Extended Data Fig. 4: Maz loss in MNs engenders features of CTCF-boundary disruption.

a, GO analysis of biological processes in differentially expressed genes in MAZ KO ESCs compared to WT ESCs. PANTHER overrepresentation test tools were used (see Methods) and GO processes with a fold enrichment > 2 were presented (FDR < 0.05). b, GO analysis of biological processes in differentially expressed genes in MAZ KO MNs compared to WT MNs. PANTHER overrepresentation test tools were used (see Methods) and GO processes with a fold enrichment > 2 were presented (FDR < 0.05). c, RNA-seq MA plots of WT versus MAZ KO ESCs at the HoxA, HoxC, and HoxD clusters. d, RNA-seq MA plots of WT versus MAZ KO MNs at the HoxA, HoxC, and HoxD clusters. RNA-seq results represent three biological replicates. Hox genes with RNA abundance ≥ 10 are represented in colors, and the rest are represented in gray (see Supplementary Data 10-11). Hox genes in 3 Hox clusters are colored based on their position with respect to the previously demonstrated CTCF-boundary in MNs. e, RT-qPCR analysis for the indicated Hox genes in HoxA cluster, HoxC cluster (f), and HoxD cluster (g) in WT, MAZ KO, and CTCF(Δ5|6:6|7) cells. RT-qPCR signal is normalized to Gapdh levels. Fold change in expression in MNs is calculated relative to baseline expression in ESCs. All RT-qPCR results are represented as mean values and error bars indicating SD across three biological replicates. Maz KO represents three independent clones. Supplementary Data 12 shows raw data for RT-qPCR and the comparison for each gene in WT versus MAZ KO and WT versus CTCF(Δ5|6:6|7) in both ESCs and MNs.