Fig. 5: PHF6 facilitates SWI/SNF function.

a Density heatmap of chromatin occupancy (ordered by PHF6) for PHF6, SMARCA4, PBRM1, BRD9, and H3K14ac in G401 cells (n = 2 independent biological replicates). b Chromatin occupancy peaks of PHF6, BRD9, PBRM1, and SMARCA4 overlapping with chromatin states defined based on ChromHMM. c PHF6 immunoprecipitation of SWI/SNF subunits from G401 nuclear extracts (n = 3 independent biological replicates) d Western blot analysis of SWI/SNF complex members from shCTRL and shPHF6 G401 nuclear lysates (n = 3 independent biological replicates). e Density sedimentation assays using 10–30% glycerol gradients performed on G401 lysates in shCTRL and shPHF6 conditions (n = 2 independent biological replicates). f Density heatmap in shCTRL and shPHF6 conditions (rank ordered by PHF6) at sites where H3K14ac is lost upon knockdown of PHF6 in G401 cells (n = 2 independent biological replicates). g Overlap of sites where BRD9, PBRM1, and SMARCA4 peaks are lost upon PHF6 knockdown in G401 with chromatin states defined based on ChromHMM. h Example locus reflecting reduced occupancy of SMARCA4, PBRM1, BRD9, H3K14ac, and RNA levels at PHF6-bound DLEU2. i Co-immunoprecipitation of PHF6 with p300, PBRM1, and SMARCC1 from nuclear extracts of G401 RT cells (n = 3 independent biological replicates). Co-immunoprecipitation of SMARCA4 with PHF6, SMARCC1, and p300 (n = 3 independent biological replicates). j Density heatmap of p300, SMARCA4, PBRM1, and BRD9 at sites (rank ordered by PHF6) of H3K14ac occupancy loss upon knockdown of PHF6 in G401 cells (n = 2 independent biological replicates). k Western blots of histone modifications in histone extracts prepared from RT cells 72 h post selection with shCTRL or shBRD9 or shPBRM1 knockdown (n = 2 independent biological replicates). l Western blot analysis of knockdown of BRD9 and PBRM1 in G401 cells reveals a role for BRD9 and PBRM1 in controlling PHF6 levels (n = 3 independent biological replicates). Source data are provided as a Source Data file.