image: Under normal conditions, HDAC3 deacetylase activity coordinates histone acetylation reprogramming and chromatin accessibility during major ZGA, thereby ensuring the proper activation of major ZGA genes and normal preimplantation embryonic development. Conversely, loss of HDAC3 deacetylase activity disrupts these epigenetic processes, leading to widespread dysregulation of major ZGA genes and ultimately resulting in developmental arrest.
Credit: ©Science Bulletin
Zygotic genome activation (ZGA) is a critical event that marks the transition from maternal control to embryonic genome-driven regulation during early embryonic development. In mice, ZGA occurs in two successive waves, with major ZGA taking place mainly at the late two-cell stage. Proper activation of this transcriptional program requires extensive epigenetic reprogramming, including dynamic changes in histone modifications and chromatin accessibility. Histone acetylation generally marks active chromatin and gene transcription, whereas histone deacetylases (HDACs) primarily remove acetyl groups from histones. HDAC3 is a class I histone deacetylase. Previous studies have demonstrated its involvement in gametogenesis and oocyte meiotic maturation. However, its role in preimplantation embryonic development remains unclear, particularly whether its deacetylase activity contributes to ZGA regulation and how it relates to chromatin states is unknown.
A study published in Science Bulletin by the team of Prof. Qing-Yuan Sun and colleagues now identifies that HDAC3 deacetylase activity is required for proper major ZGA and preimplantation embryonic development by coordinating histone acetylation reprogramming with chromatin accessibility.
The team first examined the expression pattern of HDAC3 during preimplantation development and found that HDAC3 protein remained highly expressed from the zygote to the late two-cell stage, suggesting a potential role during ZGA. Functional experiments further showed that embryos lacking HDAC3 deacetylase activity began to display developmental defects at the two-cell stage and showed progressively reduced developmental potential. Importantly, supplementation with wild-type HDAC3 partially restored embryonic development and corrected the abnormally elevated histone acetylation levels, indicating that HDAC3 deacetylase activity is essential for preimplantation embryonic development.
Transcriptomic analysis revealed widespread transcriptional dysregulation in late two-cell embryos lacking HDAC3 deacetylase activity. More than 70% of the differentially expressed transcripts were markedly downregulated, with the majority corresponding to major ZGA genes. These findings indicate that loss of HDAC3 deacetylase activity disrupts normal ZGA, ultimately leading to ZGA failure and severe embryonic developmental defects.
The researchers next investigated the epigenetic alterations underlying these transcriptional defects. Loss of HDAC3 deacetylase activity increased the levels of several histone acetylation marks, including H3K9ac, H3K18ac, H3K27ac, and H4K16ac, with H3K27ac showing the most pronounced changes. However, low-input H3K27ac CUT&Tag analysis revealed that these changes were not uniform across the genome. Instead, H3K27ac signals were reduced mainly at regions associated with major ZGA genes. These findings suggest that HDAC3 does not simply regulate global histone acetylation levels, rather its deacetylase activity contributes to the proper genomic distribution of H3K27ac during ZGA.
Using miniATAC-seq, the researchers further found that chromatin accessibility at the transcription start sites (TSSs) of major ZGA genes was significantly reduced in embryos lacking HDAC3 deacetylase activity. Notably, integrated epigenomic analysis revealed that H3K27ac signals were already markedly altered at the early two-cell stage, whereas the corresponding ATAC signals remained relatively stable. By the late two-cell stage, H3K27ac signals and chromatin accessibility exhibited more widespread coordinated decreases, suggesting that changes in H3K27ac following loss of HDAC3 deacetylase activity precede alterations in chromatin accessibility. Furthermore, experimentally reducing chromatin accessibility through SMARCC1 depletion did not cause detectable changes in H3K27ac levels in the short term, further supporting a temporal relationship between these two epigenetic events.
In addition, the researchers found that loss of HDAC3 deacetylase activity impaired the timely shutdown of the MERVL transcriptional program following ZGA. Transcriptomic analysis revealed that MERVL-int remained highly expressed at the four-cell stage, accompanied by markedly increased H3K27ac enrichment, chromatin accessibility, and Pol II occupancy at MERVL-int loci. These findings suggest that HDAC3 deacetylase activity may exert a repressive effect on MERVL-int. Furthermore, reducing MERVL-int expression improved embryonic developmental efficiency and partially restored the dysregulated gene expression profile.
Collectively, this study demonstrates that HDAC3 deacetylase activity ensures the proper activation of major ZGA genes by coordinately regulating histone acetylation reprogramming and chromatin accessibility. Conversely, loss of HDAC3 deacetylase activity disrupts these epigenetic processes, leading to widespread dysregulation of major ZGA genes and ultimately impairing embryonic development.