Guowei Bu1,2,6, Wei Zhu1,2,6, Xin Liu1,2,6, Jingjing Zhang1,2, Longtao Yu1,2, Kai Zhou1,2, Shangke Wang1,2, Zhekun Li1,2, Zhengang Fan1,2, Tingting Wang1,2, Taotao Hu1,2, Ruifeng Hu1,2, Zhiting Liu1,2, Tao Wang1,2, Linhui Wu1,2, Xia Zhang1,2, Shuhong Zhao2 and Yi-Liang Miao1,2,3,4,5 1Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; 2Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China; 3Hubei Hongshan Laboratory, Wuhan 430070, China; 4Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518120, China; 5Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

↵6 These authors contributed equally to this work.

Corresponding author: miaoylmail.hzau.edu.cn Abstract

Histone modifications are critical epigenetic indicators of chromatin state associated with gene expression. Although the reprogramming patterns of H3K4me3 and H3K27me3 have been elucidated in mouse and human preimplantation embryos, the relationship between these marks and zygotic genome activation (ZGA) remains poorly understood. By ultra-low-input native chromatin immunoprecipitation and sequencing, we profiled global H3K4me3 and H3K27me3 in porcine oocytes and in vitro fertilized (IVF) embryos. We observed sharp H3K4me3 peaks in promoters of ZGA genes in oocytes, and these peaks became broader after fertilization and reshaped into sharp peaks again during ZGA. By simultaneous depletion of H3K4me3 demethylase KDM5B and KDM5C, we determined that broad H3K4me3 domain maintenance impaired ZGA gene expression, suggesting its function to prevent premature ZGA entry. In contrast, broad H3K27me3 domains underwent global removal upon fertilization, followed by a re-establishment for H3K4me3/H3K27me3 bivalency in morulae. We also found that bivalent marks were deposited at promoters of ZGA genes, and inhibiting this deposition was correlated with the activation of ZGA genes. It suggests that promoter bivalency contributes to ZGA exit in porcine embryos. Moreover, we demonstrated that aberrant reprogramming of H3K4me3 and H3K27me3 triggered ZGA dysregulation in somatic cell nuclear transfer (SCNT) embryos, whereas H3K27me3-mediated imprinting did not exist in porcine IVF and SCNT embryos. Our findings highlight two previously unknown epigenetic reprogramming modes coordinated with ZGA in porcine preimplantation embryos. Finally, the similarities observed between porcine and human histone modification dynamics suggest that the porcine embryo may also be a useful model for human embryo research.

Received September 16, 2021. Accepted July 19, 2022.