Fig. 4:  + KTS and -KTS EWS-WT1 isoforms display shared and private chromatin binding sites and transcriptional programs. | Nature Communications

Fig. 4:  + KTS and -KTS EWS-WT1 isoforms display shared and private chromatin binding sites and transcriptional programs.

From: EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in desmoplastic small round cell tumors

Fig. 4

a Pie charts show genomic distribution of EWS-WT1 binding sites in MeT-5A cells transduced with either the EWS-WT1 -KTS or +KTS isoforms. b Top enriched DNA motifs identified in MeT-5A cells expressing either EWS-WT1 + KTS or -KTS as in Fig. 4a. Associated transcription factors for the motifs were EGR2 (top) and ZNF263 (bottom). p values were calculated based on the binomial test by the Homer software. c Pie chart shows the percentage of consensus EWS-WT1 binding sites initially identified in JN-DSRCT1 cells (as in Fig. 1a), and that are bound by either EWS-WT1 + KTS, EWS-WT1 -KTS or both upon their expression in MeT-5A cells. d Heatmaps of V5 (EWS-WT1 + KTS), HA (EWS-WT1 -KTS) and H3K27ac ChIP-seq signal densities in MeT-5A cells expressing either EWS-WT1 -KTS or +KTS, illustrating that the two isoforms bind to a majority of sites identified in JN-DSRCT1 cells (as in Fig. 1a). 10-kb windows in each panel are centered on EWS-WT1 binding sites as defined in JN-DSRCT1 cells. The categories of sites are: bound by either EWS-WT1 + KTS (n = 240), EWS-WT1 -KTS (n = 3139) or both (n = 1083). Chromatin profiling was performed twice in EWS-WT1 transduced MeT-5A cell line. e Composite plots of V5 (EWS-WT1 + KTS) and HA (EWS-WT1 -KTS) ChIP-seq signals in MeT-5A cells at each category of EWS-WT1 binding sites shown in panel (d). 10-kb windows in each panel are centered on EWS-WT1 binding sites. f Venn diagram depicting the number of genes which are shared between the ones induced by EWS-WT1 + KTS/-KTS in MeT-5A cells, and the ones connected to EWS-WT1 sites and downregulated upon EWS-WT1 knockdown in JN-DSRCT1 cells. g Pie chart showing that the vast majority (86%) of genes induced upon expression of EWS-WT1 + KTS or -KTS in MeT-5A cells are also downregulated upon EWS-WT1 knockdown in JN-DSRCT1 cells. h Heatmap shows expression levels for genes induced by either EWS-WT1 + KTS (n = 70), EWS-WT1 -KTS (n = 174) or both EWS-WT1 isoforms (n = 148) upon their expression in MeT-5A cells. Expression profiling was performed thrice in EWS-WT1 transduced MeT-5A cell line.

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