My research focuses on understanding the molecular mechanisms underlying chromatin dynamics and its role in the regulation of diverse cellular process including gene transcription and replication. High field Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography, and biochemical and molecular biology approaches are utilized determine the three-dimensional structures and functions of chromatin binding proteins implicated in heart disease, cancer and other human diseases.
The human genome is compacted into chromatin, allowing nearly three meters of DNA to fit into the small volume of the nucleus. Chromatin is composed of DNA and proteins, and this DNA-protein complex is the template for a number of essential cell processes including transcription and replication. Understanding the role of chromatin’s higher order structure in transcriptional control is important as loss of this regulation may underlie many disease processes.
The basic structural unit of chromatin is the nucleosome. Nucleosomes are comprised of 147 base pairs of DNA wrapped around a core histone octamer. The histone octamer core contains two molecules of each histone H2A, H2B, H3 and H4. Each of these core histones contains two separate functional domains; a modular domain which interacts with the DNA and other histones, and a flexible tail domain that protrudes from the nucleosome. The tail domains can be modified by the reversible addition of chemical moieties such as acetyl-, methyl- and phospho- groups.
Modifications on the histone tail have been shown to be important in altering chromatin structure, facilitating access for DNA-binding transcription factors, but they also act as markers allowing non-histone proteins to interact with the chromatin. The “Histone Code Hypothesis” suggests that histone tail modifications constitute an epigenetic (beyond genes) code, which is read by other proteins. It postulates that these proteins, and protein complexes are able to recognize/read distinct tail modifications, just like a language or code. This consequently triggers downstream events resulting in a unique and specific biological outcome, such as: cell death, cell cycle regulation, and the transcription, repair or replication of DNA.
We are investigating novel chromatin binding domains, including the PHD finger, which interact specifically with the unmodified and modified histone H3 tail. PHD finger domains are found many proteins (including the ING family of tumor suppressors), and binds to the histone tail (Figure 1).
Members of the ING family are known to interact with both Histone Acetyltransferase (HAT) and Histone Deacetyl Transferase (HDAC) complexes, which modify the chromatin structure to activate or inactivate gene expression, respectively. Interestingly, even though all of the ING family members contain a conserved PHD binding domain, some of theses proteins appear to bind to slightly different marks. Additionally, the ING-associated HATs (including MOZ/MORF and HBO1) are multi-subunit complexes that often contain additional PHD fingers and/or chromatin binding domains (Figure 2).
How these protein modules differentiate between various histone marks to read the histone code is unknown. The focus of my research is aimed at determining the structures of chromatin binding domains, including the PHD finger, in complex with the histone tail to elucidate how histone tail modifications are recognized. This research will aid in a deeper understanding of how HATs and HDACs are targeted to the chromatin and regulate gene expression. A greater understanding of how these molecular signaling pathways function and are regulated will provide insights into how they can be therapeutically manipulated, and may help to identify new diagnostic markers and targets to prevent and treat disease.