1
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Azhar M, Xu C, Jiang X, Li W, Cao Y, Zhu X, Xing X, Wu L, Zou J, Meng L, Cheng Y, Han W, Bao J. The arginine methyltransferase Prmt1 coordinates the germline arginine methylome essential for spermatogonial homeostasis and male fertility. Nucleic Acids Res 2023; 51:10428-10450. [PMID: 37739418 PMCID: PMC10602896 DOI: 10.1093/nar/gkad769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023] Open
Abstract
Arginine methylation, catalyzed by the protein arginine methyltransferases (PRMTs), is a common post-translational protein modification (PTM) that is engaged in a plethora of biological events. However, little is known about how the methylarginine-directed signaling functions in germline development. In this study, we discover that Prmt1 is predominantly distributed in the nuclei of spermatogonia but weakly in the spermatocytes throughout mouse spermatogenesis. By exploiting a combination of three Cre-mediated Prmt1 knockout mouse lines, we unravel that Prmt1 is essential for spermatogonial establishment and maintenance, and that Prmt1-catalyzed asymmetric methylarginine coordinates inherent transcriptional homeostasis within spermatogonial cells. In conjunction with high-throughput CUT&Tag profiling and modified mini-bulk Smart-seq2 analyses, we unveil that the Prmt1-deposited H4R3me2a mark is permissively enriched at promoter and exon/intron regions, and sculpts a distinctive transcriptomic landscape as well as the alternative splicing pattern, in the mouse spermatogonia. Collectively, our study provides the genetic and mechanistic evidence that connects the Prmt1-deposited methylarginine signaling to the establishment and maintenance of a high-fidelity transcriptomic identity in orchestrating spermatogonial development in the mammalian germline.
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Affiliation(s)
- Muhammad Azhar
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Caoling Xu
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Xue Jiang
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Wenqing Li
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Yuzhu Cao
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Xiaoli Zhu
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Xuemei Xing
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Limin Wu
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Jiaqi Zou
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Lan Meng
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Yu Cheng
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Wenjie Han
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Anhui, China
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2
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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3
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Zhang J, Zhang Y, You Q, Huang C, Zhang T, Wang M, Zhang T, Yang X, Xiong J, Li Y, Liu CP, Zhang Z, Xu RM, Zhu B. Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation. Science 2022; 375:1053-1058. [PMID: 35143257 DOI: 10.1126/science.abm0730] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bivalent genes are ready for activation upon the arrival of developmental cues. Here, we report that BEND3 is a CpG island (CGI)-binding protein that is enriched at regulatory elements. The cocrystal structure of BEND3 in complex with its target DNA reveals the structural basis for its DNA methylation-sensitive binding property. Mouse embryos ablated of Bend3 died at the pregastrulation stage. Bend3 null embryonic stem cells (ESCs) exhibited severe defects in differentiation, during which hundreds of CGI-containing bivalent genes were prematurely activated. BEND3 is required for the stable association of polycomb repressive complex 2 (PRC2) at bivalent genes that are highly occupied by BEND3, which suggests a reining function of BEND3 in maintaining high levels of H3K27me3 at these bivalent genes in ESCs to prevent their premature activation in the forthcoming developmental stage.
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Affiliation(s)
- Jing Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglong You
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tiantian Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China
| | - Tianwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaocheng Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Duethorn B, Groll F, Rieger B, Drexler HCA, Brinkmann H, Kremer L, Stehling M, Borowski MT, Mildner K, Zeuschner D, Zernicka-Goetz M, Stemmler MP, Busch KB, Vaquerizas JM, Bedzhov I. Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism. Nat Commun 2022; 13:610. [PMID: 35105859 PMCID: PMC8807836 DOI: 10.1038/s41467-022-28139-5] [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: 05/05/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Lima1 is an extensively studied prognostic marker of malignancy and is also considered to be a tumour suppressor, but its role in a developmental context of non-transformed cells is poorly understood. Here, we characterise the expression pattern and examined the function of Lima1 in mouse embryos and pluripotent stem cell lines. We identify that Lima1 expression is controlled by the naïve pluripotency circuit and is required for the suppression of membrane blebbing, as well as for proper mitochondrial energetics in embryonic stem cells. Moreover, forcing Lima1 expression enables primed mouse and human pluripotent stem cells to be incorporated into murine pre-implantation embryos. Thus, Lima1 is a key effector molecule that mediates the pluripotency control of membrane dynamics and cellular metabolism.
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Affiliation(s)
- Binyamin Duethorn
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Fabian Groll
- Regulatory Genomics group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Bettina Rieger
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Hannes C A Drexler
- Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Ludmila Kremer
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Marie-Theres Borowski
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Karina Mildner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.,Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, California Institute of Technology (Caltech), Pasadena, CA, 91125, USA
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Karin B Busch
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Juan M Vaquerizas
- Regulatory Genomics group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany.,MRC London Institute of Medical Sciences, Du Cane Road, W12 0NN, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany.
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5
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Lee JY, Davis I, Youth EHH, Kim J, Churchill G, Godwin J, Korstanje R, Beck S. Misexpression of genes lacking CpG islands drives degenerative changes during aging. SCIENCE ADVANCES 2021; 7:eabj9111. [PMID: 34910517 PMCID: PMC8673774 DOI: 10.1126/sciadv.abj9111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/26/2021] [Indexed: 05/14/2023]
Abstract
Cellular aging is characterized by disruption of the nuclear lamina and its associated heterochromatin. How these structural changes within the nucleus contribute to age-related degeneration of the organism is unclear. Genes lacking CpG islands (CGI− genes) generally associate with heterochromatin when they are inactive. Here, we show that the expression of these genes is globally activated in aged cells and tissues. This CGI− gene misexpression is a common feature of normal and pathological aging in mice and humans. We report evidence that CGI− gene up-regulation is directly responsible for age-related physiological deterioration, notably for increased secretion of inflammatory mediators.
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Affiliation(s)
- Jun-Yeong Lee
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Ian Davis
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Elliot H. H. Youth
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
- Brown University, Providence, RI 02912, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - James Godwin
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Samuel Beck
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
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6
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Pluripotency-State-Dependent Role of Dax1 in Embryonic Stem Cells Self-Renewal. Stem Cells Int 2021; 2021:5522723. [PMID: 34335791 PMCID: PMC8286181 DOI: 10.1155/2021/5522723] [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: 03/09/2021] [Revised: 05/18/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
Dax1(also known as Nr0b1) is regarded as an important component of the transcription factor network in mouse embryonic stem cells (ESCs). However, the role and the molecular mechanism of Dax1 in the maintenance of different pluripotency states are poorly understood. Here, we constructed a stable Dax1 knockout (KO) cell line using the CRISPR/Cas9 system to analyze the precise function of Dax1. We reported that 2i/LIF-ESCs had significantly lower Dax1 expression than LIF/serum-ESCs. Dax1KO ES cell lines could be established in 2i/LIF and their pluripotency was confirmed. In contrast, Dax1-null ESCs could not be continuously passaged in LIF/serum due to severe differentiation and apoptosis. In LIF/serum, the activities of the Core module and Myc module were significantly reduced, while the PRC2 module was activated after Dax1KO. The expression of most proapoptotic genes and lineage-commitment genes were drastically increased, while the downregulated expression of antiapoptotic genes and many pluripotency genes was observed. Our research on the pluripotent state-dependent role of Dax1 provides clues to understand the molecular regulation mechanism at different stages of early embryonic development.
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7
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Olivieri D, Castelli E, Kawamura YK, Papasaikas P, Lukonin I, Rittirsch M, Hess D, Smallwood SA, Stadler MB, Peters AHFM, Betschinger J. Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells. EMBO J 2021; 40:e106818. [PMID: 33909924 PMCID: PMC8204867 DOI: 10.15252/embj.2020106818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) are biased toward producing embryonic rather than extraembryonic endoderm fates. Here, we identify the mechanism of this barrier and report that the histone deacetylase Hdac3 and the transcriptional corepressor Dax1 cooperatively limit the lineage repertoire of mESCs by silencing an enhancer of the extraembryonic endoderm-specifying transcription factor Gata6. This restriction is opposed by the pluripotency transcription factors Nr5a2 and Esrrb, which promote cell type conversion. Perturbation of the barrier extends mESC potency and allows formation of 3D spheroids that mimic the spatial segregation of embryonic epiblast and extraembryonic endoderm in early embryos. Overall, this study shows that transcriptional repressors stabilize pluripotency by biasing the equilibrium between embryonic and extraembryonic lineages that is hardwired into the mESC transcriptional network.
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Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Eleonora Castelli
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Yumiko K Kawamura
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | | | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
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8
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Lee JY, Song J, LeBlanc L, Davis I, Kim J, Beck S. Conserved dual-mode gene regulation programs in higher eukaryotes. Nucleic Acids Res 2021; 49:2583-2597. [PMID: 33621342 PMCID: PMC7969006 DOI: 10.1093/nar/gkab108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 12/27/2022] Open
Abstract
Recent genomic data analyses have revealed important underlying logics in eukaryotic gene regulation, such as CpG islands (CGIs)-dependent dual-mode gene regulation. In mammals, genes lacking CGIs at their promoters are generally regulated by interconversion between euchromatin and heterochromatin, while genes associated with CGIs constitutively remain as euchromatin. Whether a similar mode of gene regulation exists in non-mammalian species has been unknown. Here, through comparative epigenomic analyses, we demonstrate that the dual-mode gene regulation program is common in various eukaryotes, even in the species lacking CGIs. In cases of vertebrates or plants, we find that genes associated with high methylation level promoters are inactivated by forming heterochromatin and expressed in a context-dependent manner. In contrast, the genes with low methylation level promoters are broadly expressed and remain as euchromatin even when repressed by Polycomb proteins. Furthermore, we show that invertebrate animals lacking DNA methylation, such as fruit flies and nematodes, also have divergence in gene types: some genes are regulated by Polycomb proteins, while others are regulated by heterochromatin formation. Altogether, our study establishes gene type divergence and the resulting dual-mode gene regulation as fundamental features shared in a broad range of higher eukaryotic species.
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Affiliation(s)
- Jun-Yeong Lee
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Jawon Song
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX 78758, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Davis
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel Beck
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04609, USA
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9
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Cohen I, Bar C, Ezhkova E. Activity of PRC1 and Histone H2AK119 Monoubiquitination: Revising Popular Misconceptions. Bioessays 2020; 42:e1900192. [PMID: 32196702 PMCID: PMC7585675 DOI: 10.1002/bies.201900192] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/12/2020] [Indexed: 12/21/2022]
Abstract
Polycomb group proteins are evolutionary conserved chromatin-modifying complexes, essential for the regulation of developmental and cell-identity genes. Polycomb-mediated transcriptional regulation is provided by two multi-protein complexes known as Polycomb repressive complex 1 (PRC1) and 2 (PRC2). Recent studies positioned PRC1 as a foremost executer of Polycomb-mediated transcriptional control. Mammalian PRC1 complexes can form multiple sub-complexes that vary in their core and accessory subunit composition, leading to fascinating and diverse transcriptional regulatory mechanisms employed by PRC1 complexes. These mechanisms include PRC1-catalytic activity toward monoubiquitination of histone H2AK119, a well-established hallmark of PRC1 complexes, whose importance has been long debated. In this review, the central roles that PRC1-catalytic activity plays in transcriptional repression are emphasized and the recent evidence supporting a role for PRC1 complexes in gene activation is discussed.
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Affiliation(s)
- Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
- These authors contributed equally to this work
| | - Carmit Bar
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology; Icahn School of Medicine at Mount Sinai; 1 Gustave L. Levy Place, New York, NY 10029; USA
- These authors contributed equally to this work
| | - Elena Ezhkova
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
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10
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Friman ET, Deluz C, Meireles-Filho ACA, Govindan S, Gardeux V, Deplancke B, Suter DM. Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle. eLife 2019; 8:e50087. [PMID: 31794382 PMCID: PMC6890464 DOI: 10.7554/elife.50087] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewing cell divisions and across the cell cycle is poorly understood. Here we assessed the interplay between OCT4 and SOX2 in controlling chromatin accessibility of mouse embryonic stem cells. We found that OCT4 and SOX2 operate in a largely independent manner even at co-occupied sites, and that their cooperative binding is mostly mediated indirectly through regulation of chromatin accessibility. Controlled protein degradation strategies revealed that the uninterrupted presence of OCT4 is required for post-mitotic re-establishment and interphase maintenance of chromatin accessibility, and that highly OCT4-bound enhancers are particularly vulnerable to transient loss of OCT4 expression. Our study sheds light on the constant pioneer activity required to maintain the dynamic pluripotency regulatory landscape in an accessible state.
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Affiliation(s)
- Elias T Friman
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Cédric Deluz
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Antonio CA Meireles-Filho
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Subashika Govindan
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Vincent Gardeux
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - David M Suter
- Institute of Bioengineering, School of Life SciencesEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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11
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Beck S, Rhee C, Song J, Lee BK, LeBlanc L, Cannon L, Kim J. Implications of CpG islands on chromosomal architectures and modes of global gene regulation. Nucleic Acids Res 2019. [PMID: 29529258 PMCID: PMC5961348 DOI: 10.1093/nar/gky147] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CpG islands (CGIs) have long been implicated in the regulation of vertebrate gene expression. However, the involvement of CGIs in chromosomal architectures and associated gene expression regulations has not yet been thoroughly explored. By combining large-scale integrative data analyses and experimental validations, we show that CGIs clearly reconcile two competing models explaining nuclear gene localizations. We first identify CGI-containing (CGI+) and CGI-less (CGI-) genes are non-randomly clustered within the genome, which reflects CGI-dependent spatial gene segregation in the nucleus and corresponding gene regulatory modes. Regardless of their transcriptional activities, CGI+ genes are mainly located at the nuclear center and encounter frequent long-range chromosomal interactions. Meanwhile, nuclear peripheral CGI- genes forming heterochromatin are activated and internalized into the nuclear center by local enhancer-promoter interactions. Our findings demonstrate the crucial implications of CGIs on chromosomal architectures and gene positioning, linking the critical importance of CGIs in determining distinct mechanisms of global gene regulation in three-dimensional space in the nucleus.
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Affiliation(s)
- Samuel Beck
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, Maine 04609, USA
| | - Catherine Rhee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jawon Song
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Laurie Cannon
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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12
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Illingworth RS. Chromatin folding and nuclear architecture: PRC1 function in 3D. Curr Opin Genet Dev 2019; 55:82-90. [PMID: 31323466 PMCID: PMC6859790 DOI: 10.1016/j.gde.2019.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/20/2022]
Abstract
Embryonic development requires the intricate balance between the expansion and specialisation of defined cell types in time and space. The gene expression programmes that underpin this balance are regulated, in part, by modulating the chemical and structural state of chromatin. Polycomb repressive complexes (PRCs), a family of essential developmental regulators, operate at this level to stabilise or perpetuate a repressed but transcriptionally poised chromatin configuration. This dynamic state is required to control the timely initiation of productive gene transcription during embryonic development. The two major PRCs cooperate to target the genome, but it is PRC1 that appears to be the primary effector that controls gene expression. In this review I will discuss recent findings relating to how PRC1 alters chromatin accessibility, folding and global 3D nuclear organisation to control gene transcription.
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Affiliation(s)
- Robert S Illingworth
- MRC Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, United Kingdom.
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13
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NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule. Sci Rep 2019; 9:8140. [PMID: 31148571 PMCID: PMC6544651 DOI: 10.1038/s41598-019-44597-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/20/2019] [Indexed: 11/15/2022] Open
Abstract
Recent technical advances highlight that to understand mammalian development and human disease we need to consider transcriptional and epigenetic cell-to-cell differences within cell populations. This is particularly important in key areas of biomedicine like stem cell differentiation and intratumor heterogeneity. The recently developed nucleosome occupancy and methylome (NOMe) assay facilitates the simultaneous study of DNA methylation and nucleosome positioning on the same DNA strand. NOMe-treated DNA can be sequenced by sanger (NOMe-PCR) or high throughput approaches (NOMe-seq). NOMe-PCR provides information for a single locus at the single molecule while NOMe-seq delivers genome-wide data that is usually interrogated to obtain population-averaged measures. Here, we have developed a bioinformatic tool that allow us to easily obtain locus-specific information at the single molecule using genome-wide NOMe-seq datasets obtained from bulk populations. We have used NOMePlot to study mouse embryonic stem cells and found that polycomb-repressed bivalent gene promoters coexist in two different epigenetic states, as defined by the nucleosome binding pattern detected around their transcriptional start site.
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14
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Cossec JC, Theurillat I, Chica C, Búa Aguín S, Gaume X, Andrieux A, Iturbide A, Jouvion G, Li H, Bossis G, Seeler JS, Torres-Padilla ME, Dejean A. SUMO Safeguards Somatic and Pluripotent Cell Identities by Enforcing Distinct Chromatin States. Cell Stem Cell 2018; 23:742-757.e8. [PMID: 30401455 DOI: 10.1016/j.stem.2018.10.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/10/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Understanding general principles that safeguard cellular identity should reveal critical insights into common mechanisms underlying specification of varied cell types. Here, we show that SUMO modification acts to stabilize cell fate in a variety of contexts. Hyposumoylation enhances pluripotency reprogramming in vitro and in vivo, increases lineage transdifferentiation, and facilitates leukemic cell differentiation. Suppressing sumoylation in embryonic stem cells (ESCs) promotes their conversion into 2-cell-embryo-like (2C-like) cells. During reprogramming to pluripotency, SUMO functions on fibroblastic enhancers to retain somatic transcription factors together with Oct4, Sox2, and Klf4, thus impeding somatic enhancer inactivation. In contrast, in ESCs, SUMO functions on heterochromatin to silence the 2C program, maintaining both proper H3K9me3 levels genome-wide and repression of the Dux locus by triggering recruitment of the sumoylated PRC1.6 and Kap/Setdb1 repressive complexes. Together, these studies show that SUMO acts on chromatin as a glue to stabilize key determinants of somatic and pluripotent states.
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Affiliation(s)
- Jack-Christophe Cossec
- Nuclear Organization and Oncogenesis Unit, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | - Ilan Theurillat
- Nuclear Organization and Oncogenesis Unit, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015 Paris, France; INSERM, U993, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Claudia Chica
- Bioinformatics and Biostatistics Hub - C3BI, USR 3756 Institut Pasteur & CNRS, 75015 Paris, France
| | - Sabela Búa Aguín
- Cellular Plasticity and Disease Modelling Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR3738, 75015 Paris, France
| | - Xavier Gaume
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Alexandra Andrieux
- Nuclear Organization and Oncogenesis Unit, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | - Ane Iturbide
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Gregory Jouvion
- Experimental Neuropathology Unit, Institut Pasteur, 75015 Paris, France
| | - Han Li
- Cellular Plasticity and Disease Modelling Unit, Institut Pasteur, 75015 Paris, France; CNRS UMR3738, 75015 Paris, France
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jacob-Sebastian Seeler
- Nuclear Organization and Oncogenesis Unit, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | | | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015 Paris, France; INSERM, U993, 75015 Paris, France.
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15
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Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes. Genome Res 2018; 28:1494-1507. [PMID: 30154222 PMCID: PMC6169895 DOI: 10.1101/gr.237180.118] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that play important roles in regulating gene expression during animal development. In vitro experiments have shown that PcG protein complexes can compact chromatin to limit the activity of chromatin remodeling enzymes and access of the transcriptional machinery to DNA. In fitting with these ideas, gene promoters associated with PcG proteins have been reported to be less accessible than other gene promoters. However, it remains largely untested in vivo whether PcG proteins define chromatin accessibility or other chromatin features. To address this important question, we examine the chromatin accessibility and nucleosome landscape at PcG protein-bound promoters in mouse embryonic stem cells using the assay for transposase accessible chromatin (ATAC)-seq. Combined with genetic ablation strategies, we unexpectedly discover that although PcG protein-occupied gene promoters exhibit reduced accessibility, this does not rely on PcG proteins. Instead, the Polycomb repressive complex 1 (PRC1) appears to play a unique role in driving elevated nucleosome occupancy and decreased nucleosomal spacing in Polycomb chromatin domains. Our new genome-scale observations argue, in contrast to the prevailing view, that PcG proteins do not significantly affect chromatin accessibility and highlight an underappreciated complexity in the relationship between chromatin accessibility, the nucleosome landscape, and PcG-mediated transcriptional repression.
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16
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Lee BK, Uprety N, Jang YJ, Tucker SK, Rhee C, LeBlanc L, Beck S, Kim J. Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells. Stem Cell Res 2017; 26:95-102. [PMID: 29272857 PMCID: PMC5899959 DOI: 10.1016/j.scr.2017.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/05/2017] [Accepted: 12/10/2017] [Indexed: 11/30/2022] Open
Abstract
During early development in placental mammals, proper trophoblast lineage development is essential for implantation and placentation. Defects in this lineage can cause early pregnancy failures and other pregnancy disorders. However, transcription factors controlling trophoblast development remain poorly understood. Here, we utilize Fosl1, previously implicated in trophoblast giant cell development as a member of the AP-1 complex, to trans-differentiate embryonic stem (ES) cells to trophoblast lineage-like cells. We first show that the ectopic expression of Fosl1 is sufficient to induce trophoblast-specific gene expression programs in ES cells. Surprisingly, we find that this transcriptional reprogramming occurs independently of changes in levels of ES cell core factors during the cell fate change. This suggests that Fosl1 acts in a novel way to orchestrate the ES to trophoblast cell fate conversion compared to previously known reprogramming factors. Mapping of Fosl1 targets reveals that Fosl1 directly activates TE lineage-specific genes as a pioneer factor. Our work suggests Fosl1 may be used to reprogram ES cells into differentiated cell types in trophoblast lineage, which not only enhances our knowledge of global trophoblast gene regulation but also may provide a future therapeutic tool for generating induced trophoblast cells from patient-derived pluripotent stem cells.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Nadima Uprety
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Yu Jin Jang
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Scott K Tucker
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Catherine Rhee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Lucy LeBlanc
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Samuel Beck
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States; Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Salisbury Cove, ME 04672, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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17
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Lee BK, Lee J, Shen W, Rhee C, Chung H, Kim J. Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination. Nucleic Acids Res 2017; 45:7151-7166. [PMID: 28453857 PMCID: PMC5499583 DOI: 10.1093/nar/gkx310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/13/2017] [Indexed: 12/17/2022] Open
Abstract
Histone H2B lysine 120 mono-ubiquitination (H2Bub1) catalyzed by Rnf20 has been implicated in normal differentiation of embryonic stem (ES) and adult stem cells. However, it remains unknown how Rnf20 is recruited to its specific target chromosomal loci for the establishment of H2Bub1. Here, we reveal that Fbxl19, a CxxC domain-containing protein, promotes H2Bub1 at the promoters of CpG island-containing genes by interacting with Rnf20. We show that up-regulation of Fbxl19 increases the level of global H2Bub1 in mouse ES cells, while down-regulation of Fbxl19 reduces the level of H2Bub1. Our genome-wide target mapping unveils the preferential occupancy of Fbxl19 on CpG island-containing promoters, and we further discover that chromosomal binding of Fbxl19 is required for H2Bub1 of its targets. Moreover, we reveal that Fbxl19 is critical for proper differentiation of ES cells in collaboration with Rnf20. Altogether, our results demonstrate that Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jiwoon Lee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Wenwen Shen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Rhee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Haewon Chung
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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18
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Dubois-Chevalier J, Dubois V, Dehondt H, Mazrooei P, Mazuy C, Sérandour AA, Gheeraert C, Guillaume P, Baugé E, Derudas B, Hennuyer N, Paumelle R, Marot G, Carroll JS, Lupien M, Staels B, Lefebvre P, Eeckhoute J. The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions. Genome Res 2017; 27:985-996. [PMID: 28400425 PMCID: PMC5453331 DOI: 10.1101/gr.217075.116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/05/2017] [Indexed: 02/06/2023]
Abstract
Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TRs). However, how recruitment of a myriad of TRs is orchestrated at cis-regulatory modules (CRMs) to account for coregulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRMs involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRMs), which consist of subsets of preferentially and coordinately corecruited TRs, assemble into hierarchical combinations at hepatic CRMs. Different combinations of TRMs add to a core TRM, broadly found across the whole landscape of CRMs, to discriminate promoters from enhancers. These combinations also specify distinct sets of CRM differentially organized along the genome and involved in regulation of either housekeeping/cellular maintenance genes or liver-specific functions. In addition to these TRMs which we define as obligatory, we show that facultative TRMs, such as one comprising core circadian TRs, are further recruited to selective subsets of CRMs to modulate their activities. TRMs transcend TR classification into ubiquitous versus liver-identity factors, as well as TR grouping into functional families. Hence, hierarchical superimpositions of obligatory and facultative TRMs bring about independent transcriptional regulatory inputs defining different sets of CRMs with logical connection to regulation of specific gene sets and biological pathways. Altogether, our study reveals novel principles of concerted transcriptional regulation by multiple TRs at CRMs.
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Affiliation(s)
- Julie Dubois-Chevalier
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Vanessa Dubois
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Hélène Dehondt
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Parisa Mazrooei
- The Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Claire Mazuy
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Aurélien A Sérandour
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Céline Gheeraert
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Penderia Guillaume
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Eric Baugé
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Bruno Derudas
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Nathalie Hennuyer
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Réjane Paumelle
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Guillemette Marot
- Université Lille, MODAL Team, Inria Lille-Nord Europe, 59650 Villeneuve-d'Ascq, France
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Bart Staels
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Philippe Lefebvre
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Jérôme Eeckhoute
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
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19
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Intragenic CpG islands play important roles in bivalent chromatin assembly of developmental genes. Proc Natl Acad Sci U S A 2017; 114:E1885-E1894. [PMID: 28223506 DOI: 10.1073/pnas.1613300114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
CpG, 5'-C-phosphate-G-3', islands (CGIs) have long been known for their association with enhancers, silencers, and promoters, and for their epigenetic signatures. They are maintained in embryonic stem cells (ESCs) in a poised but inactive state via the formation of bivalent chromatin containing both active and repressive marks. CGIs also occur within coding sequences, where their functional role has remained obscure. Intragenic CGIs (iCGIs) are largely absent from housekeeping genes, but they are found in all genes associated with organ development and cell lineage control. In this paper, we investigated the epigenetic status of iCGIs and found that they too reside in bivalent chromatin in ESCs. Cell type-specific DNA methylation of iCGIs in differentiated cells was linked to the loss of both the H3K4me3 and H3K27me3 marks, and disruption of physical interaction with promoter regions, resulting in transcriptional activation of key regulators of differentiation such as PAXs, HOXs, and WNTs. The differential epigenetic modification of iCGIs appears to be mediated by cell type-specific transcription factors distinct from those bound by promoter, and these transcription factors may be involved in the hypermethylation of iCGIs upon cell differentiation. iCGIs thus play a key role in the cell type-specific regulation of transcription.
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20
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Abstract
The E2F family of transcription factors is a key determinant of cell proliferation in response to extra- and intra-cellular signals. Within this family, E2F4 is a transcriptional repressor whose activity is critical to engage and maintain cell cycle arrest in G0/G1 in conjunction with members of the retinoblastoma (RB) family. However, recent observations challenge this paradigm and indicate that E2F4 has a multitude of functions in cells besides this cell cycle regulatory role, including in embryonic and adult stem cells, during regenerative processes, and in cancer. Some of these new functions are independent of the RB family and involve direct activation of target genes. Here we review the canonical functions of E2F4 and discuss recent evidence expanding the role of this transcription factor, with a focus on cell fate decisions in tissue homeostasis and regeneration.
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Affiliation(s)
- Jenny Hsu
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
| | - Julien Sage
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
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Song J, Zynda G, Beck S, Springer NM, Vaughn MW. Bisulfite Sequence Analyses Using CyVerse Discovery Environment: From Mapping to DMRs. ACTA ACUST UNITED AC 2016; 1:510-529. [DOI: 10.1002/cppb.20034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jawon Song
- Texas Advanced Computing Center, University of Texas at Austin Austin Texas
| | - Greg Zynda
- Texas Advanced Computing Center, University of Texas at Austin Austin Texas
| | - Samuel Beck
- Department of Molecular Biosciences, University of Texas at Austin Austin Texas
| | - Nathan M. Springer
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota Saint Paul Minnesota
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas at Austin Austin Texas
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High-efficiency generation of induced pluripotent mesenchymal stem cells from human dermal fibroblasts using recombinant proteins. Stem Cell Res Ther 2016; 7:99. [PMID: 27473118 PMCID: PMC4967313 DOI: 10.1186/s13287-016-0358-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/13/2016] [Accepted: 06/29/2016] [Indexed: 01/04/2023] Open
Abstract
Background Induced pluripotent mesenchymal stem cells (iPMSCs) are novel candidates for drug screening, regenerative medicine, and cell therapy. However, introduction of transcription factor encoding genes for induced pluripotent stem cell (iPSC) generation which could be used to generate mesenchymal stem cells is accompanied by the risk of insertional mutations in the target cell genome. Methods We demonstrate a novel method using an inactivated viral particle to package and deliver four purified recombinant Yamanaka transcription factors (Sox2, Oct4, Klf4, and c-Myc) resulting in reprogramming of human primary fibroblasts. Whole genome bisulfite sequencing was used to analyze genome-wide CpG methylation of human iPMSCs. Western blot, quantitative PCR, immunofluorescence, and in-vitro differentiation were used to assess the pluripotency of iPMSCs. Results The resulting reprogrammed fibroblasts show high-level expression of stem cell markers. The human fibroblast-derived iPMSC genome showed gains in DNA methylation in low to medium methylated regions and concurrent loss of methylation in previously hypermethylated regions. Most of the differentially methylated regions are close to transcription start sites and many of these genes are pluripotent pathway associated. We found that DNA methylation of these genes is regulated by the four iPSC transcription factors, which functions as an epigenetic switch during somatic reprogramming as reported previously. These iPMSCs successfully differentiate into three embryonic germ layer cells, both in vitro and in vivo. Following multipotency induction in our study, the delivered transcription factors were degraded, leading to an improved efficiency of subsequent programmed differentiation. Conclusion Recombinant transcription factor based reprogramming and derivatization of iPMSC offers a novel high-efficiency approach for regenerative medicine from patient-derived cells. Electronic supplementary material The online version of this article (doi:10.1186/s13287-016-0358-4) contains supplementary material, which is available to authorized users.
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Lee BK, Shen W, Lee J, Rhee C, Chung H, Kim KY, Park IH, Kim J. Tgif1 Counterbalances the Activity of Core Pluripotency Factors in Mouse Embryonic Stem Cells. Cell Rep 2015; 13:52-60. [PMID: 26411691 DOI: 10.1016/j.celrep.2015.08.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/24/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
Core pluripotency factors, such as Oct4, Sox2, and Nanog, play important roles in maintaining embryonic stem cell (ESC) identity by autoregulatory feedforward loops. Nevertheless, the mechanism that provides precise control of the levels of the ESC core factors without indefinite amplification has remained elusive. Here, we report the direct repression of core pluripotency factors by Tgif1, a previously known terminal repressor of TGFβ/activin/nodal signaling. Overexpression of Tgif1 reduces the levels of ESC core factors, whereas its depletion leads to the induction of the pluripotency factors. We confirm the existence of physical associations between Tgif1 and Oct4, Nanog, and HDAC1/2 and further show the level of Tgif1 is not significantly altered by treatment with an activator/inhibitor of the TGFβ/activin/nodal signaling. Collectively, our findings establish Tgif1 as an integral member of the core regulatory circuitry of mouse ESCs that counterbalances the levels of the core pluripotency factors in a TGFβ/activin/nodal-independent manner.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Wenwen Shen
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA
| | - Jiwoon Lee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Catherine Rhee
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Haewon Chung
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, the University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, the University of Texas at Austin, Austin, TX 78712, USA.
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