Fig. 8

Combination of ChIPseq and RNAseq following INTS12 depletion defines INTS12 regulome and mode of action. a Log₂ fold change of INTS12 ChIPseq binding signal versus input control across gene bodies of expressed and silenced genes in basal HBECs. b Comparison of INTS12 binding vs. corresponding gene expression in basal HBECs. Genes were ordered based on the level of INTS12 ChIPseq signal. The same sorted gene list was used to evaluate their transcription in basal un-transfected HBECs where red colour indicates higher expression derived from read counts on the corresponding gene bodies. c Average INTS12 binding profile for differentially expressed genes and genes with no evidence of differential expression following INTS12 depletion (left) as well as heatmap representation of this binding (right), with red indicating enrichment while green denoting lack of enrichment in ChIPseq sample versus input control. d Prediction of the activating and repressive function of INTS12. The cumulative fraction of genes is plotted against the regulatory potential, based on significance of representative D-siRNA A differential expression and ChIPseq evidence of binding near genes’ TSS. Regulatory potential is a product of the ranked potentials (\( R P=\frac{rank\left({S}_{g\ binding}\right)}{n}*\frac{rank\left({S}_{g\ differential\ expression}\right)}{n}\ \Big) \) as judged by distance and number of INTS12 binding sites near gene’s TSS (S _g binding  = ∑ ^k _i = 1 e ^{− (0.5 + 4Δi)}) and the potential as judged by significance of gene’s differential expression following INTS12 depletion (S _{g differential expression}  = Q − value). INTS12 depletion was equally likely to induce or suppress gene expression in Kolmogorov-Smirnov test but >90% of downregulated genes had a higher regulatory potential than upregulated genes explaining the more robust effects observed on downregulated pathways. e Probability distribution of INTS12 binding enriched DNA motif TGAxTCA across the sites at which it is present. Position at zero represents peak summit and motif appears to be centrally enriched 158 bp in each direction from this summit. The site probability curve is broad (P = 2.7 × 10⁻¹⁷) indicating indirect or cooperative binding to the DNA