1
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Huang B, Peng X, Zhai X, Hu J, Chen J, Yang S, Huang Q, Deng E, Li H, Barakat TS, Chen J, Pei D, Fan X, Chambers I, Zhang M. Inhibition of HDAC activity directly reprograms murine embryonic stem cells to trophoblast stem cells. Dev Cell 2024:S1534-5807(24)00326-5. [PMID: 38823394 DOI: 10.1016/j.devcel.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/23/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Embryonic stem cells (ESCs) can differentiate into all cell types of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which is not fully understood. Here, we show that treating mouse ESCs with sodium butyrate (NaB) increases the population of 2C-like cells and enables direct reprogramming of ESCs into trophoblast stem cells (TSCs) without a transition through a 2C-like state. Mechanistically, NaB inhibits histone deacetylase activities in the LSD1-HDAC1/2 corepressor complex. This increases acetylation levels in the regulatory regions of both 2C- and TSC-specific genes, promoting their expression. In addition, NaB-treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and form deciduae in vivo. These results identify how epigenetics restrict the totipotent and trophectoderm fate in mouse ESCs.
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Affiliation(s)
- Boyan Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Xing Peng
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Xuzhao Zhai
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China; Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jie Hu
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Junyu Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China; School of Life Science, South China Normal University, Guangzhou 510005, China
| | - Suming Yang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Qingpei Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Enze Deng
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China
| | - Huanhuan Li
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510525, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510525, China
| | - Xiaoying Fan
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China.
| | - Ian Chambers
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, Scotland.
| | - Man Zhang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510005, China; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China.
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2
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Espinosa-Martínez M, Alcázar-Fabra M, Landeira D. The molecular basis of cell memory in mammals: The epigenetic cycle. SCIENCE ADVANCES 2024; 10:eadl3188. [PMID: 38416817 PMCID: PMC10901381 DOI: 10.1126/sciadv.adl3188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Cell memory refers to the capacity of cells to maintain their gene expression program once the initiating environmental signal has ceased. This exceptional feature is key during the formation of mammalian organisms, and it is believed to be in part mediated by epigenetic factors that can endorse cells with the landmarks required to maintain transcriptional programs upon cell duplication. Here, we review current literature analyzing the molecular basis of epigenetic memory in mammals, with a focus on the mechanisms by which transcriptionally repressive chromatin modifications such as methylation of DNA and histone H3 are propagated through mitotic cell divisions. The emerging picture suggests that cellular memory is supported by an epigenetic cycle in which reversible activities carried out by epigenetic regulators in coordination with cell cycle transition create a multiphasic system that can accommodate both maintenance of cell identity and cell differentiation in proliferating stem cell populations.
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Affiliation(s)
- Mencía Espinosa-Martínez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - María Alcázar-Fabra
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
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3
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Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. Bioessays 2024; 46:e2300163. [PMID: 38058121 DOI: 10.1002/bies.202300163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, "division of labor," and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.
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Affiliation(s)
- Dmitry E Koryakov
- Lab of Molecular Cytogenetics, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
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4
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Tam PLF, Cheung MF, Chan LY, Leung D. Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions. Nat Commun 2024; 15:15. [PMID: 38167730 PMCID: PMC10762014 DOI: 10.1038/s41467-023-44578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
SETDB1 is an essential histone methyltransferase that deposits histone H3 lysine 9 trimethylation (H3K9me3) to transcriptionally repress genes and repetitive elements. The function of differential H3K9me3 enrichment between cell-types remains unclear. Here, we demonstrate mutual exclusivity of H3K9me3 and CTCF across mouse tissues from different developmental timepoints. We analyze SETDB1 depleted cells and discover that H3K9me3 prevents aberrant CTCF binding independently of DNA methylation and H3K9me2. Such sites are enriched with SINE B2 retrotransposons. Moreover, analysis of higher-order genome architecture reveals that large chromatin structures including topologically associated domains and subnuclear compartments, remain intact in SETDB1 depleted cells. However, chromatin loops and local 3D interactions are disrupted, leading to transcriptional changes by modifying pre-existing chromatin landscapes. Specific genes with altered expression show differential interactions with dysregulated cis-regulatory elements. Collectively, we find that cell-type specific targets of SETDB1 maintain cellular identities by modulating CTCF binding, which shape nuclear architecture and transcriptomic networks.
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Affiliation(s)
- Phoebe Lut Fei Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Ming Fung Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Lu Yan Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China.
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China.
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5
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Dong L, Liao H, Zhao L, Wang J, Wang C, Wang B, Sun Y, Xu L, Xia Y, Ling S, Lou X, Qin J. A functional crosstalk between the H3K9 methylation writers and their reader HP1 in safeguarding embryonic stem cell identity. Stem Cell Reports 2023; 18:1775-1792. [PMID: 37703822 PMCID: PMC10545489 DOI: 10.1016/j.stemcr.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Histone H3 lysine 9 (H3K9) methylation, as a hallmark of heterochromatin, has a central role in cell lineage and fate determination. Although evidence of a cooperation between H3K9 methylation writers and their readers has started to emerge, their actual interplay remains elusive. Here, we show that loss of H3K9 methylation readers, the Hp1 family, causes reduced expression of H3K9 methyltransferases, and that this subsequently leads to the exit of embryonic stem cells (ESCs) from pluripotency and a reciprocal gain of lineage-specific characteristics. Importantly, the phenotypes of Hp1-null ESCs can be rescued by ectopic expression of Setdb1, Nanog, and Oct4. Furthermore, Setdb1 ablation results in loss of ESC identity, which is accompanied by a reduction in the expression of Hp1 genes. Together, our data support a model in which the safeguarding of ESC identity involves the cooperation between the H3K9 methylation writers and their readers.
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Affiliation(s)
- Lixia Dong
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Huaqi Liao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Linchun Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Jingnan Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Bowen Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Yanqi Sun
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Lijun Xu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China
| | - Yin Xia
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shizhang Ling
- The Translational Research Institute for Neurological Disorders, Department of Neurosurgery, The First Affiliated Hospital (Yijishan Hospital) of Wannan Medical College, Wannan Medical College, Wuhu, China.
| | - Xin Lou
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou 311100, China.
| | - Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China.
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6
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Bi S, Tu Z, Chen D, Zhang S. Histone modifications in embryo implantation and placentation: insights from mouse models. Front Endocrinol (Lausanne) 2023; 14:1229862. [PMID: 37600694 PMCID: PMC10436591 DOI: 10.3389/fendo.2023.1229862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
Embryo implantation and placentation play pivotal roles in pregnancy by facilitating crucial maternal-fetal interactions. These dynamic processes involve significant alterations in gene expression profiles within the endometrium and trophoblast lineages. Epigenetics regulatory mechanisms, such as DNA methylation, histone modification, chromatin remodeling, and microRNA expression, act as regulatory switches to modulate gene activity, and have been implicated in establishing a successful pregnancy. Exploring the alterations in these epigenetic modifications can provide valuable insights for the development of therapeutic strategies targeting complications related to pregnancy. However, our current understanding of these mechanisms during key gestational stages remains incomplete. This review focuses on recent advancements in the study of histone modifications during embryo implantation and placentation, while also highlighting future research directions in this field.
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Affiliation(s)
- Shilei Bi
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
| | - Zhaowei Tu
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
| | - Dunjin Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
| | - Shuang Zhang
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
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7
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Abstract
While epigenetic modifications of DNA and histones play main roles in gene transcription regulation, recently discovered post-transcriptional RNA modifications, known as epitranscriptomic modifications, have been found to have a profound impact on gene expression by regulating RNA stability, localization and decoding efficiency. Importantly, genetic variations or environmental perturbations of epitranscriptome modifiers (that is, writers, erasers and readers) are associated with obesity and metabolic diseases, such as type 2 diabetes. The epitranscriptome is closely coupled to epigenetic signalling, adding complexity to our understanding of gene expression in both health and disease. Moreover, the epitranscriptome in the parental generation can affect organismal phenotypes in the next generation. In this Review, we discuss the relationship between epitranscriptomic modifications and metabolic diseases, their relationship with the epigenome and possible therapeutic strategies.
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Affiliation(s)
- Yoshihiro Matsumura
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Fan-Yan Wei
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Japan
| | - Juro Sakai
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan.
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
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8
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Lin Y, Zhang F, Chen S, Zhu X, Jiao J, Zhang Y, Li Z, Lin J, Ma B, Chen M, Wang PY, Cui C. Binary Colloidal Crystals Promote Cardiac Differentiation of Human Pluripotent Stem Cells via Nuclear Accumulation of SETDB1. ACS NANO 2023; 17:3181-3193. [PMID: 36655945 PMCID: PMC9933589 DOI: 10.1021/acsnano.3c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Biophysical cues can facilitate the cardiac differentiation of human pluripotent stem cells (hPSCs), yet the mechanism is far from established. One of the binary colloidal crystals, composed of 5 μm Si and 400 nm poly(methyl methacrylate) particles named 5PM, has been applied as a substrate for hPSCs cultivation and cardiac differentiation. In this study, cell nucleus, cytoskeleton, and epigenetic states of human induced pluripotent stem cells on the 5PM were analyzed using atomic force microscopy, molecular biology assays, and the assay for transposase-accessible chromatin sequencing (ATAC-seq). Cells were more spherical with stiffer cell nuclei on the 5PM compared to the flat control. ATAC-seq revealed that chromatin accessibility decreased on the 5PM, caused by the increased entry of histone lysine methyltransferase SETDB1 into the cell nuclei and the amplified level of histone H3K9me3 modification. Reducing cytoskeleton tension using a ROCK inhibitor attenuated the nuclear accumulation of SETDB1 on the 5PM, indicating that the effect is cytoskeleton-dependent. In addition, the knockdown of SETDB1 reversed the promotive effects of the 5PM on cardiac differentiation, demonstrating that biophysical cue-induced cytoskeletal tension, cell nucleus deformation, and then SETDB1 accumulation are critical outside-in signal transformations in cardiac differentiation. Human embryonic stem cells showed similar results, indicating that the biophysical impact of the 5PM surfaces on cardiac differentiation could be universal. These findings contribute to our understanding of material-assistant hPSC differentiation, which benefits materiobiology and stem cell bioengineering.
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Affiliation(s)
- Yongping Lin
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
- Department
of Cardiology, The Affiliated Taizhou People’s Hospital of
Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou225300, Jiangsu, China
| | - Feng Zhang
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
| | - Shaojie Chen
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
| | - Xiyu Zhu
- Department
of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical
School, Nanjing210000, China
| | - Jincheng Jiao
- State
Key Laboratory of Bioelectronics, School of Biological Science and
Medical Engineering, Southeast University, Nanjing210000, Jiangsu, China
| | - Yike Zhang
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
| | - Zhaomin Li
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
| | - Jiao Lin
- Shenzhen
Key Laboratory of Biomimetic Materials and Cellular Immunomodulation,
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518000, Guangdong, China
| | - Biao Ma
- State
Key Laboratory of Bioelectronics, School of Biological Science and
Medical Engineering, Southeast University, Nanjing210000, Jiangsu, China
| | - Minglong Chen
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
- Department
of Cardiology, The Affiliated Taizhou People’s Hospital of
Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou225300, Jiangsu, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing210000, Jiangsu, China
| | - Peng-Yuan Wang
- Oujiang
Laboratory; Key Laboratory of Alzheimer’s Disease of Zhejiang
Province, Institute of Aging, Wenzhou Medical
University, Wenzhou325000, Zhejiang, China
| | - Chang Cui
- Department
of Cardiology, The First Affiliated Hospital
of Nanjing Medical University, Nanjing210000, Jiangsu, China
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9
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Li H, Sun J, Dong Y, Huang Y, Wu L, Xi C, Su Z, Xiao Y, Zhang C, Liang Y, Li Y, Lin Z, Shen L, Zuo Y, Abudureheman A, Yin J, Wang H, Kong X, Le R, Gao S, Zhang Y. Remodeling of H3K9me3 during the pluripotent to totipotent-like state transition. Stem Cell Reports 2023; 18:449-462. [PMID: 36638787 PMCID: PMC9968986 DOI: 10.1016/j.stemcr.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
Multiple chromatin modifiers associated with H3K9me3 play important roles in the transition from embryonic stem cells to 2-cell (2C)-like cells. However, it remains elusive how H3K9me3 is remodeled and its association with totipotency. Here, we integrated transcriptome and H3K9me3 profiles to conduct a detailed comparison of 2C embryos and 2C-like cells. Globally, H3K9me3 is highly preserved and H3K9me3 dynamics within the gene locus is not associated with gene expression change during 2C-like transition. Promoter-deposited H3K9me3 plays non-repressive roles in the activation of genes during 2C-like transition. In contrast, transposable elements, residing in the nearby regions of up-regulated genes, undergo extensive elimination of H3K9me3 and are tended to be induced in 2C-like transitions. Furthermore, a large fraction of trophoblast stem cell-specific enhancers undergo loss of H3K9me3 exclusively in MERVL+/Zscan4+ cells. Our study therefore reveals the unique H3K9me3 profiles of 2C-like cells, facilitating the further exploration of totipotency.
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Affiliation(s)
- Hu Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, China
| | - Jiatong Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yu Dong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixin Huang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chenxiang Xi
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongqu Su
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yihan Xiao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chuyu Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuwei Liang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yujun Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiyi Lin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lu Shen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixing Zuo
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Abuduwaili Abudureheman
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiangyin Kong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Yanping Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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10
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Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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11
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Levinsky AJ, McEdwards G, Sethna N, Currie MA. Targets of histone H3 lysine 9 methyltransferases. Front Cell Dev Biol 2022; 10:1026406. [PMID: 36568972 PMCID: PMC9768651 DOI: 10.3389/fcell.2022.1026406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Histone H3 lysine 9 di- and trimethylation are well-established marks of constitutively silenced heterochromatin domains found at repetitive DNA elements including pericentromeres, telomeres, and transposons. Loss of heterochromatin at these sites causes genomic instability in the form of aberrant DNA repair, chromosome segregation defects, replication stress, and transposition. H3K9 di- and trimethylation also regulate cell type-specific gene expression during development and form a barrier to cellular reprogramming. However, the role of H3K9 methyltransferases extends beyond histone methylation. There is a growing list of non-histone targets of H3K9 methyltransferases including transcription factors, steroid hormone receptors, histone modifying enzymes, and other chromatin regulatory proteins. Additionally, two classes of H3K9 methyltransferases modulate their own function through automethylation. Here we summarize the structure and function of mammalian H3K9 methyltransferases, their roles in genome regulation and constitutive heterochromatin, as well as the current repertoire of non-histone methylation targets including cases of automethylation.
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Affiliation(s)
- Aidan J. Levinsky
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Gregor McEdwards
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nasha Sethna
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Mark A. Currie
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada,*Correspondence: Mark A. Currie,
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12
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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 PMCID: PMC9485127 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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13
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Lee M, Oh JN, Choe GC, Kim SH, Choi KH, Lee DK, Jeong J, Lee CK. Changes in OCT4 expression play a crucial role in the lineage specification and proliferation of preimplantation porcine blastocysts. Cell Prolif 2022; 55:e13313. [PMID: 35883229 DOI: 10.1111/cpr.13313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVES Curiosity about the role of OCT4, a core transcription factor that maintains inner cell mass (ICM) formation during preimplantation embryogenesis and the pluripotent state in embryonic development, has long been an issue. OCT4 has a species-specific expression pattern in mammalian preimplantation embryogenesis and is known to play an essential role in ICM formation. However, there is a need to study new roles for OCT4-related pluripotency networks and second-cell fate decisions. MATERIALS AND METHODS To determine the functions of OCT4 in lineage specification and embryo proliferation, loss- and gain-of-function studies were performed on porcine parthenotes using microinjection. Then, we performed immunocytochemistry and quantitative real-time polymerase chain reaction (PCR) to examine the association of OCT4 with other lineage markers and its effect on downstream genes. RESULTS In OCT4-targeted late blastocysts, SOX2, NANOG, and SOX17 positive cells were decreased, and the total cell number of blastocysts was also decreased. According to real-time PCR analysis, NANOG, SOX17, and CDK4 were decreased in OCT4-targeted blastocysts, but trophoblast-related genes were increased. In OCT4-overexpressing blastocysts, SOX2 and NANOG positive cells increased, while SOX17 positive cells decreased, and while total cell number of blastocysts increased. As a result of real-time PCR analysis, the expression of SOX2, NANOG, and CDK4 was increased, but the expression of SOX17 was decreased. CONCLUSION Taken together, our results demonstrated that OCT4 leads pluripotency in porcine blastocysts and also plays an important role in ICM formation, secondary cell fate decision, and cell proliferation.
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Affiliation(s)
- Mingyun Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jong-Nam Oh
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Gyung Cheol Choe
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Seung-Hun Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kwang-Hwan Choi
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Dong-Kyung Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinsol Jeong
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
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14
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Warrier T, El Farran C, Zeng Y, Ho B, Bao Q, Zheng Z, Bi X, Ng HH, Ong D, Chu J, Sanyal A, Fullwood MJ, Collins J, Li H, Xu J, Loh YH. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Res 2022; 50:7326-7349. [PMID: 35776115 PMCID: PMC9303280 DOI: 10.1093/nar/gkac531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene 'islands' that drive differentiation to other lineages. The 'unearthing' of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.
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Affiliation(s)
- Tushar Warrier
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chadi El Farran
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Benedict Shao Quan Ho
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Qiuye Bao
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zi Hao Zheng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Xuezhi Bi
- Proteomics Group, Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Infectious Disease Translational Research Programme, National University of Singapore, Singapore 117597, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Melissa Jane Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - James J Collins
- Howard Hughes Medical Institute, Boston, MA 02114, USA
- Institute for Medical Engineering and Science Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 MedicalDrive, Singapore 117456, Singapore
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15
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Tiana M, Lopez-Jimenez E, de Aja JS, Barral A, Victorino J, Badia-Careaga C, Rollan I, Rouco R, Santos E, Sanchez-Iranzo H, Acemel RD, Torroja C, Adan J, Andres-Leon E, Gomez-Skarmeta JL, Giovinazzo G, Sanchez-Cabo F, Manzanares M. Pluripotency factors regulate the onset of Hox cluster activation in the early embryo. SCIENCE ADVANCES 2022; 8:eabo3583. [PMID: 35857513 PMCID: PMC9286507 DOI: 10.1126/sciadv.abo3583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pluripotent cells are a transient population of the mammalian embryo dependent on transcription factors, such as OCT4 and NANOG, which maintain pluripotency while suppressing lineage specification. However, these factors are also expressed during early phases of differentiation, and their role in the transition from pluripotency to lineage specification is largely unknown. We found that pluripotency factors play a dual role in regulating key lineage specifiers, initially repressing their expression and later being required for their proper activation. We show that Oct4 is necessary for activation of HoxB genes during differentiation of embryonic stem cells and in the embryo. In addition, we show that the HoxB cluster is coordinately regulated by OCT4 binding sites located at the 3' end of the cluster. Our results show that core pluripotency factors are not limited to maintaining the precommitted epiblast but are also necessary for the proper deployment of subsequent developmental programs.
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Affiliation(s)
- María Tiana
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Elena Lopez-Jimenez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Julio Sainz de Aja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Jesus Victorino
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Claudio Badia-Careaga
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Isabel Rollan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Raquel Rouco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Elisa Santos
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Hector Sanchez-Iranzo
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO, 41013 Seville, Spain
| | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Adan
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Eduardo Andres-Leon
- Instituto de Parasitología y Biomedicina López Neyra (IPBL), CSIC, 18100 Granada, Spain
| | | | - Giovanna Giovinazzo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Fatima Sanchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, 28029 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
- Corresponding author.
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16
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Yu H, Chen M, Hu Y, Ou S, Yu X, Liang S, Li N, Yang M, Kong X, Sun C, Jia S, Zhang Q, Liu L, Hurst LD, Li R, Wang W, Wang J. Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development. Cell Stem Cell 2022; 29:1031-1050.e12. [PMID: 35803225 DOI: 10.1016/j.stem.2022.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development remains, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, promoting the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prevent pluripotent transcription factors from binding to hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in the ICM is associated with higher transcription of DNA repair genes, when compared with naive human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulation for early development has evolved in mammals.
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Affiliation(s)
- Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yuanlang Hu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Songbang Ou
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingzhu Yang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qingxue Zhang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenjun Wang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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17
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Ueshima S, Fang J. Histone H3K9 methyltransferase SETDB1 augments invadopodia formation to promote tumor metastasis. Oncogene 2022; 41:3370-3380. [PMID: 35546351 PMCID: PMC9801494 DOI: 10.1038/s41388-022-02345-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 01/04/2023]
Abstract
Non-small cell lung cancer (NSCLC) is one of leading causes of cancer-related mortality worldwide, which harbors various accumulated genetic and epigenetic abnormalities. Histone methyltransferase SETDB1 is a pivotal epigenetic regulator whose focal amplification and upregulation are commonly detected in NSCLC. However, molecular mechanisms underlying the pro-oncogenic function of SETDB1 remain poorly characterized. Here, we demonstrate that SETDB1 augments the migration and invasion capabilities of NSCLC cells by reinforcing invadopodia formation and mediated ECM degradation. At the molecular level, SETDB1 suppresses the expression of FOXA2, a crucial tumor and metastasis suppressor via coordinated epigenetic mechanisms - SETDB1 not only catalyzes histone H3K9 methylation on FOXA2 genomic locus, but also recruits DNMT3A to regulate DNA methylation on CpG island. Consequently, depletion of Setdb1 in murine lung adenocarcinoma cells completely abolished their full and spontaneous metastatic capabilities in mouse xenograft models. These findings together establish the pro-metastasis activity of SETDB1 in NSCLC and elucidate the underlying cellular and molecular mechanisms.
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Affiliation(s)
- Shuhei Ueshima
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jia Fang
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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18
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Moon HJ, Lee NY, Do EK, Lee SY, Park GT, Lim JK, Seo JK, Kim JH. Kap1 Regulates the Stability of Lin28A in Embryonic Stem Cells. Stem Cells 2022; 40:385-396. [PMID: 35262736 DOI: 10.1093/stmcls/sxac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/24/2022] [Indexed: 11/14/2022]
Abstract
Lin28A is an RNA-binding protein that controls mammalian development and maintenance of the pluripotency of embryonic stem cells (ESCs) via regulating the processing of the microRNA let-7. Lin28A is highly expressed in ESCs, and ectopic expression of this protein facilitates reprogramming of somatic cells to induced pluripotent stem cells. However, the mechanisms underlying the post-translational regulation of Lin28A protein stability in ESCs remain unclear. In the present study, we identified Kap1 (KRAB-associated protein 1) as a novel Lin28A-binding protein using affinity purification and mass spectrometry. Kap1 specifically interacted with the N-terminal region of Lin28A through its coiled-coil domain. Kap1 overexpression significantly attenuated Lin28A ubiquitination and increased its stability. However, small interfering RNA-mediated knockdown of Kap1 promoted the ubiquitination of Lin28A, leading to its proteasomal degradation. Trim71, an E3 ubiquitin ligase, induced Lin28A degradation and Kap1 knockdown accelerated the Trim71-dependent degradation of Lin28A. Mutation of the lysine 177 residue of Lin28A to arginine abrogated the ubiquitination and degradation of Lin28A which were accelerated by Kap1 silencing. Moreover, Kap1 overexpression led to the accumulation of Lin28A in the cytoplasm, but not in the nucleus, and reduced the levels of let-7 subtypes. These results suggest that Kap1 plays a key role in regulation of the stability of Lin28A by modulating the Trim71-mediated ubiquitination and subsequent degradation of Lin28A, thus playing a pivotal role in the regulation of ESC self-renewal and pluripotency.
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Affiliation(s)
- Hye Ji Moon
- Gene & Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Republic of Korea.,Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Na Yeon Lee
- Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Eun Kyoung Do
- Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Seo Yul Lee
- Gene & Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Republic of Korea.,Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Gyu Tae Park
- Gene & Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Republic of Korea.,Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Jae Kyong Lim
- Gene & Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Republic of Korea.,Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Jeong Kon Seo
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jae Ho Kim
- Gene & Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Republic of Korea.,Department of Physiology, School of Medicine, Pusan National University, Yangsan, Republic of Korea
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19
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Barral A, Pozo G, Ducrot L, Papadopoulos GL, Sauzet S, Oldfield AJ, Cavalli G, Déjardin J. SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers. Mol Cell 2022; 82:816-832.e12. [PMID: 35081363 PMCID: PMC8860380 DOI: 10.1016/j.molcel.2021.12.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/17/2022]
Abstract
Gene silencing by heterochromatin plays a crucial role in cell identity. Here, we characterize the localization, the biogenesis, and the function of an atypical heterochromatin, which is simultaneously enriched in the typical H3K9me3 mark and in H3K36me3, a histone mark usually associated with gene expression. We identified thousands of dual regions in mouse embryonic stem (ES) cells that rely on the histone methyltransferases SET domain bifurcated 1 (SETDB1) and nuclear set domain (NSD)-containing proteins to generate H3K9me3 and H3K36me3, respectively. Upon SETDB1 removal, dual domains lose both marks, gain signatures of active enhancers, and come into contact with upregulated genes, suggesting that it might be an important pathway by which genes are controlled by heterochromatin. In differentiated tissues, a subset of these dual domains is destabilized and becomes enriched in active enhancer marks, providing a mechanistic insight into the involvement of heterochromatin in the maintenance of cell identity. H3K9me3 and H3K36me3 dual domains form on thousands of regions in ES cells Dual domains depend on SETDB1 and NSD enzymes Most upregulated genes in Setdb1 KO cells are not normally heterochromatinized Dual domains become enhancers for these genes upon Setdb1 loss
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20
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Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
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Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
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21
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Somatic Reprogramming-Above and Beyond Pluripotency. Cells 2021; 10:cells10112888. [PMID: 34831113 PMCID: PMC8616127 DOI: 10.3390/cells10112888] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells, having long been considered the fountain of youth, have caught the attention of many researchers from diverse backgrounds due to their capacity for unlimited self-renewal and potential to differentiate into all cell types. Over the past 15 years, the advanced development of induced pluripotent stem cells (iPSCs) has displayed an unparalleled potential for regenerative medicine, cell-based therapies, modeling human diseases in culture, and drug discovery. The transcription factor quartet (Oct4, Sox2, Klf4, and c-Myc) reprograms highly differentiated somatic cells back to a pluripotent state recapitulated embryonic stem cells (ESCs) in different aspects, including gene expression profile, epigenetic signature, and functional pluripotency. With the prior fruitful studies in SCNT and cell fusion experiments, iPSC finds its place and implicates that the differentiated somatic epigenome retains plasticity for re-gaining the pluripotency and further stretchability to reach a totipotency-like state. These achievements have revolutionized the concept and created a new avenue in biomedical sciences for clinical applications. With the advent of 15 years’ progress-making after iPSC discovery, this review is focused on how the current concept is established by revisiting those essential landmark studies and summarizing its current biomedical applications status to facilitate the new era entry of regenerative therapy.
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22
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Vojtek M, Chambers I. Loss of Resf1 reduces the efficiency of embryonic stem cell self-renewal and germline entry. Life Sci Alliance 2021; 4:4/12/e202101190. [PMID: 34607919 PMCID: PMC8500223 DOI: 10.26508/lsa.202101190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
RESF1 supports ESC self-renewal by raising expression of transmembrane LIF receptor and key pluripotency transcription factors and increases in vitro primordial germ cell differentiation efficiency. Retroelement silencing factor 1 (RESF1) interacts with the key regulators of mouse embryonic stem cells (ESCs) OCT4 and NANOG, and its absence results in sterility of mice. However, the function of RESF1 in ESCs and germline specification is poorly understood. In this study, we used Resf1 knockout cell lines to determine the requirements of RESF1 for ESC self-renewal and for in vitro specification of ESCs into primordial germ cell-like cells (PGCLCs). We found that deletion of Resf1 in ESCs cultured in serum and LIF reduces self-renewal potential, whereas episomal expression of RESF1 has a modest positive effect on ESC self-renewal. In addition, RESF1 is not required for the capacity of NANOG and its downstream target ESRRB to drive self-renewal in the absence of LIF. However, Resf1 deletion reduces the efficiency of PGCLC differentiation in vitro. These results identify Resf1 as a novel player in the regulation of pluripotent stem cells and germ cell specification.
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Affiliation(s)
- Matúš Vojtek
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, Scotland.,Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Ian Chambers
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, Scotland .,Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
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23
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Karasek C, Ashry M, Driscoll CS, Knott JG. A tale of two cell-fates: role of the Hippo signaling pathway and transcription factors in early lineage formation in mouse preimplantation embryos. Mol Hum Reprod 2021; 26:653-664. [PMID: 32647873 PMCID: PMC7473788 DOI: 10.1093/molehr/gaaa052] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/18/2020] [Indexed: 12/26/2022] Open
Abstract
In mammals, the first cell-fate decision occurs during preimplantation embryo development when the inner cell mass (ICM) and trophectoderm (TE) lineages are established. The ICM develops into the embryo proper, while the TE lineage forms the placenta. The underlying molecular mechanisms that govern lineage formation involve cell-to-cell interactions, cell polarization, cell signaling and transcriptional regulation. In this review, we will discuss the current understanding regarding the cellular and molecular events that regulate lineage formation in mouse preimplantation embryos with an emphasis on cell polarity and the Hippo signaling pathway. Moreover, we will provide an overview on some of the molecular tools that are used to manipulate the Hippo pathway and study cell-fate decisions in early embryos. Lastly, we will provide exciting future perspectives on transcriptional regulatory mechanisms that modulate the activity of the Hippo pathway in preimplantation embryos to ensure robust lineage segregation.
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Affiliation(s)
- Challis Karasek
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Mohamed Ashry
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Chad S Driscoll
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Jason G Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
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24
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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25
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Guo SM, Mei NH, Yang J, Zhou LQ. Transcription factor OTX2 silences the expression of cleavage embryo genes and transposable elements. J Reprod Dev 2021; 67:223-228. [PMID: 33896883 PMCID: PMC8238675 DOI: 10.1262/jrd.2021-007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/28/2021] [Indexed: 11/20/2022] Open
Abstract
Upon mammalian fertilization, zygotic genome activation (ZGA) and activation of transposable elements (TEs) occur in early embryos to establish totipotency and support embryogenesis. However, the molecular mechanisms controlling the expression of these genes in mammals remain poorly understood. The 2-cell-like population of mouse embryonic stem cells (mESCs) mimics cleavage-stage embryos with transient Dux activation. In this study, we demonstrated that deficiency of the transcription factor OTX2 stimulates the expression of ZGA genes in mESCs. Further analysis revealed that OTX2 is incorporated at the Dux locus with corepressors for transcriptional inhibition. We also found that OTX2 associates with TEs and silences the subtypes of TEs. Therefore, OTX2 protein plays an important role in ZGA and TE expression in mESCs to orchestrate the transcriptional network.
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Affiliation(s)
- Shi-Meng Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Ning-Hua Mei
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Jing Yang
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
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26
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Dahlet T, Truss M, Frede U, Al Adhami H, Bardet AF, Dumas M, Vallet J, Chicher J, Hammann P, Kottnik S, Hansen P, Luz U, Alvarez G, Auclair G, Hecht J, Robinson PN, Hagemeier C, Weber M. E2F6 initiates stable epigenetic silencing of germline genes during embryonic development. Nat Commun 2021; 12:3582. [PMID: 34117224 PMCID: PMC8195999 DOI: 10.1038/s41467-021-23596-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development. DNA methylation targets CpG island promoters of germline genes to repress their expression in mouse somatic cells. Here the authors show that a transcription factor E2F6 is required to target CpG island DNA methylation and epigenetic silencing to germline genes during early mouse development.
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Affiliation(s)
- Thomas Dahlet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Matthias Truss
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Ute Frede
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Anaïs F Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, Strasbourg, France
| | - Sarah Kottnik
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Hansen
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Uschi Luz
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gonzalo Alvarez
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ghislain Auclair
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Jochen Hecht
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany.,Centre for Genomic Regulation, Barcelona, Spain
| | - Peter N Robinson
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany.,Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christian Hagemeier
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France.
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27
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Wang L, Chakraborty D, Iqbal K, Soares MJ. SUV39H2 controls trophoblast stem cell fate. Biochim Biophys Acta Gen Subj 2021; 1865:129867. [PMID: 33556426 PMCID: PMC8052280 DOI: 10.1016/j.bbagen.2021.129867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/31/2020] [Accepted: 02/01/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND The placenta is formed by the coordinated expansion and differentiation of trophoblast stem (TS) cells along a multi-lineage pathway. Dynamic regulation of histone 3 lysine 9 (H3K9) methylation is pivotal to cell differentiation for many cell lineages, but little is known about its involvement in trophoblast cell development. METHODS Expression of H3K9 methyltransferases was surveyed in rat TS cells maintained in the stem state and following differentiation. The role of suppressor of variegation 3-9 homolog 2 (SUV39H2) in the regulation of trophoblast cell lineage development was investigated using a loss-of-function approach in rat TS cells and ex vivo cultured rat blastocysts. RESULTS Among the twelve-known H3K9 methyltransferases, only SUV39H2 exhibited robust differential expression in stem versus differentiated TS cells. SUV39H2 transcript and protein expression were high in the stem state and declined as TS cells differentiated. Disruption of SUV39H2 expression in TS cells led to an arrest in TS cell proliferation and activation of trophoblast cell differentiation. SUV39H2 regulated H3K9 methylation status at loci exhibiting differentiation-dependent gene expression. Analyses of SUV39H2 on ex vivo rat blastocyst development supported its role in regulating TS cell expansion and differentiation. We further identified SUV39H2 as a downstream target of caudal type homeobox 2, a master regulator of trophoblast lineage development. CONCLUSIONS Our findings indicate that SUV39H2 contributes to the maintenance of TS cells and restrains trophoblast cell differentiation. GENERAL SIGNIFICANCE SUV39H2 serves as a contributor to the epigenetic regulation of hemochorial placental development.
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Affiliation(s)
- Lei Wang
- Institute for Reproduction and Perinatal Research, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Damayanti Chakraborty
- Institute for Reproduction and Perinatal Research, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Khursheed Iqbal
- Institute for Reproduction and Perinatal Research, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Michael J Soares
- Institute for Reproduction and Perinatal Research, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States of America; Departments of Pediatrics and Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, United States of America; Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy, Kansas City, MO, United States of America.
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28
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Zhang J, Matsumura Y, Kano Y, Yoshida A, Kawamura T, Hirakawa H, Inagaki T, Tanaka T, Kimura H, Yanagi S, Fukami K, Doi T, Osborne TF, Kodama T, Aburatani H, Sakai J. Ubiquitination-dependent and -independent repression of target genes by SETDB1 reveal a context-dependent role for its methyltransferase activity during adipogenesis. Genes Cells 2021; 26:513-529. [PMID: 33971063 DOI: 10.1111/gtc.12868] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The lysine methyltransferase SETDB1, an enzyme responsible for methylation of histone H3 at lysine 9, plays a key role in H3K9 tri-methylation-dependent silencing of endogenous retroviruses and developmental genes. Recent studies have shown that ubiquitination of human SETDB1 complements its catalytic activity and the silencing of endogenous retroviruses in human embryonic stem cells. However, it is not known whether SETDB1 ubiquitination is essential for its other major role in epigenetic silencing of developmental gene programs. We previously showed that SETDB1 contributes to the formation of H3K4/H3K9me3 bivalent chromatin domains that keep adipogenic Cebpa and Pparg genes in a poised state for activation and restricts the differentiation potential of pre-adipocytes. Here, we show that ubiquitin-resistant K885A mutant of SETDB1 represses adipogenic genes and inhibits pre-adipocyte differentiation similar to wild-type SETDB1. We show this was due to a compensation mechanism for H3K9me3 chromatin modifications on the Cebpa locus by other H3K9 methyltransferases Suv39H1 and Suv39H2. In contrast, the K885A mutant did not repress other SETDB1 target genes such as Tril and Gas6 suggesting SETDB1 represses its target genes by two mechanisms; one that requires its ubiquitination and another that still requires SETDB1 but not its enzyme activity.
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Affiliation(s)
- Ji Zhang
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihiro Matsumura
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Yuka Kano
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Laboratory of Molecular Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Ayano Yoshida
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takeshi Kawamura
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Proteomics Laboratory, Isotope Science Center, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Hirakawa
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Department of Physiology and Cell Biology, Tokyo Medical and Dental University (TMDU), Graduate School, Tokyo, Japan
| | - Takeshi Inagaki
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Toshiya Tanaka
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kiyoko Fukami
- Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Timothy F Osborne
- Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, and Medicine in the Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, St. Petersburg, FL, USA
| | - Tatsuhiko Kodama
- Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
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29
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Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells. Sci Rep 2021; 11:884. [PMID: 33441614 PMCID: PMC7806742 DOI: 10.1038/s41598-020-79601-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022] Open
Abstract
Trophoblast stem cell (TSC) is crucial to the formation of placenta in mammals. Histone demethylase JMJD2 (also known as KDM4) family proteins have been previously shown to support self-renewal and differentiation of stem cells. However, their roles in the context of the trophoblast lineage remain unclear. Here, we find that knockdown of Jmjd2b resulted in differentiation of TSCs, suggesting an indispensable role of JMJD2B/KDM4B in maintaining the stemness. Through the integration of transcriptome and ChIP-seq profiling data, we show that JMJD2B is associated with a loss of H3K36me3 in a subset of embryonic lineage genes which are marked by H3K9me3 for stable repression. By characterizing the JMJD2B binding motifs and other transcription factor binding datasets, we discover that JMJD2B forms a protein complex with AP-2 family transcription factor TFAP2C and histone demethylase LSD1. The JMJD2B-TFAP2C-LSD1 complex predominantly occupies active gene promoters, whereas the TFAP2C-LSD1 complex is located at putative enhancers, suggesting that these proteins mediate enhancer-promoter interaction for gene regulation. We conclude that JMJD2B is vital to the TSC transcriptional program and safeguards the trophoblast cell fate via distinctive protein interactors and epigenetic targets.
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30
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SETDB1-Mediated Cell Fate Transition between 2C-Like and Pluripotent States. Cell Rep 2021; 30:25-36.e6. [PMID: 31914391 DOI: 10.1016/j.celrep.2019.12.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/29/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022] Open
Abstract
Known as a histone H3K9 methyltransferase, SETDB1 is essential for embryonic development and pluripotent inner cell mass (ICM) establishment. However, its function in pluripotency regulation remains elusive. In this study, we find that under the "ground state" of pluripotency with two inhibitors (2i) of the MEK and GSK3 pathways, Setdb1-knockout fails to induce trophectoderm (TE) differentiation as in serum/LIF (SL), indicating that TE fate restriction is not the direct target of SETDB1. In both conditions, Setdb1-knockout activates a group of genes targeted by SETDB1-mediated H3K9 methylation, including Dux. Notably, Dux is indispensable for the reactivation of 2C-like state genes upon Setdb1 deficiency, delineating the mechanistic role of SETDB1 in totipotency restriction. Furthermore, Setdb1-null ESCs maintain pluripotent marker (e.g., Nanog) expression in the 2i condition. This "ground state" Setdb1-null population undergoes rapid cell death by activating Ripk3 and, subsequently, RIPK1/RIPK3-dependent necroptosis. These results reveal the essential role of Setdb1 between totipotency and pluripotency transition.
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31
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Cheng EC, Hsieh CL, Liu N, Wang J, Zhong M, Chen T, Li E, Lin H. The Essential Function of SETDB1 in Homologous Chromosome Pairing and Synapsis during Meiosis. Cell Rep 2021; 34:108575. [PMID: 33406415 DOI: 10.1016/j.celrep.2020.108575] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/03/2020] [Accepted: 12/08/2020] [Indexed: 12/28/2022] Open
Abstract
SETDB1 is a histone-lysine N-methyltransferase critical for germline development. However, its function in early meiotic prophase I remains unknown. Here, we report that Setdb1 null spermatocytes display aberrant centromere clustering during leptotene, bouquet formation during zygotene, and subsequent failure in pairing and synapsis of homologous chromosomes, as well as compromised meiotic silencing of unsynapsed chromatin, which leads to meiotic arrest before pachytene and apoptosis of spermatocytes. H3K9me3 is enriched in centromeric or pericentromeric regions and is present in many sites throughout the genome, with a subset changed in the Setdb1 mutant. These observations indicate that SETDB1-mediated H3K9me3 is essential for the bivalent formation in early meiosis. Transcriptome analysis reveals the function of SETDB1 in repressing transposons and transposon-proximal genes and in regulating meiotic and somatic lineage genes. These findings highlight a mechanism in which SETDB1-mediated H3K9me3 during early meiosis ensures the formation of homologous bivalents and survival of spermatocytes.
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Affiliation(s)
- Ee-Chun Cheng
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chia-Ling Hsieh
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Na Liu
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jianquan Wang
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mei Zhong
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - En Li
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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32
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Shibata S, Kobayashi EH, Kobayashi N, Oike A, Okae H, Arima T. Unique features and emerging in vitro models of human placental development. Reprod Med Biol 2020; 19:301-313. [PMID: 33071632 PMCID: PMC7542016 DOI: 10.1002/rmb2.12347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
Background The placenta is an essential organ for the normal development of mammalian fetuses. Most of our knowledge on the molecular mechanisms of placental development has come from the analyses of mice, especially histopathological examination of knockout mice. Choriocarcinoma and immortalized cell lines have also been used for basic research on the human placenta. However, these cells are quite different from normal trophoblast cells. Methods In this review, we first provide an overview of mouse and human placental development with particular focus on the differences in the anatomy, transcription factor networks, and epigenetic characteristics between these species. Next, we discuss pregnancy complications associated with abnormal placentation. Finally, we introduce emerging in vitro models to study the human placenta, including human trophoblast stem (TS) cells, trophoblast and endometrium organoids, and artificial embryos. Main findings The placental structure and development differ greatly between humans and mice. The recent establishment of human TS cells and trophoblast and endometrial organoids enhances our understanding of the mechanisms underlying human placental development. Conclusion These in vitro models will greatly advance our understanding of human placental development and potentially contribute to the elucidation of the causes of infertility and other pregnancy complications.
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Affiliation(s)
- Shun Shibata
- Department of Informative Genetics Tohoku University Graduate School of Medicine Sendai Japan
| | - Eri H Kobayashi
- Department of Informative Genetics Tohoku University Graduate School of Medicine Sendai Japan
| | - Norio Kobayashi
- Department of Informative Genetics Tohoku University Graduate School of Medicine Sendai Japan
| | - Akira Oike
- Department of Informative Genetics Tohoku University Graduate School of Medicine Sendai Japan
| | - Hiroaki Okae
- Department of Informative Genetics Tohoku University Graduate School of Medicine Sendai Japan
| | - Takahiro Arima
- Department of Informative Genetics Tohoku University Graduate School of Medicine Sendai Japan
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33
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Ashry M, Rajput SK, Folger JK, Yang C, Knott JG, Smith GW. Follistatin treatment modifies DNA methylation of the CDX2 gene in bovine preimplantation embryos. Mol Reprod Dev 2020; 87:998-1008. [PMID: 32776625 PMCID: PMC7670970 DOI: 10.1002/mrd.23409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/20/2020] [Accepted: 07/20/2020] [Indexed: 01/01/2023]
Abstract
CDX2 plays a crucial role in the formation and maintenance of the trophectoderm epithelium in preimplantation embryos. Follistatin supplementation during the first 72 hr of in vitro culture triggers a significant increase in blastocyst rates, CDX2 expression, and trophectoderm cell numbers. However, the underlying epigenetic mechanisms by which follistatin upregulates CDX2 expression are not known. Here, we investigated whether stimulatory effects of follistatin are linked to alterations in DNA methylation within key regulatory regions of the CDX2 gene. In vitro-fertilized (IVF) zygotes were cultured with or without 10 ng/ml of recombinant human follistatin for 72 hr, then cultured without follistatin until Day 7. The bisulfite-sequencing analysis revealed differential methylation (DM) at specific CpG sites within the CDX2 promoter and intron 1 following follistatin treatment. These DM CpG sites include five hypomethylated sites at positions -1384, -1283, -297, -163, and -23, and four hypermethylated sites at positions -1501, -250, -243, and +20 in the promoter region. There were five hypomethylated sites at positions +3060, +3105, +3219, +3270, and +3545 in intron 1. Analysis of transcription factor binding sites using MatInspector combined with a literature search revealed a potential association between differentially methylated CpG sites and putative binding sites for key transcription factors involved in regulating CDX2 expression. The hypomethylated sites are putative binding sites for FXR, STAF, OCT1, KLF, AP2 family, and P53 protein, whereas the hypermethylated sites are putative binding sites for NRSF. Collectively, our results suggest that follistatin may increase CDX2 expression in early bovine embryos, at least in part, by modulating DNA methylation at key regulatory regions.
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Affiliation(s)
- Mohamed Ashry
- Laboratory of Mammalian Reproductive Biology and Genomics, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Sandeep K. Rajput
- Laboratory of Mammalian Reproductive Biology and Genomics, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Fertility Labs of Colorado, CCRM, Lone Tree, Colorado
| | - Joseph K. Folger
- Laboratory of Mammalian Reproductive Biology and Genomics, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Chunyan Yang
- Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, China
| | - Jason G. Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - George W. Smith
- Laboratory of Mammalian Reproductive Biology and Genomics, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
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Ogawa S, Fukuda A, Matsumoto Y, Hanyu Y, Sono M, Fukunaga Y, Masuda T, Araki O, Nagao M, Yoshikawa T, Goto N, Hiramatsu Y, Tsuda M, Maruno T, Nakanishi Y, Hussein MS, Tsuruyama T, Takaori K, Uemoto S, Seno H. SETDB1 Inhibits p53-Mediated Apoptosis and Is Required for Formation of Pancreatic Ductal Adenocarcinomas in Mice. Gastroenterology 2020; 159:682-696.e13. [PMID: 32360551 DOI: 10.1053/j.gastro.2020.04.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND & AIMS SETDB1, a histone methyltransferase that trimethylates histone H3 on lysine 9, promotes development of several tumor types. We investigated whether SETDB1 contributes to development of pancreatic ductal adenocarcinoma (PDAC). METHODS We performed studies with Ptf1aCre; KrasG12D; Setdb1f/f, Ptf1aCre; KrasG12D; Trp53f/+; Setdb1f/f, and Ptf1aCre; KrasG12D; Trp53f/f; Setdb1f/f mice to investigate the effects of disruption of Setdb1 in mice with activated KRAS-induced pancreatic tumorigenesis, with heterozygous or homozygous disruption of Trp53. We performed microarray analyses of whole-pancreas tissues from Ptf1aCre; KrasG12D; Setdb1f/f, and Ptf1aCre; KrasG12D mice and compared their gene expression patterns. Chromatin immunoprecipitation assays were performed using acinar cells isolated from pancreata with and without disruption of Setdb1. We used human PDAC cells for SETDB1 knockdown and inhibitor experiments. RESULTS Loss of SETDB1 from pancreas accelerated formation of premalignant lesions in mice with pancreata that express activated KRAS. Microarray analysis revealed up-regulated expression of genes in the apoptotic pathway and genes regulated by p53 in SETDB1-deficient pancreata. Deletion of Setdb1 from pancreas prevented formation of PDACs, concomitant with increased apoptosis and up-regulated expression of Trp53 in mice heterozygous for disruption of Trp53. In contrast, pancreata of mice with homozygous disruption of Trp53 had no increased apoptosis, and PDACs developed. Chromatin immunoprecipitation revealed that SETDB1 bound to the Trp53 promoter to regulate its expression. Expression of an inactivated form of SETDB1 in human PDAC cells with wild-type TP53 resulted in TP53-induced apoptosis. CONCLUSIONS We found that the histone methyltransferase SETDB1 is required for development of PDACs, induced by activated KRAS, in mice. SETDB1 inhibits apoptosis by regulating expression of p53. SETDB1 might be a therapeutic target for PDACs that retain p53 function.
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Affiliation(s)
- Satoshi Ogawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akihisa Fukuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Yoshihide Matsumoto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuta Hanyu
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Makoto Sono
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuichi Fukunaga
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Drug Discovery Medicine, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonori Masuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Osamu Araki
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Munemasa Nagao
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takaaki Yoshikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norihiro Goto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yukiko Hiramatsu
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Motoyuki Tsuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahisa Maruno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mohammed S Hussein
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Internal Medicine, Al-Azhar University, Cairo, Egypt
| | | | - Kyoichi Takaori
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shinji Uemoto
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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35
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Patra SK. Roles of OCT4 in pathways of embryonic development and cancer progression. Mech Ageing Dev 2020; 189:111286. [PMID: 32531293 DOI: 10.1016/j.mad.2020.111286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 06/06/2020] [Indexed: 12/11/2022]
Abstract
Somatic cells may be reprogrammed to pluripotent state by ectopic expression of certain transcription factors; namely, OCT4, SOX2, KLF4 and c-MYC. However, the molecular and cellular mechanisms are not adequately understood, especially for human embryonic development. Studies during the last five years implicated importance of OCT4 in human zygotic genome activation (ZGA), patterns of OCT4 protein folding and role of specialized sequences in binding to DNA for modulation of gene expression during development. Epigenetic modulation of OCT4 gene and post translational modifications of OCT4 protein activity in the context of multiple cancers are important issues. A consensus is emerging that chromatin organization and epigenetic landscape play crucial roles for the interactions of transcription factors, including OCT4 with the promoters and/or regulatory sequences of genes associated with human embryonic development (ZGA through lineage specification) and that when the epigenome niche is deregulated OCT4 helps in cancer progression, and how OCT4 silencing in somatic cells of adult organisms may impact ageing.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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36
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Fathi Maroufi N, Hasegawa K, Vahedian V, Nazari Soltan Ahmad S, Zarebkohan A, Miresmaeili Mazrakhondi SA, Hosseini V, Rahbarghazi R. A glimpse into molecular mechanisms of embryonic stem cells pluripotency: Current status and future perspective. J Cell Physiol 2020; 235:6377-6392. [DOI: 10.1002/jcp.29616] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Nazila Fathi Maroufi
- Stem Cell and Regenerative Medicine InstituteTabriz University of Medical Sciences Tabriz Iran
- Student Research CommitteeTabriz University of Medical Sciences Tabriz Iran
- Department of Biochemistry and Clinical Laboratories, Faculty of MedicineTabriz University of Medical Sciences Tabriz Iran
| | - Kouichi Hasegawa
- Institute for Integrated Cell‐Material Sciences, Institute for Advanced StudyKyoto University Kyoto Japan
| | - Vahid Vahedian
- Department of Medical Laboratory Sciences, Faculty of MedicineIslamic Azad University Sari Iran
- Clinical Laboratory Medicine DepartmentRofeydeh Hospital University of Social Welfare and Rehabilitation Science Tehran Iran
| | - Saeed Nazari Soltan Ahmad
- Department of Biochemistry and Clinical Laboratories, Faculty of MedicineTabriz University of Medical Sciences Tabriz Iran
| | - Amir Zarebkohan
- Department of Medical Nanotechnology, Faculty of Advanced Medical SciencesTabriz University of Medical Sciences Tabriz Iran
| | | | - Vahid Hosseini
- Department of Biochemistry and Clinical Laboratories, Faculty of MedicineTabriz University of Medical Sciences Tabriz Iran
- Tuberculosis and Lung Disease Research CenterTabriz University of Medical Sciences Tabriz Iran
| | - Reza Rahbarghazi
- Tuberculosis and Lung Disease Research CenterTabriz University of Medical Sciences Tabriz Iran
- Department of Applied Cell Sciences, Faculty of Advanced Medical SciencesTabriz University of Medical Sciences Tabriz Iran
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37
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Hansel, Gretel, and the Consequences of Failing to Remove Histone Methylation Breadcrumbs. Trends Genet 2020; 36:160-176. [PMID: 32007289 PMCID: PMC10047806 DOI: 10.1016/j.tig.2019.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/20/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023]
Abstract
Like breadcrumbs in the forest, cotranscriptionally acquired histone methylation acts as a memory of prior transcription. Because it can be retained through cell divisions, transcriptional memory allows cells to coordinate complex transcriptional programs during development. However, if not reprogrammed properly during cell fate transitions, it can also disrupt cellular identity. In this review, we discuss the consequences of failure to reprogram histone methylation during three crucial epigenetic reprogramming windows: maternal reprogramming at fertilization, embryonic stem cell (ESC) differentiation, and the continuous maintenance of cell identity in differentiated cells. In addition, we discuss how following the wrong breadcrumb trail of transcriptional memory provides a framework for understanding how heterozygous loss-of-function mutations in histone-modifying enzymes may cause severe neurodevelopmental disorders.
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38
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The H3K9 Methylation Writer SETDB1 and its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells. Genes (Basel) 2019; 10:genes10100750. [PMID: 31557926 PMCID: PMC6826936 DOI: 10.3390/genes10100750] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/15/2019] [Accepted: 09/24/2019] [Indexed: 12/28/2022] Open
Abstract
SETDB1 (SET Domain Bifurcated histone lysine methyltransferase 1) is a key lysine methyltransferase (KMT) required in embryonic stem cells (ESCs), where it silences transposable elements and DNA repeats via histone H3 lysine 9 tri-methylation (H3K9me3), independently of DNA methylation. The H3K9 methylation reader M-Phase Phosphoprotein 8 (MPP8) is highly expressed in ESCs and germline cells. Although evidence of a cooperation between H3K9 KMTs and MPP8 in committed cells has emerged, the interplay between H3K9 methylation writers and MPP8 in ESCs remains elusive. Here, we show that MPP8 interacts physically and functionally with SETDB1 in ESCs. Indeed, combining biochemical, transcriptomic and genomic analyses, we found that MPP8 and SETDB1 co-regulate a significant number of common genomic targets, especially the DNA satellite repeats. Together, our data point to a model in which the silencing of a class of repeated sequences in ESCs involves the cooperation between the H3K9 methylation writer SETDB1 and its reader MPP8.
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39
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Ninova M, Fejes Tóth K, Aravin AA. The control of gene expression and cell identity by H3K9 trimethylation. Development 2019; 146:dev181180. [PMID: 31540910 PMCID: PMC6803365 DOI: 10.1242/dev.181180] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone 3 lysine 9 trimethylation (H3K9me3) is a conserved histone modification that is best known for its role in constitutive heterochromatin formation and the repression of repetitive DNA elements. More recently, it has become evident that H3K9me3 is also deposited at certain loci in a tissue-specific manner and plays important roles in regulating cell identity. Notably, H3K9me3 can repress genes encoding silencing factors, pointing to a fundamental principle of repressive chromatin auto-regulation. Interestingly, recent studies have shown that H3K9me3 deposition requires protein SUMOylation in different contexts, suggesting that the SUMO pathway functions as an important module in gene silencing and heterochromatin formation. In this Review, we discuss the role of H3K9me3 in gene regulation in various systems and the molecular mechanisms that guide the silencing machinery to target loci.
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
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40
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Hemberger M, Hanna CW, Dean W. Mechanisms of early placental development in mouse and humans. Nat Rev Genet 2019; 21:27-43. [PMID: 31534202 DOI: 10.1038/s41576-019-0169-4] [Citation(s) in RCA: 241] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
The importance of the placenta in supporting mammalian development has long been recognized, but our knowledge of the molecular, genetic and epigenetic requirements that underpin normal placentation has remained remarkably under-appreciated. Both the in vivo mouse model and in vitro-derived murine trophoblast stem cells have been invaluable research tools for gaining insights into these aspects of placental development and function, with recent studies starting to reshape our view of how a unique epigenetic environment contributes to trophoblast differentiation and placenta formation. These advances, together with recent successes in deriving human trophoblast stem cells, open up new and exciting prospects in basic and clinical settings that will help deepen our understanding of placental development and associated disorders of pregnancy.
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Affiliation(s)
- Myriam Hemberger
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada. .,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
| | - Courtney W Hanna
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Wendy Dean
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada. .,Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK. .,Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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41
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Seah MKY, Wang Y, Goy PA, Loh HM, Peh WJ, Low DHP, Han BY, Wong E, Leong EL, Wolf G, Mzoughi S, Wollmann H, Macfarlan TS, Guccione E, Messerschmidt DM. The KRAB-zinc-finger protein ZFP708 mediates epigenetic repression at RMER19B retrotransposons. Development 2019; 146:dev.170266. [PMID: 30846446 PMCID: PMC6803371 DOI: 10.1242/dev.170266] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
Abstract
Global epigenetic reprogramming is vital to purge germ cell-specific epigenetic features to establish the totipotent state of the embryo. This process transpires to be carefully regulated and is not an undirected, radical erasure of parental epigenomes. The TRIM28 complex has been shown to be crucial in embryonic epigenetic reprogramming by regionally opposing DNA demethylation to preserve vital parental information to be inherited from germline to soma. Yet the DNA-binding factors guiding this complex to specific targets are largely unknown. Here, we uncover and characterize a novel, maternally expressed, TRIM28-interacting KRAB zinc-finger protein: ZFP708. It recruits the repressive TRIM28 complex to RMER19B retrotransposons to evoke regional heterochromatin formation. ZFP708 binding to these hitherto unknown TRIM28 targets is DNA methylation and H3K9me3 independent. ZFP708 mutant mice are viable and fertile, yet embryos fail to inherit and maintain DNA methylation at ZFP708 target sites. This can result in activation of RMER19B-adjacent genes, while ectopic expression of ZFP708 results in transcriptional repression. Finally, we describe the evolutionary conservation of ZFP708 in mice and rats, which is linked to the conserved presence of the targeted RMER19B retrotransposons in these species. Summary: Analysis of the function and targets of a maternal KRAB-zinc-finger protein, ZFP708, found to specifically mediate maintenance of DNA methylation at a subset of LTR retrotransposons during embryonic epigenetic reprogramming.
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Affiliation(s)
- Michelle K Y Seah
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Yaju Wang
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Pierre-Alexis Goy
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore
| | - Hui Mun Loh
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Wen Jun Peh
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Diana H P Low
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Brenda Y Han
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Esther Wong
- KOre - Knock Out resource, IMB, A*STAR, 138648, Singapore
| | - Ei Leen Leong
- KOre - Knock Out resource, IMB, A*STAR, 138648, Singapore
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Slim Mzoughi
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Heike Wollmann
- NGS Unit of DNA Sequencing Facility, IMCB, A*STAR, 138673, Singapore
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
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42
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Rissi VB, Glanzner WG, De Macedo MP, Gutierrez K, Baldassarre H, Gonçalves PBD, Bordignon V. The histone lysine demethylase KDM7A is required for normal development and first cell lineage specification in porcine embryos. Epigenetics 2019; 14:1088-1101. [PMID: 31216927 DOI: 10.1080/15592294.2019.1633864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is growing evidence that histone lysine demethylases (KDMs) play critical roles in the regulation of embryo development. This study investigated if KDM7A, a lysine demethylase known to act on mono-(me1) and di-(me2) methylation of H3K9 and H3K27, participates in the regulation of early embryo development. Knockdown of KDM7A mRNA reduced blastocyst formation by 69.2% in in vitro fertilized (IVF), 48.4% in parthenogenetically activated (PA), and 48.1% in somatic cell nuclear transfer (SCNT) embryos compared to controls. Global immunofluorescence (IF) signal in KDM7A knockdown compared to control embryos was increased for H3K27me1 on D7, for H3K27me2 on D3 and D5, for H3K9me1 on D5 and D7, and for H3K9me2 on D5 embryos, but decreased for H3K9me1, me2 and me3 on D3. Moreover, KDM7A knockdown altered mRNA expression, including the downregulation of KDM3C on D3, NANOG on D5 and D7, and OCT4 on D7 embryos, and the upregulation of CDX2, KDM4B and KDM6B on D5 embryos. On D3 and D5 embryos, total cell number and mRNA expression of embryo genome activation (EGA) markers (EIF1AX and PPP1R15B) were not affected by KDM7A knockdown. However, the ratio of inner cell mass (ICM)/total number of cells in D7 blastocysts was reduced by 45.5% in KDM7A knockdown compared to control embryos. These findings support a critical role for KDM7A in the regulation of early development and cell lineage specification in porcine embryos, which is likely mediated through the modulation of H3K9me1/me2 and H3K27me1/me2 levels, and changes in the expression of other KDMs and pluripotency genes.
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Affiliation(s)
- Vitor Braga Rissi
- Laboratory of Biotechnology and Animal Reproduction - BioRep, Federal University of Santa Maria (UFSM) , Santa Maria , RS , Brazil
| | - Werner Giehl Glanzner
- Department of Animal Science, McGill University , Sainte Anne de Bellevue , QC , Canada
| | | | - Karina Gutierrez
- Department of Animal Science, McGill University , Sainte Anne de Bellevue , QC , Canada
| | - Hernan Baldassarre
- Department of Animal Science, McGill University , Sainte Anne de Bellevue , QC , Canada
| | - Paulo Bayard Dias Gonçalves
- Laboratory of Biotechnology and Animal Reproduction - BioRep, Federal University of Santa Maria (UFSM) , Santa Maria , RS , Brazil
| | - Vilceu Bordignon
- Department of Animal Science, McGill University , Sainte Anne de Bellevue , QC , Canada
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Nicetto D, Zaret KS. Role of H3K9me3 heterochromatin in cell identity establishment and maintenance. Curr Opin Genet Dev 2019; 55:1-10. [PMID: 31103921 DOI: 10.1016/j.gde.2019.04.013] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023]
Abstract
Compacted, transcriptionally repressed chromatin, referred to as heterochromatin, represents a major fraction of the higher eukaryotic genome and exerts pivotal functions of silencing repetitive elements, maintenance of genome stability, and control of gene expression. Among the different histone post-translational modifications (PTMs) associated with heterochromatin, tri-methylation of lysine 9 on histone H3 (H3K9me3) is gaining increased attention. Besides its known role in repressing repetitive elements and non-coding portions of the genome, recent observations indicate H3K9me3 as an important player in silencing lineage-inappropriate genes. The ability of H3K9me3 to influence cell identity challenges the original concept of H3K9me3-marked heterochromatin as mainly a constitutive type of chromatin and provides a further level of understanding of how to modulate cell fate control. Here, we summarize the role of H3K9me3 marked heterochromatin and its dynamics in establishing and maintaining cellular identity.
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Affiliation(s)
- Dario Nicetto
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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Moreno-Romero J, Del Toro-De León G, Yadav VK, Santos-González J, Köhler C. Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm. Genome Biol 2019; 20:41. [PMID: 30791924 PMCID: PMC6385439 DOI: 10.1186/s13059-019-1652-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression. RESULTS In this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles, we are able to predict known PEGs at high accuracy and identify several new PEGs that we confirm using INTACT-based transcriptomes generated in this study. CONCLUSIONS The presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows prediction of genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.
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Affiliation(s)
- Jordi Moreno-Romero
- Present Address: Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Gerardo Del Toro-De León
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Vikash Kumar Yadav
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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Kwon J, Li YH, Jo YJ, Oh Y, Namgoong S, Kim NH. Inhibition of MEK1/2 and GSK3 (2i system) affects blastocyst quality and early differentiation of porcine parthenotes. PeerJ 2019; 6:e5840. [PMID: 30643672 PMCID: PMC6327883 DOI: 10.7717/peerj.5840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Inhibition of both MEK1/2 and glycogen synthase kinase-3 (GSK3; 2i system) facilitates the maintenance of naïve stemness for embryonic stem cells in various mammalian species. However, the effect of the inhibition of the 2i system on porcine early embryogenesis is unknown. We investigated the effect of the 2i system on early embryo development, expression of pluripotency-related genes, and epigenetic modifications. Inhibition of MEK1/2 (by PD0325901) and/or GSK3 (by CHIR99021) did not alter the developmental potential of porcine parthenogenetic embryos, but improved blastocyst quality, as judged by the blastocyst cell number, diameter, and reduction in the number of apoptotic cells. The expression levels of octamer-binding transcription factor 4 and SOX2, the primary transcription factors that maintain embryonic pluripotency, were significantly increased by 2i treatments. Epigenetic modification-related gene expression was altered upon 2i treatment. The collective results indicate that the 2i system in porcine embryos improved embryo developmental potential and blastocyst quality by regulating epigenetic modifications and pluripotency-related gene expression.
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Affiliation(s)
- Jeongwoo Kwon
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - Ying-Hua Li
- Department of Animal Sciences, Agricultural College, Yanbian University, Yanji, China
| | - Yu-Jin Jo
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - YoungJin Oh
- Genetic Engineering, Cheongchungbuk-do Veterinary Service Laboratory, Cheongju, Cheongchungbuk-do, Republic of Korea
| | - Suk Namgoong
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungcheongbuk-do, Republic of Korea
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Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages. Nat Commun 2018; 9:4189. [PMID: 30305613 PMCID: PMC6180096 DOI: 10.1038/s41467-018-06666-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
The establishment of the embryonic and trophoblast lineages is a developmental decision underpinned by dramatic differences in the epigenetic landscape of the two compartments. However, it remains unknown how epigenetic information and transcription factor networks map to the 3D arrangement of the genome, which in turn may mediate transcriptional divergence between the two cell lineages. Here, we perform promoter capture Hi-C experiments in mouse trophoblast (TSC) and embryonic (ESC) stem cells to understand how chromatin conformation relates to cell-specific transcriptional programmes. We find that key TSC genes that are kept repressed in ESCs exhibit interactions between H3K27me3-marked regions in ESCs that depend on Polycomb repressive complex 1. Interactions that are prominent in TSCs are enriched for enhancer-gene contacts involving key TSC transcription factors, as well as TET1, which helps to maintain the expression of TSC-relevant genes. Our work shows that the first developmental cell fate decision results in distinct chromatin conformation patterns establishing lineage-specific contexts involving both repressive and active interactions.
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Gonzalez-Munoz E, Cibelli JB. Somatic Cell Reprogramming Informed by the Oocyte. Stem Cells Dev 2018; 27:871-887. [DOI: 10.1089/scd.2018.0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Elena Gonzalez-Munoz
- LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
- Department of Cell Biology, Genetics and Physiology, University of Málaga, Málaga, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBN), Málaga, Spain
| | - Jose B. Cibelli
- LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
- Department of Animal Science, Michigan State University, East Lansing, MI
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI
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Asf1a resolves bivalent chromatin domains for the induction of lineage-specific genes during mouse embryonic stem cell differentiation. Proc Natl Acad Sci U S A 2018; 115:E6162-E6171. [PMID: 29915027 DOI: 10.1073/pnas.1801909115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bivalent chromatin domains containing repressive H3K27me3 and active H3K4me3 modifications are barriers for the expression of lineage-specific genes in ES cells and must be resolved for the transcription induction of these genes during differentiation, a process that remains largely unknown. Here, we show that Asf1a, a histone chaperone involved in nucleosome assembly and disassembly, regulates the resolution of bivalent domains and activation of lineage-specific genes during mouse ES cell differentiation. Deletion of Asf1a does not affect the silencing of pluripotent genes, but compromises the expression of lineage-specific genes during ES cell differentiation. Mechanistically, the Asf1a-histone interaction, but not the role of Asf1a in nucleosome assembly, is required for gene transcription. Asf1a is recruited to several bivalent promoters, partially through association with transcription factors, and mediates nucleosome disassembly during differentiation. We suggest that Asf1a-mediated nucleosome disassembly provides a means for resolution of bivalent domain barriers for induction of lineage-specific genes during differentiation.
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Kang YK. Surveillance of Retroelement Expression and Nucleic-Acid Immunity by Histone Methyltransferase SETDB1. Bioessays 2018; 40:e1800058. [DOI: 10.1002/bies.201800058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/31/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Yong-Kook Kang
- Development and Differentiation Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Department of Functional Genomics; University of Science and Technology (UST); Yuseong-gu Daejeon 34141 South Korea
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50
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Zhang Y, Huang J, Li Q, Chen K, Liang Y, Zhan Z, Ye F, Ni W, Chen L, Ding Y. Histone methyltransferase SETDB1 promotes cells proliferation and migration by interacting withTiam1 in hepatocellular carcinoma. BMC Cancer 2018; 18:539. [PMID: 29739365 PMCID: PMC5941371 DOI: 10.1186/s12885-018-4464-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 04/30/2018] [Indexed: 11/24/2022] Open
Abstract
Background SETDB1 is a histone H3K9 methyltransferase, which plays a significant role in the occurrence and progression of tumors. Previous studies have confirmed that T-lymphom invasion and metastasis gene (Tiam1) is a protein associated with the metastasis of hepatocellular carcinoma (HCC); however, we have not yet been successful in elucidating the specific mechanism of HCC. Methods Yeast two-hybrid test was conducted to screen proteins that interacted with Tiam1 gene. Glutathione-S-transferase (GST) pull-down and crosslinking-immunoprecipitation (CLIP) assays were performed to determine whether SETDB1 can interact with Tiam1 gene. A series of related experiments were performed to explore role of SETDB1 on cell proliferation, migration, and invasion in HCC. Recovery experiment was performed to investigate the effect of Tiam1 knockdown on cell proliferation and migration, which was caused by SETDB1 overexpression in HCC cells. The expression of SETDB1 was frequently upregulated in HCC tissues and positively correlated with Tiam1. Results GST pull-down and CLIP assays were performed to elucidate the interaction between SETDB1 and Tiam1. Cell proliferation, migration, and epithelial mesenchymal transformation (EMT) in HCC cells was promoted with the overexpression of SETDB1. Following the knockdown of Tiam1 gene, the effect of SETDB1 on cell proliferation and migration was reversed in HCC cells. The expression of SETDB1 was frequently up-regulated in HCC tissues, and it was positively correlated with Tiam1 gene. Conclusions Ours is the first study to prove that SETDB1 promotes the proliferation and migration of cells by forming SETDB1-Tiam1 compounds. We found that SETDB1-Tiam1 compounds were involved in a novel pathway, which regulated epigenetic modification of gene expression in HCC samples. Electronic supplementary material The online version of this article (10.1186/s12885-018-4464-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuqin Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jing Huang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Qisheng Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Keli Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yonghao Liang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zetao Zhan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Wen Ni
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Longhua Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Yi Ding
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China.
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