Fig. 7

TAF1 is critical for the association of AE with chromatin. a Knockdown of TAF1 reduces the association of AE with chromatin in Kasumi-1 cells. Kasumi-1 cells were transduced with scrambled shRNA or TAF1 shRNAs for 5 days and then the subcellular fractionations were isolated. Total indicates the whole-cell lysate; cyto indicates the cytoplasm fraction; NS indicates the nuclear soluble fraction; chrom indicates the chromatin fraction. b Pie charts illustrate the distribution of AE peaks or TAF1 peaks across the genome. AE or TAF1 peaks were mapped to closest Refseq gene. Distal intergenic region is the region greater than 3 kb from either upstream or downstream of transcription start sites. The distance in the parentheses was measured from transcription start site. c Venn diagram illustrates the numbers of total AE peaks or TAF1 peaks or AE and TAF1 overlapping peaks in Kasumi-1 cells. Enrichment analysis for KEGG gene sets was performed on genes adjacent to overlapping TAF1 and AE peaks. d, e Venn diagram illustrates the numbers of AE peaks or TAF1 peaks or AE and TAF1 overlapping peaks at the TSS (within 1 kb of the transcription start sites) (d) (p < 1.0e-5) or at non-TSS regions (>1 kb of transcription start site including enhancers) (e) (p < 1.0e-3). P values were estimated using a Monte Carlo simulation of shuffled peaks within either the TSS background or the non-TSS genomic background. The fractions of TAF1 unique peaks, TAF1/AE co-bound peaks, and AE unique peaks at putative enhancers or non-enhancers are plotted (e, right panel). Enhancers were defined as the regions with both H3K4me and H3K27Ac peaks excluding TSS regions. f Venn diagram illustrates the numbers of AE peaks, TAF1 peaks, p300 peaks, and their overlapping peaks. g The representative picture of the peaks of p300, TAF1, AE, polymerase II (pol II), histone H3 lysine 27 acetylation (H3K27Ac), and H3 lysine 4 monomethylation (H3K4me1) at AE-activated gene ID1