Extended Data Fig. 3: YAP/TEAD1 control the enhancer activity of LTR7s.
a, Western blot validation of YAP and TEAD1 knockout (KO) efficiency in hESCs. b, AP staining and morphology analysis showing that YAP and TEAD1 KO does not impair hESC pluripotency maintenance. c, d, RT-qPCR analysis of (c) pluripotency genes and (d) HERVH-int expression in WT, YAP-KO, and TEAD1-KO hESCs. P = 0.016, 0.25, 0.18, 0.85, 0.95, 0.056, 0.43, 0.06, 0.76, 0.49, 0.96, 0.0058(c); 0.011, 0.0099, 0.011, 0.0082 (d). n = 3 biologically independent experiments. e, MA scatter plot showing RNA expression changes of HERVH-int in YAP-KO versus WT hESCs. Downregulated HERVH-int loci are highlighted in blue, while upregulated loci are in red (fold change > 1.2). f, Density plot showing the genomic distance between LTR7 elements and the nearest transcription start site (TSS). 97.1% of YAP/TEAD1-co-bound LTR7s are located more than 2 kb from a TSS. g, Pie chart summarizing histone modifications at 342 YAP/TEAD1-co-occupied LTR7s that do not overlap with TSSs. h, i, Luciferase reporter assays quantifying the enhancer activity of LTR7 elements in a minimal promoter reporter construct in WT hESCs (h) and in YAP-KO and TEAD1-KO hESCs (i). P = 0.0086 (h), P = 0.0.0029, P = 0.0069, P = 0.03, P = 0.011(i) n = 3 biologically independent experiments. j, Volcano plot showing differential BRD4 binding at genomic loci. BRD4 peaks overlapping with LTR7s are predominantly downregulated in YAP-KO or TEAD1-KO hESCs compared to WT control hESCs, indicating reduced enhancer activity. P values were calculated by the two-tailed Student’s t-test (c, d, h, i). NS, not significant. Data in (c, d, h, i) represent mean ± s.e.m. Source numerical data and unprocessed blots are available in source data.
