Fig. 6: Genome-wide analysis of the cooperativity between p85β and BCLAF1 in transcriptional control.
From: p85β acts as a transcription cofactor and cooperates with BCLAF1 in the nucleus
A ChIP-seq was performed using anti-BCLAF1 antibody or anti-HA antibody in DOV13 cells stably expressing PIK3R2. Average plot (top) and heatmap (bottom) of BCLAF1 or HA-p85β ChIP-seq read density within ±3 kb from an annotated transcription start site (TSS) are shown. B Top, distribution of BCLAF1 or HA-p85β ChIP-seq peaks relative to the closest TSS. Bottom, pie charts showing distribution of annotated genomic features of BCLAF1 or HA-p85β ChIP-seq peaks. C Venn diagram of overlapping binding regions between BCLAF1 and HA-p85β. D Top, distribution of BCLAF1 and HA-p85β overlapping ChIP-seq peaks relative to the closest TSS. Bottom, distribution of annotated genomic features of BCLAF1 and HA-p85β overlapping ChIP-seq peaks. E Average plot (top) and heatmap view (bottom) of BCLAF1 and HA-p85β overlapping ChIP-seq peaks within TSS ± 3 kb regions. F De novo motif enrichment on BCLAF1 and HA-p85β overlapping ChIP-seq peaks using MEME and TOMTOM. Shown are matches ranked top 3 by statistical significance. P-values were obtained by two-sided likelihood ratio test. G DOV13 cells stably expressing vector or PIK3R2 (R2-OX) were mock-transfected or transfected with BCLAF1 siRNA for 72 hr prior to RNA-seq. The heatmaps show log2-transformed fold changes of p85β-induced differentially expressed genes (DEGs) mediated by BCLAF1, which were defined when the changes observed in R2-OX were reversed upon BCLAF1 depletion (R2-OX+BCLAF1si). H Overlap between genes associated with p85β and BCLAF1 overlapping ChIP-seq peaks and p85β-induced DEGs mediated by BCLAF1. I Gene Ontology (GO) classification of the potential p85β and BCLAF1 co-regulated genes (n = 102). Y-axis represents GO biological process terms and X-axis represents the gene ratio (the number of DEGs against the number of genes associated with the GO term). Classified processes with gene ratio>0.1 are shown. J mRNA levels of CCND1, ADAMTS1 and ALCAM from RNA-seq data. Data represent mean ± SD. P-values were obtained using two-way ANOVA with Tukey’s post hoc test. These ChIP-seq and RNA-seq data were generated from biological triplicates. Source data are provided as a Source Data file.
