This work delineates how Setd2-mediated epigenetic reprogramming overcomes developmental barriers in cloned embryos. Comparative analysis revealed that SCNT embryos exhibit excessive H3K4me3 and H3K27me3 co-occupancy (bivalent domains) at promoters during ZGA compared to natural embryos, correlating with suppressed expression of genes essential for embryogenesis. Mechanistically, Setd2 counteracts aberrant H3K27me3 by depositing H3K36me3 across gene bodies, which spatially excludes Polycomb-repressive complexes from promoters. Pharmacological inhibition of H3K4me3 (via WDR5-0103) partially rescued embryonic development, while Setd2 overexpression synergistically normalized H3K4me3/H3K27me3 levels and restored transcriptional fidelity. Crucially, Setd2-reconstituted embryos showed 1.7-fold higher blastocyst rates, with rescued expression of 82% ZGA-related bivalent genes, including Dux and Zscan4 families. These findings position Setd2 as a master regulator of chromatin state transitions during nuclear reprogramming..

Key findings from the study include:

1. Pathological Bivalent Chromatin in SCNT Embryos​​: Aberrant co-enrichment of H3K4me3 (activating) and H3K27me3 (repressive) marks at promoters during ZGA silences developmental genes (Dux, Zscan4), stalling SCNT embryo development.
2. H3K36me3-Driven Epigenetic Antagonism​​: Setd2-mediated deposition of H3K36me3 at gene bodies displaces Polycomb Repressive Complex 2 (PRC2)-dependent H3K27me3 via spatial chromatin exclusion, reactivating transcription of ZGA-critical loci.
3. Therapeutic Rescue Strategies:

1. Pharmacological inhibition of H3K4me3 (WDR5-0103) increases blastocyst rates by 40% in murine SCNT models.
2. Setd2 overexpression restores H3K4me3/H3K27me3 balance, elevating blastocyst formation 1.7-fold through transcriptional rebalancing.

1. Evolutionarily Conserved Mechanism​​: Setd2 orchestrates hierarchical histone crosstalk (H3K36me3→H3K4me3/H3K27me3 equilibrium) to license embryonic competency, a paradigm conserved across mammalian reprogramming systems.

This study establishes Setd2 as a chromatin architect resolving SCNT-specific epigenetic barriers. By antagonizing pathological bivalency via H3K36me3-driven spatial remodeling, Setd2 overexpression unlocks ZGA fidelity and cloning efficiency. The conserved logic of histone modification hierarchies offers a universal blueprint for enhancing nuclear reprogramming in regenerative medicine and agricultural biotechnology.The work entitled “Setd2 overexpression rescues bivalent gene expression during SCNT-mediated ZGA” was published on Protein & Cell (published on Feb. 13, 2025).
DOI：https://doi.org/10.1093/procel/pwaf010