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. 2023 Jun 16;51(13):6684–6701. doi: 10.1093/nar/gkad506

Figure 6.

Figure 6.

ETS1 loss induces aberrant expression of cilia genes by remodelling the signals of flanking CAAs. (A) Heatmaps and enrichment plots showing normalized read densities of ATAC-seq signals after down-regulation of ETS1 expression in hTERT RPE-1 cells. Tracks are centred at the peaks and extend ± 3 kb. (B) The enrichment of ATAC-seq signals at CAAs after down-regulation of ETS1 expression in control (siCtrl) and ETS1-depleted (siETS1) hTERT RPE-1 cells. Tracks are centred at the peaks and extend ± 3 kb. (C) Spearman's correlation of CAA accessibility changes and regions that close after ETS1 suppression in hTERT RPE-1 cells (r = –0.727). (D) Enrichment plots showing normalized read densities of ATAC-seq signals from hTERT RPE-1 cells at the TSS for randomly selected genes (n = 700, left) and SCGSv2 genes (right) after ETS1 knockdown. Tracks are centred at the TSS and extend ± 3 kb. (E) IGV snapshot showing the ATAC-seq, CUT&Tag and RNA-seq signals from hTERT RPE-1 cells in loci of KDM3A and SMO genes. (F) Immunoblots of Gli1 and Gli3 in control (siCtrl), ETS1-depleted (siETS1) and ETS1-rescued (siETS1 + Flag-ResETS1) hTERT RPE-1 cells. The intensity of Gli1 and the ratio of Gli3-FL/Gli3-R was quantified. Tubulin was used as a loading control. (G and H) Immunostaining of Gli3 (green) (G) or Smo (green) (H) and γ-tubulin (cyan) in control, ETS1-depleted and ETS1-rescued hTERT RPE-1 cells transfected with mCherry–Arl13b (red) with (right) or without (left) Smoothened agonist (SAG). Scale bars, 1 μm.