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. 2024 Apr 11;43(10):1965–1989. doi: 10.1038/s44318-024-00086-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Strategy for generating of Tead2-FLAG-AviTag knock-in cell lines in 2iL- and SL-ESCs. (B) Western blot analysis for BIOTIN and V5 with cell lysates from Tead2-FLAG-AviTag-knock-in 2iL- and SL-ESC lines. β-ACTIN was used as a loading control. (C) Motif-enrichment analysis of BIOTIN-binding sites in 2iL- and SL-ESCs. P-value was calculated by using hypergeometric enrichment calculations from Homer software. (D) Heatmap showing the comparison of TEAD2 binding sites between 2iL- and SL-ESCs. (E) Number of 2iL- and SL-ESCs-specific TEAD2 binding peaks. (F) Pie charts showing the genomic distribution of 2i-specific TEAD2 peaks. (G) Heatmaps of sequence read density for ATAC-seq in 2i-specific TEAD2 binding peaks. (H) Bar plot showing the number of 2i-specific TEAD2 peaks that overlap with both promoters and enhancers. (I) Tag-density pileup showing H3K4me1, H3K27ac, H3K4me3, H3K27me3, H3K9me3, and H3K36me3 ChIP-seq signals at the 2i-specific TEAD2 binding sites in both 2iL- and SL-ESCs. (J) Venn plots showing the overlap among 2i-specific TEAD2 target genes and cluster 5 genes. (K) Boxplots showing expression level of overlapping genes in (J) between wild-type and Tead2-knockout cells at day 6 of the transition. The centerline indicates the median value, while the box and whiskers represent the interquartile range (IQR) and 1.5 × IQR, respectively, n = 192. P-value was calculated by Mann–Whitney U test. (L) GO categories of the overlapping genes shown in (J). The enrichment p-value was calculated by using Metascape software. (M) Genomic views of enrichment for TEAD2 and histone modifications in the B4galt6 gene. Source data are available online for this figure.