Molecular mechanisms of chromatin signaling and epigenetic regulation

PROJECT SUMMARY DNA methylation and histone post-translational modifications (PTMs) are key epigenetic regulators of chromatin accessibility, interaction, and function. Changes in the composition, abundance, and distribution of DNA methylation and histone PTMs, and associated rearrangements in chromatin structure, are defining features of human cancer and other diseases. While much progress has been made connecting epigenetic regulation to cellular function and disease, it is still not clear how these regulatory functions are accomplished with spatial and temporal precision, how these epigenetic signals translate to functional outcomes in chromatin regulation, and how these changes contribute to disease states. Our long-term goal is to translate basic mechanistic understanding of chromatin regulatory function into new strategies for the treatment of human diseases. Toward this goal, we develop and use cutting edge biochemical, genomic, and proteomic technologies to understand the interconnected molecular activities of chromatin regulatory proteins that “read,” “write,” and “erase” DNA methylation and histone PTMs. Our past work focused on defining molecular mechanisms regulating the epigenetic inheritance of DNA methylation through cell divisions. We revealed complex mechanisms involving multivalent DNA and histone associations and allosteric regulation that influence DNA methyltransferase chromatin targeting and substrate specificity. These studies also contributed to the appreciation that DNA methyltransferases utilize ubiquitin-dependent protein interactions to facilitate their enzymatic activities, but the mechanistic details of how DNA methylation and ubiquitin signaling interface are unclear. Our goals in the next five years are to define regulatory and pathologic mechanisms that connect ubiquitin signaling to the epigenetic inheritance of DNA methylation. Toward accomplishing these goals, we will study roles for protein ubiquitination in big picture questions of: 1) how, when, and where DNA methylation regulators are targeted in the genome to carry out their enzymatic functions; 2) how abnormal 5mC patterns arise in cancer and aging cells; and 3) how these changes contribute to other molecular hallmarks of these disease and disease-associated states. To facilitate these studies, we will also 4) develop a new class of ubiquitinated histone affinity reagents that is generalizable for the enrichment of singly and combinatorially modified histone PTM states. Collectively, our studies will continue to define fundamental mechanisms regulating DNA methylation inheritance, reveal pathologic mechanisms associated with abnormal DNA methylation signaling, and introduce new reagents and methods for this field.