Fig. 5

Pre- and post-treatment effects of chromatin-modifying reagents and cells with cohesin mutations on DA. a–e. Ladder plots compare fraction of DA (i.e. expressed as a percentage along y axis) with (+) and without (−) chromatin-modifying reagents at various concentrations (x axis). Fraction of DA is illustrated with solid and dashed lines for GM06326 and GM10958 cells, respectively. Each line color corresponds to a different probe (indicated in key; RGS7, CACNA1B, ADORA2B, PMP22:IVS3, SNRPN, HERC2) or control probes exhibiting equal accessibility (C9orf66, PMP22:IVS4-Ex5). a-c In all cases, greater than two-thirds of the cells analyzed (n = 20–100, μ = 43 cells/per target) maintained DA pre- and post- reagent treatment in both cell lines at all concentrations tested. Black dotted line indicates threshold for DA. This suggests allelic chromatin accessibility differences were not reversed with chromatin-modifying reagents targeting histone proteins. This was also true for chromatin-modifying reagents that prevent (panel d) cytosine methylation or cohesin mutations (panel e) in cells from individuals with Cornelia de Lange Syndrome (CdLS) and SC-phocomelia Syndrome. Probes that do not detect DA, C9orf66 and PMP22:IVS4-Ex5, were hybridized to cell lines with cohesin mutations, as controls. Outlier in panel D (PMP22:IVS3) refers to ~ 60 % of the cells (n = 41 cells total) with DA in cell line GM06326 following 5-AZC [17.5 μM]