Fig. 4: MacroH2A2 contributes to both compacted and accessible chromatin at neurodevelopmental genes in GBM.
From: macroH2A2 antagonizes epigenetic programs of stemness in glioblastoma
a Heatmap of differentially accessible regions (n = 270) in two biological replicates of MACROH2A2/macroH2A2 knockdown versus control cells. b CIBERSORTx deconvolution of estimated cell states in control versus knockdown cells, averaged across two biological replicates (p value 0.02 for NPC1, 0.03 for OPC; 0.14 for MES2; 0.12 for AC; 0.28 for NPC2). P values by T-test with Welch’s correction. c Top ten motifs enriched in peaks gained upon macroH2A2 knockdown (P value by hypergeometric test). d Top ten motifs enriched in peaks lost upon macroH2A2 knockdown (P value by hypergeometric test). e Top process terms resulting from Gene Ontology term analysis of peaks gained upon macroH2A2 knockdown (P value by hypergeometric test). f, g Permutation analysis of accessible regions gained (f) and lost (g) upon MACROH2A2/macroH2A2 knockdown at enhancer elements genome-wide. Results were obtained from n = 500 permutations of n = 94 (f) and n = 176 (g) independent genomic regions. The boxplot line represents the median, hinges at 25th and 75th percentiles, and whiskers at 1.5 × IQR. P value by hypergeometric test.
