Figure 3 ∣.

Vitamin C deficiency induces a Tet1−/− like expression profile in the developing germline.

a, Diagram of experiments to determine the molecular impact of Vitamin C deficiency in the embryonic germline. Pregnant mice were deprived of Vitamin C as before and Oct4/EGFP+ germ cells were isolated from single E13.5 embryos.

b, Principle component analysis (PCA) of the transcriptional profile of E13.5 germ cells identifies a clear separation of samples according to Vitamin C availability along PC1. Each grey or red dot represents the germ cell transcriptome from a single Ctrl or -VitC female embryo, respectively. N=6 biological replicates per condition were measured. The Ctrl sample closest to the -VitC samples in the PCA plot clusters with them in hierarchical clustering (see Extended Data Fig. 5b). This sample is transcriptionally intermediate between Ctrl and -VitC samples, for reasons unknown.

c, MA plot of the differential expression between Ctrl and -VitC samples. The 98 gold dots represent genes significantly up-regulated in -VitC germ cells. The 314 blue dots represent genes down-regulated in -VitC germ cells. Select germline genes previously identified as Tet1- dependent in female germ cells⁸, induced by Vitamin C in ES culture¹¹ and validated by qRT-PCR (see Extended Data Fig. 1f-i) are highlighted in pink.

d, Gene Set Enrichment Analysis (GSEA) highlights the similarities between -VitC (this study) and Tet1−/−⁸ female E13.5 germ cells. Both up-regulated or down-regulated genes in Tet1−/− germ cells are highly biased to be up-regulated or down-regulated, respectively, in -VitC E13.5 germ cells. Statistical significance is calculated by a weighted Kolmogorov-Smirnov-like statistic and adjusted for multiple hypothesis testing.