Extended Data Fig. 5: Depletion of INTS11 reduces immediate early responsive gene expression and induces PROMPT accumulation.
From: Transcription directionality is licensed by Integrator at active human promoters
a. Flow diagram illustrating the EGF / IFN-β induced experiments in INTS11-AID cells. b. Selection of immediate responsive genes (FDR < 0.05). Volcano plots showing the IEG genes b. c. Venn diagram showing the overlap between EGF-induced IEG genes and genes with PROMPT after INTS11 depletion. d. Volcano plots showing the PROMPT regions with significantly upregulated RNA levels and IEG genes with downregulated pre-mRNA levels upon EGF treatment. In total 1026 IEG genes were included in the analyses. e. Quantitative boxplots of transcription distribution for 1026 EGF-induced IEG genes and their PROMPTs upon INTS11 depletion. P values were calculated by two-sided Mann-Whitney test. See Extended Data Fig. 1 for description of boxplots. f. Quantitative RT-PCR results of the EGF-induced NR4A1 gene and PROMPT locus upon INTS11 depletion. Data are presented as mean ± SD. P values were calculated by unpaired t-test (n = 3 independent experiments). (*) p < 0.05. (***) p < 0.001. g. Like in (a) but for IFN-β. h. Like in (b) but for IFN-β genes. i. IGV tracks of DDX58 and IFIT1 gene loci before and after IFN-β induction with or without INTS11 depletion. j. Quantitative RT-PCR results of the IFN-β induced IFIT1 gene and its PROMPT locus before and after the depletion of INTS11. Data are presented as mean ± SD. P values were calculated by unpaired t-test (n = 3 independent experiments). (***) p < 0.001. k-l. IEG genes and their PROMPTs before and after INTS11 depletion. The total represents the combined levels of pre-mRNA and PROMPT fold change for each locus. P values were calculated by two-sided Mann-Whitney test. See Extended Data Fig. 1 for description of boxplots.
