Figure 5
VC promotes the reorganization of histone H3 as well as H3K4me3- and H3K27me3-modified nucleosomes during transition from pre-iPSCs to iPSCs.
(A) Induction of iPSCs from pre-iPSCs by treatment with VC and Setdb1 siRNA. Cells were first treated with Setdb1 siRNA and grown in mES medium supplemented with VC for 48 h and 96 h, respectively. RNA-seq data show the upregulated (Ddx4, Zfp42 and Nanog) and downregulated genes (Inhba and Vcam1) during the pre-iPS to iPS transition. (B) Dynamics of nucleosome deposition at the Ddx4, Zfp42 and Nanog promoters, quantified by ChIP-qPCR in pre-iPSCs cultured with mES medium containing VC. Ddx4 H3 ChIP (D2 vs. D0 *p = 0.0462, D4 vs. D0 *p = 0.0102); Zfp42 H3 ChIP (D2 vs. D0 **p = 0.0018, D4 vs. D0 ***p = 0.0002); Nanog H3 ChIP (D2 vs. D0 **p = 0.0050, D4 vs. D0 ***p = 0.0010). (C) Dynamics of H3K4me3 at the Ddx4, Zfp42 and Nanog promoters, quantified by ChIP-qPCR in pre-iPSCs cultured with mES medium containing VC. Ddx4 H3K4me3 ChIP (D4 vs. D0 ***p = 0.0002); Zfp42 H3K4me3 ChIP (D2 vs. D0 **p = 0.0041, D4 vs. D0 ***p = 7.86 × 10−5); Nanog H3K4me3 ChIP (D4 vs. D0 *p = 0.0249). (D) Dynamics of H3K27me3 at the Ddx4, Zfp42 and Nanog promoters, quantified by ChIP-qPCR in pre-iPSCs cultured with mES medium containing VC. Ddx4 H3K27me3 ChIP (D2 vs. D0 *p = 0.0432, D4 vs. D0 *p = 0.0215); Zfp42 H3K27me3 ChIP (D2 ***p = 0.0003, D4 vs. D0 ***p = 0.0002); Nanog H3K27me3 ChIP (D2 vs. D0 **p = 0.0017, D4 vs. D0 **p = 0.0015). (E) Dynamics of nucleosome deposition at the Inhba and Vcam1 promoters, quantified by ChIP-qPCR in pre-iPSCs cultured with mES medium containing VC. Inhba H3 ChIP (D4 vs. D0 ***p = 0.0005); Vcam1 H3 ChIP (D2 vs. D0 *p = 0.0108, D4 vs. D0 **p = 0.0071). (F) Dynamics of H3K4me3 at the Inhba and Vcam1 promoters, quantified by ChIP-qPCR in pre-iPSCs cultured with mES medium containing VC. Inhba H3K4me3 ChIP (D2 vs. D0 *p = 0.0140, D4 vs. D0 **p = 0.0068); Vcam1 H3K4me3 ChIP (D2 vs. D0 **p = 0.0022, D4 vs. D0 **p = 0.0017). Data represent the mean ± s.d. of triplicates.
