Fig. 3

PU.1 increases binding at HDACi-opened DHS sites. a PU.1 motif enrichment detected in NaBut and SAHA-opened DHS sites with motif logo, expected (E) value, and top JASPAR database motif match found. See Additional file 4: Fig. S2 for all top motif enrichments. ChIP-qPCR was performed for six DHS sites that open in K562 cells following HDACi treatment and a control site that does not change accessibility. The fold-change of PU.1 pull-down enrichment following SAHA (b) or NaBut (c) 72-h treatment is plotted for each site. Error bars are SEM (n = 3 replicates). d ChIP-qPCR for the same six DHS sites for H3K4me1 immunoprecipitation. The fold-change of H3K4me1 pull-down enrichment following 72-h SAHA treatment is plotted for each site. Error bars are SEM (n = 3 replicates). e Representative example of ChIP-seq data for PU.1 binding in K562 cells before and after 72-h SAHA treatment. The two sites highlighted increase in both DNase and PU.1 binding signal (n = 3 replicates). f The proportion of differential DHS sites overlapped by PU.1 ChIP-seq peaks. g Relationship between total PU.1 ChIP signal found in vehicle controls and SAHA-treated K562 at all PU.1 peaks. ChIP-seq signal is normalized by total number of mapped reads in each condition (Spearman’s correlation = 0.811)