We develop new tools to delineate mechanisms by which metabolism is linked to genomic regulation via histone post-translational modifications (PTMs).
The eukaryotic genome is regulated by a variety of epigenetic mechanisms that establish and maintain proper gene expression profiles to control cell identity and fate. One of these vital mechanisms is accomplished by chromatin, which is the packaging medium for genomic DNA. The chromatin polymer consists of individual nucleosomes in which the DNA is wrapped around an octamer of the canonical histone proteins H2A, H2B, H3, and H4. The histone proteins are highly post-translationally modified, and these modifications (PTMs) act as dynamic signals to delineate specific chromatin states. Importantly, when histone PTMs and other epigenetic processes are dysregulated, this leads to aging and diseases including cancer and metabolic and developmental disorders.
Our lab’s goal is to understand how the deposition, removal, and recognition of these PTMs are regulated and what downstream effects these PTMs have on DNA-mediated processes. In particular, we want to understand how metabolism is linked to genomic regulation via histone PTMs. Thus, we seek to elucidate mechanisms by which the metabolic state of the cell (e.g., acetyl-CoA level) is reported to the genome via chromatin (e.g., histone acetylation) to lead to changes in DNA transcription, translation, or repair. To do so, my lab utilizes a range of techniques across organic chemistry, peptide/protein chemistry, biochemistry, and molecular and cell biology.
Metabolite biosensors for live cell imaging
Fluorescent biosensors are powerful tools for studying cell signaling dynamics, giving us a window into these processes as they are occurring in live cells. We are developing new genetically-encoded biosensors for imaging metabolites, focusing on core metabolites for which no biosensors currently exist. With these sensors, we are able to track subcellular metabolite levels in real time as cells respond to stimuli such as nutrient changes, DNA damage, and inhibitor treatments. Since we are particularly interested in chromatin, we are using our sensors to understand how metabolite compartmentalization impacts histone PTM regulation.
Non-canonical histone acylations
The expansion of mass spectrometric characterization of histone PTMs has led to a recent surge in the identification of histone acylations beyond acetylation (e.g., succinylation, lactylation). While initial evidence suggests that at least some of these acylations perform distinct chromatin regulatory roles from acetylation and one another, these functions remain poorly-defined. We are using biochemical and in cell methods to delineate the mechanisms by which non-canonical acylations impact chromatin structure and function. We are also defining regulatory feedback loops between the metabolic pathways that produce these acyl-CoAs and the effects on gene expression from the corresponding histone acylation.
Poly-ADP-ribosylation in the DNA damage response
Cancer cells are marked by genomic instability, rendering them reliant on DNA damage repair (DDR) to proliferate. This dependence has led to the development of drugs that target DDR pathways, including inhibitors of the enzyme poly-ADP-ribose polymerase 1 (PARP1). PARP1 deposits poly-ADP-ribose (PAR) chains on (PARylates) proteins near DNA strand breaks, and this PAR then recruits repair proteins and modulates DNA accessibility to facilitate repair. Finally, the PAR is degraded by hydrolase enzymes to properly complete the repair process. While PARP inhibitors are already used in the clinic, the development of inhibitors that target proteins downstream of PARP1, including PAR binding proteins and hydrolases, has lagged despite such inhibitors’ potential as cancer therapies. We are developing novel chemical probes for PAR that will enable us to obtain a detailed characterization of PAR function and regulation in a biochemical and cellular setting and to develop screening platforms for inhibitors of PAR binding proteins and hydrolases.
Metabolic regulation of histone deacetylases
The sirtuins are a class of NAD+-dependent protein deacetylases that play a critical role in controlling the acetylation status of a multitude of proteins, including histones. Dysregulation of nuclear sirtuins, SIRT1, 6, and 7, is known to lead to deleterious changes in gene expression associated with aging, cancer, metabolic disorders, and neurodegeneration. We are investigating how these proteins are regulated by metabolites including NAD+ and endogenous allosteric activators like fatty acids. By understanding how the cell modulates sirtuin activity, we can identify new therapeutic approaches that inhibit or activate sirtuins to treat aging-related diseases.