Fig. 2
From: KDM6A facilitates Xist upregulation at the onset of X inactivation
Kdm6a KO leads to increased gene expression from the Xi in differentiated cells. A Allelic X-linked gene expression ratios (129:cast) in Tsix-stop wt, CRISPR control, and KO cells (Tsix-Kdm6aΔEΔE17 and Tsix-Kdm6aΔEΔE21) at D0 and D15 of differentiation. Ratios between expressed X-linked genes (> 1TPM) are shown. There is increased gene expression from the 129 X-chromosome (Xi) following Kdm6a KO differentiation. B, C Plots of expression from the Xi (B) and the Xa (C) (average for Tsix-Kdm6aΔEΔE17 and Tsix-Kdm6aΔEΔE21) at D15. Kdm6a and the XIC are highlighted. Log2 TPM fold change (KO/wt) is shown. Genes with a decrease of expression in KO versus wt are in blue, and with an increase in red. Gene expression from the Xi is selectively increased following KO. D Top, scatter plots of average log2 expression between Tsix-stop wt and KO clones (average for Tsix-Kdm6aΔEΔE17 and Tsix-Kdm6aΔEΔE21) at D15 for X-linked genes categorized as those silenced early, silenced at an intermediate time, silenced late, and not silenced (escape) during XCI [3, 25]. KO clones show higher expression of genes in each category compared to wt. n indicates the number of genes in each category. Bottom, histograms of median allelic expression of genes silenced at different times during XCI and of genes that escape XCI is increased in Tsix-stop KO clones compared to wt and CRISPR controls for all categories, while there is little change in expression from the Xa. n indicates the number of genes in each category. E Expression fold changes of individual escape genes from the Xi in Tsix-stop KO clones (average for Tsix-Kdm6aΔEΔE17 and Tsix-Kdm6aΔEΔE21) compared to wt at D15. Most genes show increased expression