Setd2 overexpression rescues bivalent gene expression during SCNT-mediated ZGA by enhancing H3K36me3 at gene bodies and excluding H3K27me3 from promoters [RNA-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. To investigate the function of small molecule inhibitor WDR5-0103 during SCNT-mediated reprogramming, we added WDR5-0103 into the culture medium of SCNT embryos. To investigate the function of Setd2 during SCNT-mediated reprogramming, the SCNT embryos were injected with Setd2 mRNA after activation. We then performed gene expression profiling analysis using data obtained from Smart-seq2 of 2-cell stage and/or 4-cell stage SCNT embryos after WDR5-0103 addition and Setd2 mRNA injection.