The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq]. The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq]

Pigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only contribute to assisted reproduction technologies of pigs but also will shed light into early human development. We generated 3D chromatin profiles for pig somatic cells, IVF, PA and AG preimplantation embryos. We found that the chromosomes in the pig preimplantation embryos are enriched for superdomains, i.e., the larger than 10M compartment domains, which are much rarer in mice. Wheras, p(s) curves, compartments and TADs, are largely conserved in somatic cells, and are gradually establishing during preimplantation embryogenesis. In the uniparental pig embryos, the establishment of chromatin architecture was highly asynchronized at all levels from IVF embryos, and a remarkably strong decompartmentalization was observed during zygotic genome activation (ZGA). Finally, chromosomes originating from oocytes always establish TADs faster than chromosomes originating from sperm, both before and during ZGA. Overall design: We generated two histone modifications and CTCF binding profiles for pig embryonic fibroblasts (PEFs).

猪是农业与生物医学研究的重要模式动物，其辅助生殖技术亟待优化升级。解析体外受精（IVF）、孤雌生殖（PA）与雄核发育（AG）来源的猪植入前胚胎早期的表观遗传重编程潜在机制，不仅可推动猪辅助生殖技术的发展，亦能为人类早期发育研究提供重要参考。本研究构建了猪体细胞、IVF、PA及AG来源植入前胚胎的三维染色质图谱。研究发现，猪植入前胚胎的染色体富集超结构域——即尺寸大于10Mb的区室结构域，此类结构在小鼠中极为罕见。而p(s)曲线、区室结构与拓扑关联结构域（TADs）在体细胞中整体保守，并在植入前胚胎发育过程中逐步建立完善。相较于IVF胚胎，单亲性猪胚胎的染色质结构在各层级的建立过程均呈现高度异步性，且在合子基因组激活（ZGA）阶段可观察到显著的区室解离现象。此外，无论在ZGA发生前还是激活过程中，卵母细胞来源的染色体始终比精子来源的染色体更快完成TAD结构的建立。研究设计概况：本研究获取了猪胚胎成纤维细胞（PEFs）的两种组蛋白修饰及CTCF结合图谱。