Mass Spectrometry-Based Protein Footprinting Defines the Binding Pocket of Crotonylated H3K14 in the PHD1 Domain of BAF45D within the BAF Chromatin Remodeling Complex

The BRG-/BRM-associated factor (BAF) chromatin remodeling complex is a central actor in transcription. One mechanism by which BAF affects gene expression is via its various histone mark readers, including double plant homeodomains (DPF), located in the BAF45D subunit. DPF domains recognize lysine acetyl and acylations, including crotonylation, localized at promoters and enhancers. Despite a significant degree of conservation between DPF domains, attempts to crystallize BAF45D with a crotonylated histone 3 peptide (H3K14Cr) were unsuccessful. In addition, recent cryoEM and modeled structures failed to define the Req domain of BAF45D, which is responsible for reading lysine modifications. Thus, the precise mechanism of crotonyl group recognition and binding by BAF45D within the BAF complex remains unclear. We turned to protein footprinting mass spectrometry to map the binding interface between H3K14Cr and BAF45D. This technique is able to demarcate protein-binding interfaces by modifying surface-accessible residues and is not limited by protein size or composition. Experiments performed in the isolated DPF domain of BAF45D (BAF45D_DPF)-delineated H3K14Cr peptide binding across the PHD1 and PHD2 pockets. We observed markedly similar effects on the BAF45D subunit when assessing H3K14Cr binding in the purified full BAF complex. The ATPase motor, BRM, also displayed H3K14Cr-protected peptides in two separate domains that were subsequently evaluated in direct binding assays. These data confirm the BAF45D–crotonylamide interaction within its obligate complex and are the first to demonstrate H3K14Cr direct binding to BRM.