Fig. 5: HEXIM1 and AFF1 colocalize to directly suppress rapid-response targets.

a Venn diagram showing the significant overlap between AFF1 and HEXIM1 ChIP-seq peaks (Fisher’s exact test, two-tailed, P = 1×10⁻²⁶⁸). b Violin plot showing the significant enrichment of total Pol II counts at ChIP-seq categories: AFF1 unique peaks, HEXIM1 unique peaks, and peaks with Pol II but no HEXIM1 or AFF1 relative to overlapping AFF1 and HEXIM1 peaks (****P < 0.0001, two-tailed, unpaired t test). c Pie chart showing the peak distribution of AFF1 and HEXIM1 ChIP-seq data in promoters (transcription start site (TSS) ± 1 kb), gene bodies (TSS ± 1 kb through transcription end site), or intergenic regions. d Average profile plot showing the overlapping enrichment of AFF1 and HEXIM1 ChIP-seq signal near the promoters of their shared target genes. e Shared target genes among AFF1 ChIP-seq, HEXIM1 ChIP-seq, and the significantly upregulated genes in keratinocytes with 3-hr KL treatment. f Relative expression of the 92 AFF1-HEXIM1-KL(3 hr) shared target genes, ranked from low to high, in keratinocytes treated with KL versus DMSO for 3 hours. The top two upregulated genes ATF3 and DUSP1, as well as RND3, are highlighted in orange. g Heatmap showing differential expression of rapid-response and differentiation-activating genes with 1-hour and 3-hour nascent RNA-seq. h, i qRT-PCR showing the upregulation of ATF3, DUSP1, and RND3 with AFF1 or HEXIM1 knockdown (n = 3 technical replicates, data are presented as mean values ± standard deviation). j–l Genome browser tracks showing the enrichment of AFF1, HEXIM1, CDK9, undifferentiated (UD) Pol II, and differentiated (DF) Pol II ChIP-seq signal at ATF3, DUSP1, and RND3. Source data are provided as a Source Data file.