Additional file 11 of KDM6A facilitates Xist upregulation at the onset of X inactivation

Additional file 11 Supplemental figure S6. Epigenetic and expression changes at known KDM6A target genes. (A) IGV browser views of profiles of H3K27me3 enrichment and peaks at known KDM6A target genes in differentiated Tsix-stop wt cells (blue) and KO clones (Tsix-Kdm6aΔEΔE17) (red). Peaks are represented by colored bars below the signal profiles. Below are RNA-seq expression profiles (black) in wt and KO cells. Histograms show TPM expression values for T and Pitx2 in two differentiated wt clones and KO clones. For Wnt3 and Gata4, both changes in expression at D0-7 obtained by qRT-PCR during differentiation and histograms of TPM values following differentiation are shown (*p<0.05). KO represents an average for the Tsix-Kdm6aΔEΔE17 and Tsix-Kdm6aΔEΔE21 clones. Values are normalized to Actinβ. (B) Same analysis as in (A), but for Nsdhl and Araf, two genes that do not show significant downregulation following Kdm6a KO. (C) Same analysis as in (A), but at the Dlk1/Meg3 imprinted locus at D15 where H3K27me3 markedly increases at the promoter of Meg3 in KO cells, including at the imprinting control region ICR (2) and the intergenic ICR (1). The scales of the profiles shown in (A), (B) and (C) are indicated in the upper right corners.