Setd2 overexpression rescues bivalent gene expression during SCNT-mediated ZGA by enhancing H3K36me3 at gene bodies and excluding H3K27me3 from promoters [ChIP-seq]

Successful cloning through somatic cell nuclear transfer (SCNT) face significant challenges due to epigenetic obstacles. Recent studies have highlighted the roles of H3K4me3 and H3K27me3 as potential epigenetic barriers. However, the underlying mechanisms remain largely unclear. In this study, we generated genome-wide maps of H3K4me3 and H3K27me3 from mouse pre-implantation NT embryos. Our analysis revealed aberrant over-representation of H3K4me3 and H3K27me3 bivalent in 2-cell stage NT embryos, potentially linked to the deficiency of H3K36me3. Notably, the overexpression of Setd2, a H3K36me3 methyltransferase, successfully restored multiple epigenetic marks, including H3K36me3, H3K4me3 and H3K27me3. Additionally, it reinstated the expression levels of ZGA-related genes by re-establishing H3K36me3 at gene body regions to exclude H3K27me3 from bivalent regions, and ultimately improved cloning efficiency. These findings highlight the excessive bivalent state as a potent barrier and emphasize the removal of these barriers as a promising approach to achieving higher cloning efficiency. Overall design: Ultra-low-input chromatin immunoprecipitation followed by sequencing (ULI-NChIP-seq) for histone moifications H3K4me3, H3K27me3 and H3K36me3 in mouse somatic cell nuclear transfer embryos.