Figure 2: VELs are recurrent and associated with altered gene expression.
From: Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome
(a) Normalized H3K27ac ChIP-seq tracks at the FOXQ1 locus. Red bars (top) denote gained VELs present in 10 or more CRC cell lines (G10+). Colours and labels as in Fig. 1a. Track heights are all equal. (b) Quantification of gained (red) and lost (blue) VEL recurrence. Arrows correspond to two different thresholds of recurrence: Permutation *P<0.001, FDR<0.05; **P<0.001, FDR<1 × 10−5. Examples of genes associated with VELs present in all 31 CRC lines are shown at lower right. (c) Per cent of VELs validated in primary tumours at each recurrence rate. (d) Expression levels of recurrent gained and lost VEL genes in normal colon tissue and CRC patient tumours. (e) Normalized H3K27ac ChIP-seq track for HCT116 compared with CRC and normal colon H3K27ac super-tracks (median binned signal of all normal crypts or all CRC cell lines) at the PHLDA1 locus. Guide RNA target sites for the three CRISPR–Cas9 edits performed are indicated by arrows. (f) Barplots indicate PHLDA1 RNA levels in the parental HCT116 cell line and cells disrupted by CRISPR/Cas9 at each of the sites indicated in Fig. 2e (relative to GAPDH, mean±95% confidence interval of quadruplicates). **T-test P<0.0001. (g) Gene ontology networks for genes associated with recurrent gained (G10+, left) and lost (L14+, right) VELs. Circles represent gene ontology categories with size proportional to number of genes and coloured based on enrichment FDR. Green lines connect categories with overlapping gene sets with the line weight proportional to the degree of overlap.
