Molecular Mechanisms of Histone Acetyltransferases

University Of Wisconsin-Madison, Madison WI

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Abstract

PROJECT SUMMARY / ABSTRACT Organization of eukaryotic DNA into a macromolecular histone complex (chromatin) allows the cell to utilize regulatory mechanisms that control gene activation and chromosomal stability. This epigenetic process can explain how genetically equivalent stem cells differentiate into diverse cell types, how penetrance of disease is modulated by nutrition and environment, and how organogenesis, tissue formation, and aging occur. The majority of emergent research in epigenetics describes phenomenological data, but progress on the molecular understanding of the pathways has lagged. Chromatin modifying enzymes are responsible for generating and removing chemical 'marks' on histone proteins. By dynamically altering the structure and function of chromatin, these modifying enzymes regulate transcription and all DNA-templated processes. It is postulated that the complex array of posttranslational modifications (PTMs) gives rise to a 'histone code' that is a major epigenetic mechanism for controlling transcriptional programs. Mounting evidence suggests that inappropriate chromatin PTMs and misinterpretation of the code is linked to an array of diseases, including many forms of cancer and a host of developmental defects. How this histone code is 'read', 'written' or 'erased' is poorly understood. How do PTM enzymes 'read' pre-existing marks and perform the appropriate histone modification? A major roadblock towards de-coding this information has been the shear complexity of the PTMs presented on even short stretches of amino acids within histone proteins. The cataloguing of these dynamic modifications has been accomplished through use of modification-specific antibodies and mass spectral methods. However, unbiased dissection of the combinatorial PTM patterns recognized by chromatin binding proteins requires a platform for rapidly and comprehensively surveying binding affinity. To begin to address these questions, recently we have developed combinatorial PTM libraries and screening methodologies to probe the histone code recognized by chromatin proteins/enzymes. Here, we will utilize these novel methodologies to investigate how the epigenetic code is read, written or erased. We propose that a histone code is generated, read and interpreted by enzyme complexes that can discriminate the PTM codes at two molecular levels: a.) catalytic domain selectivity and b.) modular histone-binding domains that recognize distinct patterns of PTMs. Utilizing a number of innovative biochemical tools to address these questions, three major aims are proposed: 1.) To determine the mechanisms of specific but multi-site acetylation by histone acetyltransferase complexes. 2.) To elucidate the 'histone code' read by modular chromatin-binding domains. 3.) To determine the function of chromatin-binding modules in substrate selection and catalytic efficiency by chromatin PTM complexes.