Cells and ultimately organisms tightly regulate essential pathways to support complex biological processes such as homeostasis, growth, and differentiation. Increasing evidence suggests that these pathways operate in a highly integrated and coordinated manner, rather than functioning in isolation. The overarching aim of this proposal was to deepen our understanding of the mechanistic regulation of key cellular pathways, with a particular focus on the interplay between metabolism and epigenetics (i.e. chromatin metabolism). Building on previous findings and expertise from our laboratory - specifically the discovery of a functional interaction between the folate enzyme MTHFD1 and the histone acetylation reader protein BRD4 - we hypothesized that similar metabolism-centric regulatory relationship(s) may exist with YEATS domain-containing reader proteins, which recognize histone acylation marks. Moreover, although dysregulation of YEATS proteins has been linked to various diseases, most notably in different types of cancer, their overall function, particularly the context and consequences of their histone acylation reading ability, remain only partially understood. Thus, to investigate potential functional relationships, we proposed a series of work packages (WPs) within the proposal: While WP1 focused on characterizing the baseline functions of YEATS proteins under various metabolite-enriched conditions, WP2 aimed to identify functional interactions between YEATS proteins and metabolic enzymes, that require further in-depth characterization, as proposed in WP3.
To address these WPs, we planned to develop YEATS-perturbation-dependent fluorescent reporter systems, that could respond upon genetic or chemical perturbation, thus linking these phenotypes to YEATS protein function. In the absence of suitable chemical tool compounds for all YEATS proteins, we aimed to generate dTAG-YEATS cell lines that enable targeted protein degradation upon incubation with the corresponding PROTAC.
