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Fig. 6 | Cell Regeneration

Fig. 6

From: Rif1 interacts with non-canonical polycomb repressive complex PRC1.6 to regulate mouse embryonic stem cells fate potential

Fig. 6

Rif1 modulates the genomic distribution of the PRC1.6 complex and regulates a group of 2C genes. A Motif analysis of Rif1-binding sites in mESCs reveals significant enrichment in C-Myc, Max, E2F4, and E2F6 binding motifs. B Correlation matrix showing the unbiased and pairwise comparisons of genomic distributions of the indicated proteins or histone modifications in mESCs. Color bar represents Pearson correlation coefficient. C Venn diagram comparing the Rif1 binding sites (12,729 peaks) with that of Pcgf6 (22,911 peaks), RNF2 (19,408 peaks), and H2AK119ub (8928 peaks). D Top: heatmaps showing the densities of Rif1, Pcgf6, RNF2, and H2AK119ub ChIP-seq reads on the Rif1-bound regions (±1 kb) in control or Rif1 downregulated mESCs. The genomic regions are centered according to the Rif1 ChIP-seq signals in the WT mESCs. Bottom: the averaged ChIP-seq signals of Pcgf6, RNF2, or H2AK119ub on Rif1-bound regions in the presence (blue lines) or absence (green lines) of Rif1. E Selected Gene Ontology (GO) analysis results of the genes in the Rif1 and Pcgf6 co-occupied genomic regions which showed decreased Pcgf6 binding upon Rif1 knockdown. F Venn diagrams comparing the Rif1-bound genes that showed decreased Pcgf6 binding upon Rif1 knockdown with the 2C genes. Hypergeometric p value < 0.01. G Gene set enrichment analysis (GSEA) illustrating the upregulation of 2C genes in the mESCs depleted of Rif1 or Pcgf6. The normalized enrichment scores (NES) > 1 and p < 0.05 is considered significantly enriched. H Heatmap of RNA-seq data showing the expression of the 2C genes in Rif1 CKO and Pcgf6 KD mESCs. The number of 2C genes in each cluster is shown. I Averaged Rif1 and Pcgf6 ChIP-seq profiles in the corresponding clusters. J Integrative Genomics Viewer (IGV) showing ChIP-seq intensity of indicated proteins and the RNA-seq signals on Zfp352

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