The Role of Insulators and Transcription Factors in Genome Organization and Function in Drosophila

Epigenetic changes can alter the genome function without altering their base composition. These differences can be inherited and can provide an important source of variation within populations that can be acted upon by natural selection. Epigenetic changes in gene expression can take place via covalent modifications of histone or DNA as well as the three-dimensional organization of chromatin in the nucleus. Insulators mediate chromatin interactions in cis or trans between different regions of the genome and may be important factors regulating the 3D organization of the genome. BEAF-32 is an insulator protein highly conserved in Drosophila but not found in other species. Here I describe an analysis of the epigenetic function of BEAF-32 in Drosophila. I identify the BEAF-32 insulator as a cis regulatory element separating genes arranged in a head-to-head orientation. I then compare the genome-wide binding landscapes of the BEAF-32 in four different Drosophila species and highlight the evolutionarily conserved presence of this protein between close adjacent genes. During the formation of new Drosophila species, binding of BEAF-32 in the genome is altered along with changes in genome organization caused by DNA re-arrangements. The alterations of BEAF-32 distribution correlate with new gene expression profiles, which in turn translate into specific and distinct phenotypes. Epigenetic information encoded in the 3D organization of the genome mediated by insulators needs to be faithfully transmitted through mitosis and meiosis in order to effect evolutionary change. To address this issue, I have also studied the function of the Myc transcription factor. I found that a subset of Myc sites remain on mitotic chromatin and overlap with aligned insulator proteins binding sites. These sites are enriched at the boundaries of topological chromosome domains, suggesting they may be important for maintaining chromosome structure throughout the cell cycle. Together, these results suggest a mechanism for the establishment of differences in transcription patterns during evolution and may help to decipher the role of epigenetic changes in evolution.