Aberrant H3K4me3 and H3K27me3 modifications in porcine SCNT embryos. (A) Heat maps and aggregate profile plots showing the H3K4me3 and H3K27me3 enrichment at gene promoters in somatic cell nuclear transfer (SCNT) embryos at the four-cell and blastocyst stages, as well as the difference between IVF and SCNT embryos (Δ[SCNT-IVF]: SCNT enrichment values minus IVF enrichment values). Gene clusters were defined in Figure 2A. (B) Heat maps and aggregate profile plots showing the H3K4me3 and H3K27me3 enrichment in oocyte PMDs of SCNT embryos at the four-cell and blastocyst stages, as well as the difference between IVF and SCNT embryos (Δ[SCNT-IVF]). (C) Bar plot showing the fraction of differentially expressed genes (DEGs) between IVF and SCNT four-cell embryos that are porcine ZGA genes. SCNT four-cell embryos contained 78 down-regulated (IVF vs. SCNT, FC > 2, FDR < 0.05) and 569 up-regulated (SCNT vs. IVF, FC > 2, FDR < 0.05). (D) Bar plot showing the fraction of DEGs located in H3K27me3-enhanced PMDs that are porcine ZGA genes. (E) Genome browser snapshots showing the H3K4me3 and H3K27me3 enriched at candidate genes in IVF and SCNT embryos at the four-cell and blastocyst stages. DNA methylation levels (mCG) in oocyte and spermatozoa are also shown.
