Hou Changliang, Tian Geng G, Hu Shuanggang, Chen Beili, Li Xiaoyong, Xu Bo, Cao Yuedi, Le Wei, Hu Rong, Chen Hao, Zhang Yan, Fang Qian, Zhang Man, Wang Zhaoxia, Zhang Zhiguo, Zhang Jinfu, Wei Zhaolian, Yao Guangxin, Wang Yefan, Yin Ping, Guo Ya, Tong Guoqing, Teng Xiaoming, Sun Yun, Cao Yunxia, Wu Ji
Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Genome Med. 2025 May 19;17(1):57. doi: 10.1186/s13073-025-01476-y.
Three-dimensional (3D) chromatin architecture undergoes dynamic reorganization during mammalian gametogenesis and early embryogenesis. While mouse studies have shown species-specific patterns as well as mechanisms underlying de novo organization, these remain poorly characterized in humans. Although RNA polymerases II and III have been shown to regulate chromatin structure, the potential role of RNA polymerase I (Pol I), which drives ribosomal RNA production, in shaping 3D genome organization during these developmental transitions has not been investigated.
We employed a modified low-input in situ Hi-C approach to systematically compare 3D genome architecture dynamics from gametogenesis through early embryogenesis in human and mouse. Complementary Smart-seq2 for low-input transcriptomics, CUT&Tag for Pol I profiling, and Pol I functional inhibition assays were performed to elucidate the mechanisms governing chromatin organization.
Our study revealed an extensive reorganization of the 3D genome from human oogenesis to early embryogenesis, displaying significant differences with the mouse, including dramatically attenuated topologically associating domains (TADs) at germinal vesicle (GV) stage oocytes. The 3D genome reconstruction timing is a fundamental difference between species. In human, reconstruction initiates at the 4-cell stage embryo in human, while in mouse, it commences at the 2-cell stage embryo. We discovered that Pol I is crucial for establishing the chromatin structures during mouse embryogenesis, but not in human embryos. Intriguingly, the absence of Pol I transcription weakens TAD structure in mouse female germline stem cells, whereas it fortifies it in human counterparts.
These observed interspecies distinctions in chromatin organization dynamics provide novel insights into the evolutionary divergence of chromatin architecture regulation during early mammalian development. Our findings provide mechanistic insights into species-specific chromatin organization during germ cell and embryonic development and have potential implications for fertility preservation and birth defect prevention.
在哺乳动物配子发生和早期胚胎发育过程中，三维（3D）染色质结构会发生动态重组。虽然小鼠研究已经揭示了物种特异性模式以及从头组织的潜在机制，但这些在人类中仍未得到充分表征。尽管已证明RNA聚合酶II和III可调节染色质结构，但驱动核糖体RNA产生的RNA聚合酶I（Pol I）在这些发育转变过程中塑造3D基因组组织的潜在作用尚未得到研究。
我们采用改良的低输入原位Hi-C方法，系统地比较了人类和小鼠从配子发生到早期胚胎发育过程中的3D基因组结构动态。进行了用于低输入转录组学的互补Smart-seq2、用于Pol I分析的CUT&Tag以及Pol I功能抑制试验，以阐明染色质组织的调控机制。
我们的研究揭示了从人类卵子发生到早期胚胎发育过程中3D基因组的广泛重组，与小鼠表现出显著差异，包括在生发泡（GV）期卵母细胞中拓扑相关结构域（TADs）明显减弱。3D基因组重建时间是物种之间的一个根本差异。在人类中，重建在4细胞期胚胎开始，而在小鼠中，它在2细胞期胚胎开始。我们发现Pol I对于小鼠胚胎发育过程中建立染色质结构至关重要，但在人类胚胎中并非如此。有趣的是，Pol I转录的缺失会削弱小鼠雌性生殖系干细胞中的TAD结构，而在人类对应细胞中则会增强它。
这些在染色质组织动态方面观察到的种间差异为早期哺乳动物发育过程中染色质结构调控的进化分歧提供了新的见解。我们的发现为生殖细胞和胚胎发育过程中物种特异性染色质组织提供了机制性见解，并对生育力保存和出生缺陷预防具有潜在意义。
