mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome

Bromodomains regulate gene expression by recognizing protein motifs containing acetyllysine. Although originally characterized as histone-binding proteins, it has since become clear that these domains interact with other acetylated proteins, perhaps most prominently transcription factors. The likely transient nature and low stoichiometry of such modifications, however, has made it challenging to fully define the interactome of any given bromodomain. To begin to address this knowledge gap in an unbiased manner, we carried out mRNA display screens against a bromodomain - the N-terminal bromodomain of BRD3 - using peptide libraries that contained either one or two acetyllysine residues. We discovered peptides with very strong consensus sequences and with affinities that are significantly higher than typical bromodomain-peptide interactions. X-ray crystal structures also revealed modes of binding that have not been seen with natural ligands. Intriguingly, however, our selected sequences are not found in the human proteome, perhaps suggesting that strong binders to bromodomains might have been selected against.