Molecular Insights into the Recognition of N-Terminal Histone Modifications by the BRPF1 Bromodomain

Abstract

The monocytic leukemic zinc-finger (MOZ) histone acetyltransferase (HAT) acetylates free histones H3, H4, H2A, and H2B in vitro and is associated with up-regulation of gene transcription. The MOZ HAT functions as a quaternary complex with the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5), and hEaf6 subunits. BRPF1 links the MOZ catalytic subunit to the ING5 and hEaf6 subunits, thereby promoting MOZ HAT activity. Human BRPF1 contains multiple effector domains with known roles in gene transcription, and chromatin binding and remodeling. However, the biological function of the BRPF1 bromodomain remains unknown. Our findings reveal novel interactions of the BRPF1 bromodomain with multiple acetyllysine residues on the N-terminus of histones, and show it preferentially selects for H2AK5ac, H4K12ac and H3K14ac. We used chemical shift perturbation data from NMR titration experiments to map the BRPF1 bromodomain ligand binding pocket and identified key residues responsible for coordination of the post-translationally modified histones. Extensive molecular dynamics simulations were used to generate structural models of bromodomain-histone ligand complexes, to analyze H-bonding and other interactions, and to calculate the binding free energies. Our results outline the molecular mechanism driving binding specificity of the BRPF1 bromodomain for discrete acetyllysine residues on the N-terminal histone tails. Together these data provide insights on how histone recognition by the bromodomain directs the biological function of BRPF1, ultimately targeting the MOZ HAT complex to chromatin substrates.

MOZ and MORF acetyltransferases: Molecular interaction, animal development and human disease

“…3A) [36]. The bromodomain of BRPF1 has acetyllysine-binding ability [57], whereas the PZP modules of BRPF1 and BRPF2 recognize the unmodified N-terminus of histone H3 [46,58] and the second PHD finger of BRPF2 is also known to bind directly [78,79,130,134]. Abbreviations: CBP, CREB-binding protein; p300, E1A-associated p300 kDa protein (paralogous to CBP); TIF2, transcription intermediary factor 2 (known to bind p300 and CBP).…”

Regulation of KAT6 Acetyltransferases and Their Roles in Cell Cycle Progression, Stem Cell Maintenance, and Human Disease

“…The BRPF1 bromodomain has recently been shown to recognize acetylated histones, including the active marks acetylated histone H2A lysine 5 (H2AK5ac), H4K12ac, and H3K14ac (37,38), and its PWWP domain was demonstrated to be an H3K36me3 reader (39). Similarly, the PWWP domain in yeast Pdp3 also recognizes the H3K36me3 mark, and Pdp3 has been shown to contribute to the transcription of NuA3 target genes (21,22).…”

Expression atlas of the multivalent epigenetic regulator Brpf1 and its requirement for survival of mouse embryos

“…4 The bromodomain and PWWP domain of BRPF1 have the ability to bind specifically to acetylated and methylated forms of histone H3, respectively. [15][16][17] BRPFs contain two more sequence motifs flanking the PZP module and displaying similarity to EPC (enhancer of polycomb) proteins. 10,18 Biochemical purification revealed that, in HeLa cells, BRPFs form tetrameric complexes with the histone acetyltransferase MOZ (or the paralog MORF), ING5 and EAF6.…”