Fig. 5: VGLL1 regulates histone acetylation levels and chromatin accessibility at TE target loci.

a Western blotting analysis for the indicated histone marks in 4CL H9 ESCs transduced with shLuc, shVGLL1−2 or shVGLL1−4 at day 5 of TELC differentiation. Representative of three independent experiments. b Venn diagram showing the overlap between VGLL1- and TEAD4-bound sites and H3K27ac-enriched sites in CUT&Tag of TELC-D5 cells differentiated from 4CL H9 ESCs. Representative cell cycle and TE genes corresponding to the overlapping regions are shown in the boxes. c Enriched GO terms for VGLL1, TEAD4 and H3K27ac co-occupied genes in CUT&Tag of TELC-D5 differentiated from 4CL H9 ESCs. P value was calculated using a hypergeometric test (one-sided) and adjusted for multiple testing using the Benjamini-Hochberg correction. d Co-occupancy analysis by signal density pileups of TEAD4 CUT&Tag peaks in 4CL H9 ESCs and TEAD4 CUT&Tag peaks in TELC-D5 cells differentiated from them. Peaks were divided into three categories: naïve-specific, shared and TE-specific. Example genes are shown for each category. e Signal intensity of H3K27ac in 4CL H9 ESCs (Naïve-H3K27ac) and TELC-D5 cells (TELC-D5-H3K27ac), and VGLL1 in TELC-D5 cells (TELC-D5-VGLL1) from the three categories defined in d. f Venn diagram showing the overlap between VGLL1- and TEAD4-binding at H3K27ac-enriched sites in CUT&Tag with chromatin accessibility peaks (ATAC-seq) in TELC-D5 cells differentiated from H9 4CL naïve ESCs. Representative cell cycle and TE genes corresponding to the overlapping regions are shown in the boxes. g Co-occupancy analysis by signal density pileups of VGLL1, TEAD4, H3K27ac CUT&Tag peaks and chromatin accessibility (ATAC-seq) peaks in TELC-D5 cells differentiated from 4CL H9 ESCs. h Enriched GO terms for open chromatin genes (ATAC-seq) co-occupied by VGLL1, TEAD4 and H3K27ac (CUT&Tag) of TELC-D5 cells differentiated from 4CL H9 ESCs. P value was calculated using a hypergeometric test (one-sided) and adjusted for multiple testing using the Benjamini-Hochberg correction. i Genome browser tracks showing VGLL1, TEAD4, H3K27ac genomic enrichment peaks (CUT&Tag) and chromatin accessibility peaks (ATAC-seq) for representative TE gene loci of TELC-D5 cells differentiated from 4CL H9 ESCs. j Signal intensity of TEAD4 at VGLL1-bound sites in WT and VGLL1-KO clone 68 (VGLL1^-/--C68) at day 5 of TELC induction from 4CL H9 ESCs. k Signal intensity of H3K27ac at VGLL1-binding sites in WT and VGLL1-KO clone 68 (VGLL1^-/--C68) at day 5 of TELC induction from 4CL H9 ESCs. l Signal intensity of chromatin openness at VGLL1-binding sites in WT and VGLL1-KO clone 68 (VGLL1^-/--C68) at day 5 of TELC induction from 4CL H9 ESCs.