My lab is interested in understanding the molecular basis of essential processes that regulate gene expression. We use biophysical, biochemical methods, and structural methods, including X-ray crystallography. Our insights into these fundamental mechanisms will contribute to a better understanding and ability to regulate gene expression processes involved in human diseases from cancer and heart disease to bacterial infections and will assist in drug development efforts.
Our studies focus on the following questions:
- How is chromatin structure modulated for DNA-dependent processes?
- How do transcription factors and pioneering factors activate gene expression?
- How are genes coordinately regulated by quorum sensing in bacterial pathogens?
Modulation of chromatin structure
The eukaryotic genome is packaged by histones into nucleosomes that together with non-histone proteins form higher order structures known as chromatin. This chromatin structure must be dismantled for factors that carry out the processes of transcription, replication, DNA repair, and recombination to gain access to the DNA. Numerous protein-DNA interactions, protein-protein interactions, and covalent modifications actively regulate DNA accessibility, but the molecular mechanisms by which this dynamic remodeling of chromatin occurs are still not well understood. Therefore, we will need to understand chromatin assembly, disassembly, nucleosome remodeling and accessibility, and gene regulatory processes at the molecular level in order to achieve the ultimate goal of being able to modulate the activity of genes at will.
Nucleosome dynamics play an important role in activated gene expression. We are studying the histone chaperone Asf1, because of its central role in chromatin dynamics. Asf1 binds to a dimer of histones H3 and H4, carrying the histones for post-translational modifications and hand-off to other histone chaperones in the cell. Chromatin assembly and disassembly systems are essential and fundamental to all DNA-dependent cellular functions, and are also important in human cancer and aging processes.
HMGB proteins. The structure of chromatin is also modulated by abundant proteins that bind DNA non-sequence-specifically. The high mobility group (HMGB) proteins are among the most abundant of these ‘non-sequence-specific proteins’ with the exception of histones in the typical human cell. We study the HMGB proteins to understand how they recognize DNA, form higher order structures in chromatin, and facilitate transcriptional activation of target genes. HMGB proteins bend DNA dramatically and participate in nucleosome positioning and mobility.
Progesterone receptor-coregulator interactions.
Regulation of gene expression through changes in chromatin structure is important in human hormone dependent malignancies mediated by steroid receptor transcription factors. The steroid hormone receptors, in particular, are affected by HMGB proteins and Jun dimerization protein 2 (JDP-2) binding through currently unknown mechanisms. We are determining the mechanisms by which these proteins coactivate gene expression of the progesterone receptor. Since these factors regulate the activity of the steroid hormone receptors, blocking these interactions may prove to be an effective way to decrease hormone activity in certain cancers.
As we have entered the post-antibiotic era, it is more important now than ever before to understand the molecular and structural basis of bacterial pathogenicity. Opportunistic bacteria infect immune-compromised, cystic fibrosis and cancer chemotherapy patients, and cause serious complications in their treatment. A mechanism called quorum sensing regulates bacterial virulence by altering gene expression on a global scale. Quorum sensing is the ability of the bacteria to sense their local concentration, and in gram negative bacteria depends on a simple lipid mediator called acyl-homoserinelactone (AHL) that is synthesized by an AHL-synthase (LasI for example). The AHL is detected by a transcription factor, in this case LasR. We are studying the quorum sensing systems in several Gram negative species to understand the mechanistic basis for AHL synthesis and specificity as well as AHL detection. These studies provide the foundation for the development of pharmacological agents for treatment of persistent as well as multi-drug resistant forms of bacterial infection.