Fig. 3: Nanog^BiD increases chromatin accessibility and pluripotent gene expression.

a Heatmap of the expression dynamics during Nanog^WT and Nanog^BiD reprogramming path as well as MEF and mESC for all differentially expressed genes. These genes were grouped into 12 clusters according to their similarity of expression dynamics. D indicates day. b Line plots show the expression dynamics trends of different gene clusters defined in (a). c, d Functional enrichment analysis of the C1 and C12 genes, respectively. e Heatmap of the chromatin accessibility dynamics during Nanog^WT and Nanog^BiD reprogramming path as well as MEF and mESC. Loci of open chromatin were arranged into groups depending upon the day of Nanog^BiD reprogramming they changed from closed to open (CO) or open to closed (OC). f Motif of transcription factors significantly enriched in each group of chromatin loci of Nanog^BiD reprogramming path (as defined in (e)) and Nanog^WT reprogramming path (as defined in Fig. S3e.). Motifs with at least 3-fold enrichment and less than 1 × 10⁻⁵ p-value are marked with asterisk. g Bar plots show the number of peaks specifically affected by Nanog^BiD (Failed) and both affected by Nanog^BiD and Nanog^WT. h, i The motif enrichments of pluripotency factors and somatic factors in the Nanog^BiD specifically affected CO and OC regions, respectively. The dots were colored by the percentage of each motif in targets. j Functional enrichment analysis of Nanog^BiD specifically affected CO regions demonstrated in heatmap. k Genome track view of the ATAC-seq data for the pluripotency gene cluster miR302a-d. l Venn diagram shows the overlapped gene number of C1 and Nanog^BiD specifically affected CO genes. The 43 transcription factors are listed. m Functional enrichment analysis of the overlapped genes in (l).