Nucleosome organization of mouse embryos during pre-implantation development
Abstract Sexual reproduction begins with sperm–oocyte fusion to form a zygote, where chromatin undergoes dramatic reorganization to establish totipotency. Although nucleosomes- the basic units of eukaryotic chromatin and key epigenetic regulators- are extensively remodeled during early embryogenesis...
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Nature Portfolio
2025-07-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-05642-5 |
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| author | Jitao Zeng Xiaojuan Tu Siming Qu Xichan Chen Ying Wang Xiaona Liu Enchuan Kang Yi Tian Qianming Xiang Binbin Lai Weiwu Gao Bing Ni Wei He |
| author_facet | Jitao Zeng Xiaojuan Tu Siming Qu Xichan Chen Ying Wang Xiaona Liu Enchuan Kang Yi Tian Qianming Xiang Binbin Lai Weiwu Gao Bing Ni Wei He |
| author_sort | Jitao Zeng |
| collection | DOAJ |
| description | Abstract Sexual reproduction begins with sperm–oocyte fusion to form a zygote, where chromatin undergoes dramatic reorganization to establish totipotency. Although nucleosomes- the basic units of eukaryotic chromatin and key epigenetic regulators- are extensively remodeled during early embryogenesis, their dynamic repositioning mechanisms and biological implications remain unclear. Here, we employed single-cell MNase sequencing (scMNase-seq) to map genome-wide nucleosome positioning and chromatin accessibility in individual mammalian embryos. We found that nucleosome positioning mirrored somatic cell patterns until the 4-cell stage, with nucleosome depletion and phasing at CTCF sites not fully established until morula formation. By integrating H3K4me3 localization and transcriptomic data, we revealed that nucleosome sparsity at transcription start sites (TSS) and flanking regions correlated with expression levels of genes critical for preimplantation development. Notably, these nucleosome-depleted regions likely serve as regulatory hubs influencing histone modification dynamics. Our study systematically delineates nucleosome reorganization principles during mammalian embryogenesis and provides a high-resolution resource for understanding chromatin remodeling in early development. |
| format | Article |
| id | doaj-art-057288b85cb54abeaf8f9ec936c849b2 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-057288b85cb54abeaf8f9ec936c849b22025-08-20T03:37:22ZengNature PortfolioScientific Reports2045-23222025-07-0115111710.1038/s41598-025-05642-5Nucleosome organization of mouse embryos during pre-implantation developmentJitao Zeng0Xiaojuan Tu1Siming Qu2Xichan Chen3Ying Wang4Xiaona Liu5Enchuan Kang6Yi Tian7Qianming Xiang8Binbin Lai9Weiwu Gao10Bing Ni11Wei He12Reproductive Medical Center, Southwest Hospital, Army Medical UniversityReproductive Medical Center, Southwest Hospital, Army Medical UniversityOrgan Transplantation Center, The First Affiliated Hospital of Kunming Medical UniversityInstitute of Immunology People’s Liberation Army (PLA) and Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University)Reproductive Medical Center, Southwest Hospital, Army Medical UniversityReproductive Medical Center, Southwest Hospital, Army Medical UniversityReproductive Medical Center, Southwest Hospital, Army Medical UniversityInstitute of Immunology People’s Liberation Army (PLA) and Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University)Department of Dermatology and Venereology, Peking University First HospitalDepartment of Dermatology and Venereology, Peking University First HospitalInstitute of Immunology People’s Liberation Army (PLA) and Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University)Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical UniversityReproductive Medical Center, Southwest Hospital, Army Medical UniversityAbstract Sexual reproduction begins with sperm–oocyte fusion to form a zygote, where chromatin undergoes dramatic reorganization to establish totipotency. Although nucleosomes- the basic units of eukaryotic chromatin and key epigenetic regulators- are extensively remodeled during early embryogenesis, their dynamic repositioning mechanisms and biological implications remain unclear. Here, we employed single-cell MNase sequencing (scMNase-seq) to map genome-wide nucleosome positioning and chromatin accessibility in individual mammalian embryos. We found that nucleosome positioning mirrored somatic cell patterns until the 4-cell stage, with nucleosome depletion and phasing at CTCF sites not fully established until morula formation. By integrating H3K4me3 localization and transcriptomic data, we revealed that nucleosome sparsity at transcription start sites (TSS) and flanking regions correlated with expression levels of genes critical for preimplantation development. Notably, these nucleosome-depleted regions likely serve as regulatory hubs influencing histone modification dynamics. Our study systematically delineates nucleosome reorganization principles during mammalian embryogenesis and provides a high-resolution resource for understanding chromatin remodeling in early development.https://doi.org/10.1038/s41598-025-05642-5scMNase-seqEmbryosNucleosome positionChromatin organizationH3K4me3 |
| spellingShingle | Jitao Zeng Xiaojuan Tu Siming Qu Xichan Chen Ying Wang Xiaona Liu Enchuan Kang Yi Tian Qianming Xiang Binbin Lai Weiwu Gao Bing Ni Wei He Nucleosome organization of mouse embryos during pre-implantation development Scientific Reports scMNase-seq Embryos Nucleosome position Chromatin organization H3K4me3 |
| title | Nucleosome organization of mouse embryos during pre-implantation development |
| title_full | Nucleosome organization of mouse embryos during pre-implantation development |
| title_fullStr | Nucleosome organization of mouse embryos during pre-implantation development |
| title_full_unstemmed | Nucleosome organization of mouse embryos during pre-implantation development |
| title_short | Nucleosome organization of mouse embryos during pre-implantation development |
| title_sort | nucleosome organization of mouse embryos during pre implantation development |
| topic | scMNase-seq Embryos Nucleosome position Chromatin organization H3K4me3 |
| url | https://doi.org/10.1038/s41598-025-05642-5 |
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