TDG is a pig-specific epigenetic regulator with insensitivity to H3K9 and H3K27 demethylation in nuclear transfer embryos

Summary Pig cloning by somatic cell nuclear transfer (SCNT) frequently undergoes incomplete epigenetic remodeling during the maternal-to-zygotic transition, which leads to a significant embryonic loss before implantation. Here, we generated the first genome-wide landscapes of histone methylation in pig SCNT embryos. Excessive H3K9me3 and H3K27me3, but not H3K4me3, were observed in the genomic regions with unfaithful embryonic genome activation and donor-cell-specific gene silencing. A combination of H3K9 demethylase KDM4A and GSK126, an inhibitor of H3K27me3 writer, were able to remove these epigenetic barriers and restore the global transcriptome in SCNT embryos. More importantly, thymine DNA glycosylase (TDG) was defined as a pig-specific epigenetic regulator for nuclear reprogramming, which was not reactivated by H3K9me3 and H3K27me3 removal. Both combined treatment and transient TDG overexpression promoted DNA demethylation and enhanced the blastocyst-forming rates of SCNT embryos, thus offering valuable methods to increase the cloning efficiency of genome-edited pigs for agricultural and biomedical purposes.
Graphical abstract
Highlights • Identification of reprogramming-resistant genes and regions in porcine SCNT embryos • H3K9me3 and H3K27me3 are enriched in reprogramming-resistant genes and regions • Removing H3K9me3 and H3K27me3 by KDM4A and GSK126 facilitates nuclear reprogramming • Transient TDG overexpression promotes DNA demethylation and improves reprogramming
In this article, Miao and colleagues show that H3K9me3 and H3K27me3 are epigenetic barriers to porcine SCNT-mediated reprogramming. Removal of these modifications by KDM4A and GSK126 improves SCNT embryonic development, but does not reactivate TDG during embryonic genome activation. Meanwhile, transient TDG overexpression promotes DNA demethylation and also improves SCNT embryonic development in pigs.