Katharine Diehl

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) have an impact on the local chromatin environment through both direct biophysical perturbations and recruitment of downstream effectors. Different PTM chemotypes (e.g., methylation, acetylation, ADP-ribosylation) at different sites within the histones act as dynamic signals to delineate specific chromatin states. Thus, far from being a passive scaffold for the genome, chromatin actively controls access to the underlying genetic material to aid in regulating transcription, translation, and repair. Importantly, when histone PTMs and other epigenetic factors are disrupted, these processes are misregulated leading to diseases such as cancer and developmental disorders.

Our lab studies how the deposition, removal, and recognition of these histone PTMs are regulated and what downstream effects these PTMs have on DNA-mediated processes. In particular, our focus is studying how metabolism is linked to genomic regulation via the metabolites that fuel chromatin dynamics. 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.

Current project areas include:

1. Metabolite biosensors: We use protein engineering approaches to develop genetically encoded fluorescent biosensors for metabolites like acetyl-CoA that we use for live cell tracking of the metabolite levels in a subcellular fashion
2. Histone acyl PTMs: We use biochemical and cell-based approaches to elucidate how non-canonical histone acyl PTMs, like histone lactylation, are regulated by writer/eraser/reader proteins, such as sirtuins and bromodomains, and how these PTMs link gene expression to metabolic state, like glycolysis/lactate metabolism. One of the key tools we use for these studies is the synthesis of site-specifically acylated nucleosomes using peptide chemistry and protein semi-synthesis.
3. ADP-ribosylation in nuclear regulation: We recently discovered that sirtuin 6 (SIRT6) mono-ADP-ribosylates ("mARylates") proteins that contain a poly-histidine (polyHis) sequence. PolyHis proteins are relatively rare in the human proteome, and the majority of them are nuclear proteins including about 30 transcription factors. We are now using biochemical and cell-based assays to understand how this PTM modulates the polyHis proteins' function.