| One of the greatest challenges in modern biology is to understand how cellular programs of gene expression are established and maintained. The packaging of DNA into chromatin is an important mechanism of gene regulation. Several proteins, such as chromatin remodeling factors, linker histones, HMG proteins, and heterochromatin proteins are believed to control the gene expression by modulating this packaging. However, the mechanisms of action of these proteins and their intricate network of combinatorial interactions in the living cell are poorly understood. Here, a systematic "in vivo chromatin genomics" approach is proposed to reveal the roles and functions of proteins that control chromatin structure. In particular, the mechanisms of action of these proteins in the regulation of gene expression will be dissected. Several in vivo whole-genome approaches will be integrated, using the fruit fly Drosophila melanogaster as a model system. We will perform systematic mapping of in vivo binding sites for a large set of representative proteins involved in the regulation of chromatin structure, using a whole-genome assay developed by the applicant. Furthermore, new techniques will be developed for genome-wide mapping of structural features of chromatin. The resulting global maps of protein binding and chromatin structure will cover the entire fly genome at a resolution of ~2kb. These maps will be complemented by whole-genome studies of gene regulation, employing RNAi and genetic techniques. Finally, all data will be integrated and modeled using state-of-the-art bioinformatics methods. This project will provide a wealth of new insights into the principles of gene regulation by chromatin in vivo, in the natural context of the entire genome. |
