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Xu R, Zhu Q, Zhao Y, Chen M, Yang L, Shen S, Yang G, Shi Z, Zhang X, Shi Q, Kou X, Zhao Y, Wang H, Jiang C, Li C, Gao S, Liu X. Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos. Nat Commun 2023; 14:4807. [PMID: 37558707 PMCID: PMC10412629 DOI: 10.1038/s41467-023-40496-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. We find redundant H3K9me3 marks are closely related to defective minor zygotic genome activation. Moreover, SCNT blastocysts show severely indistinct lineage-specific H3K9me3 deposition. We identify MAX and MCRS1 as potential H3K9me3-related transcription factors and are essential for early embryogenesis. Overexpression of Max and Mcrs1 significantly benefits SCNT embryo development. Notably, MCRS1 partially rescues lineage-specific H3K9me3 allocation, and further improves the efficiency of full-term development. Importantly, our data confirm the conservation of deficient H3K9me3 differentiation in Sertoli cell-derived SCNT embryos, which may be regulated by alternative mechanisms.
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Affiliation(s)
- Ruimin Xu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Qianshu Zhu
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Yuyan Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Mo Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, 400013, Chongqing, China
| | - Lingyue Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Shijun Shen
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Guang Yang
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Zhifei Shi
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Xiaolei Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Qi Shi
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Cizhong Jiang
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Chong Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
| | - Xiaoyu Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
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Gatto A, Forest A, Quivy JP, Almouzni G. HIRA-dependent boundaries between H3 variants shape early replication in mammals. Mol Cell 2022; 82:1909-1923.e5. [PMID: 35381196 DOI: 10.1016/j.molcel.2022.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/16/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
The lack of a consensus DNA sequence defining replication origins in mammals has led researchers to consider chromatin as a means to specify these regions. However, to date, there is no mechanistic understanding of how this could be achieved and maintained given that nucleosome disruption occurs with each fork passage and with transcription. Here, by genome-wide mapping of the de novo deposition of the histone variants H3.1 and H3.3 in human cells during S phase, we identified how their dual deposition mode ensures a stable marking with H3.3 flanked on both sides by H3.1. These H3.1/H3.3 boundaries correspond to the initiation zones of early origins. Loss of the H3.3 chaperone HIRA leads to the concomitant disruption of H3.1/H3.3 boundaries and initiation zones. We propose that the HIRA-dependent deposition of H3.3 preserves H3.1/H3.3 boundaries by protecting them from H3.1 invasion linked to fork progression, contributing to a chromatin-based definition of early replication zones.
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Affiliation(s)
- Alberto Gatto
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Audrey Forest
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
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Kermi C, Aze A, Maiorano D. Preserving Genome Integrity During the Early Embryonic DNA Replication Cycles. Genes (Basel) 2019; 10:genes10050398. [PMID: 31137726 PMCID: PMC6563053 DOI: 10.3390/genes10050398] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
During the very early stages of embryonic development chromosome replication occurs under rather challenging conditions, including a very short cell cycle, absence of transcription, a relaxed DNA damage response and, in certain animal species, a highly contracted S-phase. This raises the puzzling question of how the genome can be faithfully replicated in such a peculiar metabolic context. Recent studies have provided new insights into this issue, and unveiled that embryos are prone to accumulate genetic and genomic alterations, most likely due to restricted cellular functions, in particular reduced DNA synthesis quality control. These findings may explain the low rate of successful development in mammals and the occurrence of diseases, such as abnormal developmental features and cancer. In this review, we will discuss recent findings in this field and put forward perspectives to further study this fascinating question.
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Affiliation(s)
- Chames Kermi
- Laboratoire Surveillance et Stabilité du Génome, Institut de Génétique Humaine, UMR9002, CNRS, Université de Montpellier, 34090 Montpellier, France.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
| | - Antoine Aze
- Laboratoire Surveillance et Stabilité du Génome, Institut de Génétique Humaine, UMR9002, CNRS, Université de Montpellier, 34090 Montpellier, France.
| | - Domenico Maiorano
- Laboratoire Surveillance et Stabilité du Génome, Institut de Génétique Humaine, UMR9002, CNRS, Université de Montpellier, 34090 Montpellier, France.
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Horn V, Triantafyllopoulou A. DNA damage signaling and polyploid macrophages in chronic inflammation. Curr Opin Immunol 2017; 50:55-63. [PMID: 29202328 DOI: 10.1016/j.coi.2017.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/30/2017] [Accepted: 11/17/2017] [Indexed: 01/01/2023]
Abstract
Whole genome duplications, an important step in cancer development, also occur in the macrophage lineage in disease: large multinucleated macrophages found within compact, ordered aggregates of immune cells, called granulomas, are a well-known histologic entity. Very recent work suggests that granuloma macrophages remarkably acquire epithelial cell features and the genotoxic stress response instructs granuloma macrophage genome duplications, suggesting that granuloma macrophages and pre-malignant epithelial cells may share common mechanisms of adaptation to chronic genotoxic stress. Exploring these mechanisms is key for a better understanding of the pathogenesis of chronic inflammatory diseases. Here we review the mechanisms of macrophage polyploidization, the role of DNA damage signaling in this process and the function of polyploid macrophages, with a focus on chronic inflammation.
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Affiliation(s)
- Veronika Horn
- Department of Rheumatology and Clinical Immunology, Charité University Medical Center, D-10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, D-79106 Freiburg, Germany
| | - Antigoni Triantafyllopoulou
- Department of Rheumatology and Clinical Immunology, Charité University Medical Center, D-10117 Berlin, Germany; Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, D-79106 Freiburg, Germany; German Rheumatism Research Center, A Leibniz Institute, D-10117 Berlin, Germany; Institute of Microbiology, Charité University Medical Center, D-12203 Berlin, Germany.
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