Figure 6

Two-cell embryo-specific genes are induced in HP1α, HP1β, KAP1 and G9a KO mESCs. A list of two-cell (2C) specific genes was produced from single blastomere expression data [52] by identifying genes expressed at levels 4-fold higher at the 2C stage than the oocyte or 8C stages (Oo < 2C > 8C). (A-B) Venn diagrams illustrating the overlap between this gene list and the list of genes upregulated at least 4-fold in KAP1, G9a [12, 28], HP1α or HP1β KO mESCs are shown. The percentage of genes upregulated in the KO that are also 2C-specific is displayed above, while the percentage of 2C-specific genes that are also upregulated in the KO are presented below. (C) The nine genes upregulated in all four KO lines are listed, along with the distance of the nearest MERVL LTR (MT2) to the transcription start site (TSS). (D) Confirmation of the expression pattern of previously identified 2C-specific genes. RPKM values, derived by division of reads per million (RPM) values from RNA-seq data generated from pooled single blastomeres [52] by transcript length, are presented for Zfp352, Zscan4d, Zscan4c, Tdpoz3 and Tdpoz4 genes. (E) Expression levels of these 2C-specific genes was determined in G9a, KAP1, HP1α and HP1β KO mESCs as well as their wt parent lines using our RNA-seq data (HP1α and HP1β) or previously published RNA-seq data (G9a and KAP1 [12, 28]), and Z-score values (see Materials and Methods) for each are presented.