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

Abstract

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.

Molecular Insights into the Recognition of Acetylated Histone Modifications by the BRPF2 Bromodomain

“…More recent studies on the family IV bromodomains revealed that BRPF1 recognizes H3K14ac and H2AK5ac ligands with a moderate affinity, and the BRPF3 and ATAD2/B forms transient interactions with the histone H2AK5ac ligand (34-36,38,39). We also tested the binding affinity of the BRPF2 bromodomain with histone peptides H3K14ac (9-19) and H2AK5ac (1-12).…”

“…However, it is not clear how BRPF2 directs the recruitment of HBO1 HAT to chromatin to regulate the gene transcription. Recent studies on the BRPF3 bromodomain demonstrate that it recognizes multiple acetylated lysine residues on the N-terminal tails of histone H4 and shows preferential interactions with H4K5ac and H4K5acK12ac marks (36). Since the sequence similarity between the BRPF2 and BRPF3 bromodomains is high, most likely, the BRPF2 bromodomain recognizes a similar set of acetylated histone modifications.…”

“…The bromodomains of BRPF2 and BRPF3 share high sequence similarity and function as part of the HBO1 HAT complex, but there is limited information on which histone ligands they bind. We recently identified multiple acetylated histone ligands recognized by the BRPF3 bromodomain using high-throughput virtual screening and in-vitro methods (36). Considering the high sequence similarity between the bromodomains of BRPF2 and BRPF3, they are likely to recognize a similar subset of acetylated histone modifications.…”

“…Recent studies on the BRPF1 bromodomain revealed that it recognizes multiple acetyllysine residues on the histone H2A, H3, and H4 and preferentially binds to diacetylated histone H4K5acK8ac and H4K5acK12ac ligands (34,35). Similarly, the BRPF3 bromodomain has a strong affinity for histone ligands such as H4K5ac and H4K5acK12ac (36). Although, it is reported that the BRPF2 bromodomain binds weakly to diacetylated (H4K5acK8ac) and dipropionylated (H4K5prK8pr) histone ligands (37), there is still limited histone ligand information available for the BRPF2 bromodomain (Figure 1C).…”

“…34, 35 Similarly, the BRPF3 bromodomain has a strong affinity for histone ligands such as H4K5ac and H4K5acK12ac. 36 Although, it is reported that the BRPF2 bromodomain binds weakly to diacetylated (H4K5acK8ac) and dipropionylated (H4K5prK8pr) histone ligands, 37 there is still limited histone ligand information available for the BRPF2 bromodomain (Figure 1C). We sought to identify novel acetylated histone ligands recognized by the BRPF2 bromodomain through a series of computational, biophysical, and biochemical methods.…”