Extended Data Fig. 9: Chromatin proteins can bind H4Kacme, and proposed models for biological roles of Kacme.

a-c, Western blots of bromo- and YEATS ___domain-containing proteins enriched by biotinylated peptides incubated with HEK293T nuclear extract. Blots were repeated independently twice with similar results. See Table S1 for peptide sequences. The input for GAS41 is shown from a different exposure to avoid overexposure. d, ChIP-seq density of BRD2 (SRX6913085) and BRD3 (SRX6913048) across Kacme ChIP-seq peaks. e-g, Crystal structure of BRD2 BD1 bound to H4Kacme peptide (PDB 8SB6). Views demonstrate the binding pocket and local residues (e), hydrogen bond interactions (f), and overlay with structure of BRD2 BD1 bound to a H4Kac peptide (g, PDB 2DVQ²⁷). The repositioned waters are outlined in yellow. h, ITC traces of H4, H4K5me1, and H4K5pr peptides binding to BRD2 BD1. Data are representative of three independent replicates. i, ITC traces of H4 peptides binding to BRD2 BD1 N156A. Data are representative of two independent replicates and are corrected for heats of dilution. j-k, Peptide dot blots of Kac and Kacme peptides with selected antibodies. In j, the data represent two independent replicates, and the experiment in k was performed once. Yellow boxes indicate Kacme peptides. See Methods for antibody identification. l, Kacme may be recognized by specific Kacme-binding proteins. m, Kacme may be recognized by some but not other Kac-binding proteins providing differential binding at Kacme versus Kac marked loci. n, Kacme may mask Kme1 marks allowing KATs and HDACs to mask and reveal the methylation, thereby providing a way to effectively install and remove methylation without KMT/KDM enzymes. o, Regardless of whether they share downstream functions, Kacme and Kac demonstrate altered kinetics of installation and removal by KATs and HDACs, providing differential regulation of Kacme versus Kac marked loci.