Extended Data Fig. 9: YAP and mechanical cues regulate TE-gene chromatin interactions in DE cells.

a, b, Aggregate Peak Analysis (APA) of 1,463 TE enhancer-promoter (E-P) interactions co-occupied by YAP/CTCF under stiff and soft conditions in hESC-derived DE cells. APA plots are shown in (a), and box plots quantifying interaction strength are shown in (b), revealing a substantial weakening of these interactions under soft conditions. n = 2 biologically independent experiments. c, mRNA expression of genes associated with the 1,463 TE E-P pairs is substantially reduced under soft conditions in DE cells. n = 2 biologically independent experiments. d, e, Aggregate Peak Analysis (APA) of 1,463 TE enhancer-promoter (E-P) interactions co-occupied by YAP/CTCF in DE cells derived from YAP KO vs WT control hESCs. APA plots are shown in (d), and box plots quantifying interaction strength are shown in (e), revealing a marked weakening of these interactions under soft conditions. n = 2 biologically independent experiments. f, mRNA expression of genes associated with the 1,463 TE E-P pairs is markedly reduced in YAP KO hESC-derived DE cells. n = 2 biologically independent experiments. In box plots (b, c, e, f), center lines represent the median value, box limits the 25th and 75th percentiles, and whiskers denote minima and maxima (1.5× the interquartile range). Source numerical data are available in source data.