Extended Data Fig. 5: ETV6 constrains EWS/FLI-induced gene expression.
a. Scatter plot comparing log2 fold-change in EWS/FLI binding to log2 fold-change in H3K27ac abundance detected by ChIP-seq at 6 hours in EW8 ETV6-dTAG cells (n = 2 biological replicates). Pearson correlation value (R) is shown. b. Plot comparing genes mapped from significantly altered EWS/FLI binding sites (n = 2 biological replicates) to Log2 Fold-change in expression measured by RNA-seq in EW8 ETV6-dTAG cells (n = 3 biological replicates) at 72 hours. Gray boxes indicate median and first and third quartiles. Red diamond and error bars indicate mean expression ±standard deviation (FLI1 Up n = 404 mean=0.3; FLI1 Down n = 1,042 mean = -0.062; No Change n = 8,252 mean=0.033). FLI1 Up vs. No Change p = 1.99e-12, FLI1 Down vs. No Change p = 2.81e-18, paired t-test, Benjamini-Hochberg corrections. c and d. Gviz-generated views of the SEMA5B (c) and BCL11B (d) loci. ETV6 tracks show CUT&Tag of ETV6-FKBP12F36V-HA in A673 ETV6-dTAG cells at 24 hours. FLI1 tracks show ChIP-seq for EWS/FLI performed at 6 hours, H3K27ac tracks show ChIP-seq for H3K27ac at 6 hours, and ATAC tracks show ATAC-seq at 72 hours. FLI1 (EW8) tracks show ChIP-seq for EWS/FLI at 6 hours in EW8 ETV6-dTAG cells. GGAA tracks indicate locations of tandem GGAA motif repeats.
