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.

附加文件11 补充图S6。已知KDM6A靶基因的表观遗传与表达变化。(A) 分化后的Tsix-stop野生型（wt）细胞（蓝色）与KDM6A敲除（KO）克隆（Tsix-Kdm6aΔEΔE17，红色）中，已知KDM6A靶基因的H3K27me3富集及峰分布的IGV浏览器视图。峰以信号曲线下方的彩色柱状图表示。下方为野生型与敲除细胞的RNA测序（RNA-seq）表达谱（黑色）。柱状图展示了两个分化野生型克隆与敲除克隆中T和Pitx2的每百万转录本（TPM）表达值。对于Wnt3与Gata4，同时展示了分化过程中第0-7天的实时定量逆转录聚合酶链反应（qRT-PCR）检测得到的表达变化，以及分化后的TPM值柱状图（*p<0.05）。此处KO指代Tsix-Kdm6aΔEΔE17与Tsix-Kdm6aΔEΔE21克隆的平均值，所有数值均以β-肌动蛋白（Actinβ）进行标准化。(B) 与(A)采用相同分析方法，但针对Nsdhl与Araf这两个经Kdm6a敲除后未出现显著下调的基因。(C) 与(A)采用相同分析方法，但针对分化第15天的Dlk1/Meg3印记基因座：敲除细胞中Meg3启动子区域的H3K27me3水平显著升高，该区域包含印记控制区ICR(2)与基因间印记控制区ICR(1)。(A)、(B)、(C)中展示的信号曲线刻度标注于各图的右上角。