Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain

Bromodomains are evolutionarily conserved reader modules that recognize acetylated lysine residues on the histone tails to facilitate gene transcription. The bromodomain and PHD finger containing protein 3 (BRPF3) is a scaffolding protein that forms a tetrameric complex with HBO1 histone acetyltransferase (HAT) and two other subunits, which is known to regulate the HAT activity and substrate specificity. However, its molecular mechanism, histone ligands, and biological functions remain unknown. Herein, we identify mono‐ (H4K5ac) and di‐ (H4K5acK12ac) acetylated histone peptides as novel interacting partners of the BRPF3 bromodomain. Consistent with this, pull‐down assays on purified histones from human cells confirm the interaction of BRPF3 bromodomain with acetylated histone H4. Further, MD simulation studies highlight the binding mode of acetyllysine (Kac) and the stability of bromodomain‐histone peptide complexes. Collectively, our findings provide a key insight into how histone targets of the BRPF3 bromodomain direct the recruitment of HBO1 complex to chromatin for downstream transcriptional regulation. The BRPF3 is a chromatin reader that forms a complex with the HBO1 histone acetyltransferase (HAT) and enhances its HAT activity. However, it is unclear whether HBO1 and BRPF3 utilize their histone binding domains to interact with chromatin. We found that the BRPF3 bromodomain preferentially binds to H4K5ac and H4K5acK12ac modifications. These results provide insights into how histone targets of the BRPF3 bromodomain direct the HBO1 to chromatin.