Additional Supporting Information may be found in the online version of this article.

sc-12-0724_sm_SupplFigure1.tif2615KSupplementary Figure 1. A. Average binding profile of PRDM14 at active and poised enhancers. Average ChIP-Seq signal of PRDM14 occupancy in human ESCs at active class 1 enhancers (black line) and at poised class 2 enhancers (red line). B. Average ChIP-Seq signal for PRDM14 (solid line) and p300 (dotted line) across the genome in association with H3K27me3, H3K27ac and H3K4me1 in human ESCs. PRDM14 and p300 peaks were divided into three equally sized groups according to binding strength. H3K27me3 are enriched at peaks with strong PRDM14 binding signal and H3K27ac are enriched at peaks with strong p300 binding. Levels of H3K4me1 correlates with the binding intensity of both p300 and PRDM14, reflecting the enrichment of p300 and PRDM14 binding at enhancers. C. Correlation of PRDM14 binding sites with histone modifications. The calculated Pearson correlation between ChIP-Seq signal strength of PRDM14 and 11 histone modifications within 4kb of the PRDM14 binding sites. Enrichment of H3K27me3 modifications is significant compared to the 10 other histone modifications.
sc-12-0724_sm_SupplFigure2.tif2615KSupplementary Figure 2 A. Average ChIP-Seq signal for INPUT DNA, EZH2, H3K27me3 and H3K27ac within ±2000bp of PRDM14 and NANOG binding sites. B. Protein levels of PRC2 components and histones after PRDM14 depletion for 40hrs. Chromatin lysate of cells harvested for ChIP after PRDM14 depletion was used for the Western blot analysis. Levels of H3K4me1, H3K27me3, EZH2, SUZ12, histone H3 and NANOG remain unchanged compared to PRDM14, which is decreased in the PRDM14 depleted sample compared to the control. The GAPDH protein level served as a loading control. C. NANOG binding at target genes are not affected in PRDM14 depleted human ESCs. D. Histone H3 ChIP at the PRDM14-bound loci.
sc-12-0724_sm_SupplFigure3.tif2615KSupplementary Figure 3 A. Time course expression analysis of PRDM14 and pluripotency genes NANOG, CDH1 and TDGF during 4F mediated iPSC reprogramming. Total RNA was extracted from MRC-5 cells infected with retroviruses over-expressing GFP (control) or the reprogramming factors O, S, K and M. The relative expression was obtained by normalizing against the control sample. All values are means ± s.e.m from 3 independent experiments (n=3)

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