Discovering and Exploiting Selectivity in BET Tandem Bromodomain Recognition of Epigenetic Lysine Acylation
Authors: Smith Brian C. , Olp Michael D. , Sprague Daniel J. 
Published: June 2021

Bromodomains are chromatin interaction domains that bind acetyl‐lysine residues on histones and transcription factors, thereby controlling gene expression by directing assembly of transcriptional complexes on chromatin. Members of the bromodomain and extra‐terminal domain (BET) family (Brd2, Brd3, Brd4, Brdt) each contain two bromodomains within a single polypeptide sequence. Pan‐BET bromodomain inhibitors are currently in phase I/II clinical trials for multiple cancers and phase III trials for type 2 diabetes subjects with coronary artery disease. Despite these achievements, the acetyl‐lysine sites on histones and transcription factors recognized by BET bromodomains and how tandem bromodomains work in concert to regulate transcription is poorly characterized. For example, BET 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 structural and biophysical approaches. This scaffolding ability is consistent with our hypothesis that tandem bromodomains act as a scaffold for 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 potentially 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 directly linking metabolism to transcription. Yet, the broader lysine acylation binding specificity of bromodomains is poorly understood. We are addressing this knowledge gap by determining how metabolically‐derived acylations tune BET 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 BET bromodomain biology: the lack of inhibitors and chemical probes that selectively target individual BET proteins. Currently, all existing BET inhibitors target Brd2, Brd3, Brd4, and Brdt with equal nanomolar potency. This lack of selectivity may be responsible for the side effects of memory loss and lymphoid toxicity recently associated with existing pan‐BET inhibitors. We are overcoming these barriers with a novel fragment‐based ligand discovery strategy to discover selective Brd4 inhibitors by covalently targeting a unique cysteine within Brd4. These chemical tools will be necessary to distinguish the differential activities of BET proteins in cell and rodent models of disease and may lead to therapeutics targeting the Brd4 axis in cancer and diabetes.

Support or Funding Information

This work was supported by an American Heart Association Scientist Development Grant 15SDG25830057, Institutional Research Grants 14‐247‐29‐IRG and 86‐004‐26‐IRG from the American Cancer Society, the Medical College of Wisconsin Cancer Center, the Medical College of Wisconsin Cardiovascular Center, the Michael Keelan, Jr., MD, Research Foundation, the Advancing a Healthier Wisconsin Endowment, and a National Science Foundation Grant 1708829. Michael Olp is a member of the Medical Scientist Training Program at Medical College of Wisconsin, which is supported in part by National Institutes of Health Training Grant T32‐GM080202 from the National Institute of General Medical Sciences.

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.