs must share common DNA sequence features. Several short motifs that are required for PRE/TRE function have been identified. These include binding sites for three sequence-specific DNA binding proteins: the Pleiohomeotic protein (PHO), a PcG member, and the GAGA factor (GAF) and the zeste protein (Z), both of which are trxG members. Identifying PRE/TREs by searching for these motifs is limited by the shortness of the GAF binding site and the degeneracy of the PHO and Z consensus sites, and so all of them will occur with a certain frequency at random in any DNA sequence. Furthermore, GAF and Z regulate many genes independently of the PcG/trxG system, and thus functional sites occur in many regulatory regions that are not PRE/TREs. The same may also be true for PHO. Thus, for these motifs to contribute to true PRE/TRE function, additional features such as their spacing relative to one another, or other motifs, must put them in their correct context. We developed a search tool and applied it to the prediction of PRE/TREs in the Drosophila melanogaster genome. We were able to identify over 100 candidate PRE/TREs and their associated genes. Furthermore, we showed that predicted PRE/TREs are bound and regulated by PcG proteins in vivo. This analysis expanded the current repertoire of PRE/TRE sequences and associated genes tremendously, providing new opportunities for insights into PRE/TRE function.

predicted PRE/TREs