Discovering and Exploiting Selectivity in Bromodomain Recognition of Epigenetic Lysine Acylation

Abstract

Bromodomains are promising epigenetic targets in cancer, diabetes, and other inflammatory disorders, and bromodomain inhibitors are in clinical trials for multiple cancers and cardiovascular disease. Bromodomains bind sites of lysine acetylation on histones and transcription factors. Interestingly, nearly half of human bromodomains exist in tandem with at least one other bromodomain on a single polypeptide. These tandem bromodomain-containing proteins are localized disproportionately at super-enhancers, genomic regions with large clusters of elements that enhance gene transcription. The basis of this localization is unknown but important given that super-enhancers are enriched at loci with oncogenic potential. Here, we show that tandem bromodomains can scaffold nucleosomes in an acetylation-dependent manner using biochemical, structural, biophysical, cellular, bioinformatic, and other computational approaches. This scaffolding is consistent with our hypothesis that tandem bromodomains enact acetylation-dependent reorganization of chromatin; for instance, joining promotors with their corresponding distal enhancers to facilitate enhancer-driven oncogenic gene transcription. This mechanism of chromatin reorganization is paradigm-shifting with broad implications on the cellular role of tandem bromodomain proteins. We also hypothesize that changes in acyl-CoA metabolism induce distinct lysine acylations on histones that are selectively recognized by bromodomains, thereby linking metabolism to transcription. Yet, the broader lysine acylation binding specificity of bromodomains is only beginning to be characterized. Here, we address this knowledge gap by determining how metabolically-derived acylations tune bromodomain binding to histones using biophysical, structural biology, and proteomic techniques. To aid mechanistic inquiries, we are removing a critical barrier in the study of bromodomain biology: the lack of inhibitors and chemical probes that selectively target individual bromodomains. This lack of selectivity may be responsible for the dose-limiting toxicity reported in clinical trials of existing bromodomain inhibitors. Here, we report the identification of a novel ligandable site on a bromodomain outside the acetyl-lysine binding site and novel inhibitors that target individual bromodomains. These chemical tools will be necessary to distinguish the differential activities of bromodomain-containing proteins in cell and rodent models of disease and may lead to therapeutics targeting the bromodomain axis in cancer, diabetes, and cardiovascular disease. Overall, the insight gained through these studies will pave the way for safer and more effective therapies targeting bromodomains.