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Gilbert G, Renaud Y, Teste C, Anglaret N, Bertrand R, Hoehn S, Jurkowski TP, Schuettengruber B, Cavalli G, Waltzer L, Vandel L. Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity. SCIENCE ADVANCES 2024; 10:eadn5861. [PMID: 38701218 PMCID: PMC11068012 DOI: 10.1126/sciadv.adn5861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS.
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Affiliation(s)
- Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Camille Teste
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Nadège Anglaret
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Sven Hoehn
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Tomasz P. Jurkowski
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
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Yang X, Zhou W, Zhou J, Li A, Zhang C, Fang Z, Wang C, Liu S, Hao A, Zhang M. Pcgf5: An important regulatory factor in early embryonic neural induction. Heliyon 2024; 10:e27634. [PMID: 38533065 PMCID: PMC10963245 DOI: 10.1016/j.heliyon.2024.e27634] [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: 11/15/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Abstract
Polycomb group RING finger (PCGF) proteins, a crucial subunits of the Polycomb complex, plays an important role in regulating gene expression, embryonic development, and cell fate determination. In our research, we investigated Pcgf5, one of the six PCGF homologs, and its impact on the differentiation of P19 cells into neural stem cells. Our findings revealed that knockdown of Pcgf5 resulted in a significant decrease in the expression levels of the neuronal markers Sox2, Zfp521, and Pax6, while the expression levels of the pluripotent markers Oct4 and Nanog increased. Conversely, Pcgf5 overexpression upregulated the expression of Sox2 and Pax6, while downregulating the expression of Oct4 and Nanog. Additionally, our analysis revealed that Pcgf5 suppresses Wnt3 expression via the activation of Notch1/Hes1, and ultimately governs the differentiation fate of neural stem cells. To further validate our findings, we conducted in vivo experiments in zebrafish. We found that knockdown of pcgf5a using morpholino resulted in the downregulated expression of neurodevelopmental genes such as sox2, sox3, and foxg1 in zebrafish embryos. Consequently, these changes led to neurodevelopmental defects. In conclusion, our study highlights the important role of Pcgf5 in neural induction and the determination of neural cell fate.
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Affiliation(s)
- Xuan Yang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Wenjuan Zhou
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Juan Zhou
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Anna Li
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Changqing Zhang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Zhenya Fang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Chunying Wang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
| | - Shiyu Liu
- International Center, Jinan Foreign Language School, Jinan, 250108, China
| | - Aijun Hao
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Meihua Zhang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, 250014, China
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Wu J, Fu G, Luo C, Chen L, Liu Q. Cuproptosis-related ceRNA axis triggers cell proliferation and cell cycle through CBX2 in lung adenocarcinoma. BMC Pulm Med 2024; 24:85. [PMID: 38355480 PMCID: PMC10865584 DOI: 10.1186/s12890-024-02887-0] [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: 08/09/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) has high morbidity and mortality. Despite substantial advances in treatment, the prognosis of patients with LUAD remains unfavorable. The ceRNA axis has been reported to play an important role in the pathogenesis of LUAD. In addition, cuproptosis is considered an important factor in tumorigenesis. The expression of CBX2 has been associated with the development of multiple tumors, including LUAD. However, the precise molecular mechanisms through which the cuproptosis-related ceRNA network regulates CBX2 remain unclear. METHODS The DEGs between tumor and normal samples of LUAD were identified in TCGA database. The "ConsensusClusterPlus" R package was used to perform consensus clustering based on the mRNA expression matrix and cuproptosis-related gene expression profile. Then, LASSO-COX regression analysis was performed to identify potential prognostic biomarkers associated with cuproptosis, and the ceRNA network was constructed. Finally, the mechanisms of ceRNA in LUAD was studied by cell experiments. RESULTS In this study, the AC144450.1/miR-424-5p axis was found to promote the progression of LUAD by acting on CBX2. The expression of AC144450.1 and miR-424-5p can be altered to regulate CBX2 and is correlated with cell proliferation and cell cycle of LUAD. Mechanistically, AC144450.1 affects the expression of CBX2 by acting as the ceRNA of miR-424-5p. In addition, a cuproptosis-related model were constructed in this study to predict the prognosis of LUAD. CONCLUSIONS This study is the first to demonstrate that the AC144450.1/miR-424-5p/CBX2 axis is involved in LUAD progression and may serve as a novel target for its diagnosis and treatment.
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Affiliation(s)
- Jiang Wu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Guang Fu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Chao Luo
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Liang Chen
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China
| | - Quanxing Liu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, 400037, Chongqing, China.
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Del Vecchio A, Mulé P, Fernández-Pérez D, Amato S, Lattanzi G, Zanotti M, Rustichelli S, Pivetti S, Oldani P, Mariani A, Iommazzo F, Koseki H, Facciotti F, Tamburri S, Ferrari KJ, Pasini D. PCGF6 controls murine Tuft cell differentiation via H3K9me2 modification independently of Polycomb repression. Dev Cell 2024; 59:368-383.e7. [PMID: 38228142 DOI: 10.1016/j.devcel.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Cell fate is determined by specific transcription programs that are essential for tissue homeostasis and regeneration. The E3-ligases RING1A and B represent the core activity of the Polycomb repressive complex 1 (PRC1) that deposits repressive histone H2AK119 mono-ubiquitination (H2AK119ub1), which is essential for mouse intestinal homeostasis by preserving stem cell functions. However, the specific role of different PRC1 forms, which are defined by the six distinct PCGF1-6 paralogs, remains largely unexplored in vivo. We report that PCGF6 regulates mouse intestinal Tuft cell differentiation independently of H2AK119ub1 deposition. We show that PCGF6 chromatin occupancy expands outside Polycomb repressive domains, associating with unique promoter and distal regulatory elements. This occurs in the absence of RING1A/B and involves MGA-mediated E-BOX recognition and specific H3K9me2 promoter deposition. PCGF6 inactivation induces an epithelial autonomous accumulation of Tuft cells that was not phenocopied by RING1A/B loss. This involves direct PCGF6 association with a Tuft cell differentiation program that identified Polycomb-independent properties of PCGF6 in adult tissues homeostasis.
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Affiliation(s)
- Annachiara Del Vecchio
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Patrizia Mulé
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Georgia Lattanzi
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Samantha Rustichelli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Silvia Pivetti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Paola Oldani
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Mariani
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Fabiola Iommazzo
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Haruhiko Koseki
- RIKEN Centre for Integrative Medical Sciences, Laboratory for Developmental Genetics, 1-7-22 Suehiuro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Federica Facciotti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza, 2, 20126 Milan, Italy
| | - Simone Tamburri
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy
| | - Karin J Ferrari
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
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Chen-Xi G, Jin-Fu X, An-Quan H, Xiao Y, Ying-Hui W, Suo-Yuan L, Cong S, Tian-Ming Z, Jun S. Long non-coding RNA PRR7-AS1 promotes osteosarcoma progression via binding RNF2 to transcriptionally suppress MTUS1. Front Oncol 2023; 13:1227789. [PMID: 38033505 PMCID: PMC10687407 DOI: 10.3389/fonc.2023.1227789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Osteosarcoma is a common bone malignant tumor in adolescents with high mortality and poor prognosis. At present, the progress of osteosarcoma and effective treatment strategies are not clear. This study provides a new potential target for the progression and treatment of osteosarcoma. Methods The relationship between lncRNA PRR7-AS1 and osteosarcoma was analyzed using the osteosarcoma databases and clinical sample testing. Cell function assays and tumor lung metastasis were employed to study the effects of PRR7-AS1 on tumorigenesis in vivo and in vitro. Potential downstream RNF2 of PRR7-AS1 was identified and explored using RNA pulldown and RIP. The GTRD and KnockTF database were used to predict the downstream target gene, MTUS1, and ChIP-qPCR experiments were used to verify the working mechanismy. Rescue experiments were utilized to confirm the role of MTUS1 in the pathway. Results Deep mining of osteosarcoma databases combined with clinical sample testing revealed a positive correlation between lncRNA PRR7-AS1 and osteosarcoma progression. Knockdown of PRR7-AS1 inhibited osteosarcoma cell proliferation and metastasis in vitro and in vivo. Mechanistically, RNA pulldown and RIP revealed that PRR7-AS1 may bind RNF2 to play a cancer-promoting role. ChIP-qPCR experiments were utilized to validate the working mechanism of the downstream target gene MTUS1. RNF2 inhibited the transcription of MTUS1 through histone H2A lysine 119 monoubiquitin. Rescue experiments confirmed MTUS1 as a downstream direct target of PRR7-AS1 and RNF2. Discussion We identified lncRNA PRR7-AS1 as an important oncogene in osteosarcoma progression, indicating that it may be a potential target for diagnosis and prognosis of osteosarcoma.
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Affiliation(s)
- Gu Chen-Xi
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Xu Jin-Fu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Huang An-Quan
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yu Xiao
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Wu Ying-Hui
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Li Suo-Yuan
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Shen Cong
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Zou Tian-Ming
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Shen Jun
- Department of Orthopedic Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
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Ko T, Choi R, Issa K, Gupta R, Llinas E, Morey L, Finlay JB, Goldstein BJ. Polycomb repressive complex 2 regulates basal cell fate during adult olfactory neurogenesis. Stem Cell Reports 2023; 18:2283-2296. [PMID: 37832538 PMCID: PMC10679661 DOI: 10.1016/j.stemcr.2023.09.008] [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: 03/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023] Open
Abstract
Adult neurogenesis occurs in the mammalian olfactory epithelium to maintain populations of neurons that are vulnerable to injury yet essential for olfaction. Multipotent olfactory basal stem cells are activated by damage, although mechanisms regulating lineage decisions are not understood. Using mouse lesion models, we focused on defining the role of Polycomb repressive complexes (PRCs) in olfactory neurogenesis. PRC2 has a well-established role in developing tissues, orchestrating transcriptional programs via chromatin modification. PRC2 proteins are expressed in olfactory globose basal cells (GBCs) and nascent neurons. Conditional PRC2 loss perturbs lesion-induced neuron production, accompanied by altered histone modifications and misexpression of lineage-specific transcription factors in GBCs. De-repression of Sox9 in PRC2-mutant GBCs is accompanied by increased Bowman's gland production, defining an unrecognized role for PRC2 in regulating gland versus neuron cell fate. Our findings support a model for PRC2-dependent mechanisms promoting sensory neuronal differentiation in an adult neurogenic niche.
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Affiliation(s)
- Tiffany Ko
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rhea Choi
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Khalil Issa
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rupali Gupta
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Edward Llinas
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center and Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - John B Finlay
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bradley J Goldstein
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, NC 27710, USA.
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Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
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Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
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Li R, Huang D, Zhao Y, Yuan Y, Sun X, Dai Z, Huo D, Liu X, Helin K, Li MJ, Wu X. PR-DUB safeguards Polycomb repression through H2AK119ub1 restriction. Cell Prolif 2023; 56:e13457. [PMID: 36959757 PMCID: PMC10542648 DOI: 10.1111/cpr.13457] [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: 01/06/2023] [Revised: 03/01/2023] [Accepted: 03/11/2023] [Indexed: 03/25/2023] Open
Abstract
Polycomb group (PcG) proteins are critical chromatin regulators for cell fate control. The mono-ubiquitylation on histone H2AK119 (H2AK119ub1) is one of the well-recognized mechanisms for Polycomb repressive complex 1 (PRC1)-mediated transcription repression. Unexpectedly, the specific H2AK119 deubiquitylation complex composed by additional sex comb-like proteins and BAP1 has also been genetically characterized as Polycomb repressive deubiquitnase (PR-DUB) for unclear reasons. However, it remains a mystery whether and how PR-DUB deficiency affects chromatin states and cell fates through impaired PcG silencing. Here through a careful epigenomic analysis, we demonstrate that a bulk of H2AK119ub1 is diffusely distributed away from promoter regions and their enrichment is positively correlated with PRC1 occupancy. Upon deletion of Asxl2 in mouse embryonic stem cells (ESCs), a pervasive gain of H2AK119ub1 is coincident with increased PRC1 sampling at chromatin. Accordingly, PRC1 is significantly lost from a subset of highly occupied promoters, leading to impaired silencing of associated genes before and after lineage differentiation of Asxl2-null ESCs. Therefore, our study highlights the importance of genome-wide H2AK119ub1 restriction by PR-DUB in safeguarding robust PRC1 deposition and its roles in developmental regulation.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Dandan Huang
- Wuxi School of MedicineJiangnan UniversityWuxi214000China
| | - Yingying Zhao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Ye Yuan
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Xiaoyu Sun
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Zhongye Dai
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Dawei Huo
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Xiaozhi Liu
- Pediatric Center, Tianjin Key Laboratory of Epigenetics for Organ Development of Premature InfantsThe Fifth Central Hospital of TianjinTianjin300450China
| | - Kristian Helin
- Biotech Research and Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Institute of Cancer Research (ICR)LondonUK
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300070China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
- Department of OrthopedicsTianjin Medical University General HospitalTianjin300052China
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Chen Y, Wu Y, Li J, Chen K, Wang W, Ye Z, Feng K, Yang Y, Xu Y, Kang J, Guo X. Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation. Cell Death Discov 2023; 9:244. [PMID: 37452012 PMCID: PMC10349095 DOI: 10.1038/s41420-023-01548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The zinc finger proteins (ZNFs) mediated transcriptional regulation is critical for cell fate transition. However, it is still unclear how the ZNFs realize their specific regulatory roles in the stage-specific determination of cardiomyocyte differentiation. Here, we reported that the zinc fingers and homeoboxes 1 (Zhx1) protein, transiently expressed during the cell fate transition from mesoderm to cardiac progenitors, was indispensable for the proper cardiomyocyte differentiation of mouse and human embryonic stem cells. Moreover, Zhx1 majorly promoted the specification of cardiac progenitors via interacting with hnRNPA1 and co-activated the transcription of a wide range of genes. In-depth mechanistic studies showed that Zhx1 was bound with hnRNPA1 by the amino acid residues (Thr111-His120) of the second Znf domain, thus participating in the formation of cardiac progenitors. Together, our study highlights the unrevealed interaction of Zhx1/hnRNPA1 for activating gene transcription during cardiac progenitor specification and also provides new evidence for the specificity of cell fate determination in cardiomyocyte differentiation.
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Affiliation(s)
- Yang Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianguo Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Kai Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Wuchan Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zihui Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Ke Feng
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yiwei Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Institute for Advanced Study, Tongji University, Shanghai, 200092, China.
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10
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Henry S, Kokity L, Pirity MK. Polycomb protein RYBP activates transcription factor Plagl1 during in vitro cardiac differentiation of mouse embryonic stem cells. Open Biol 2023; 13:220305. [PMID: 36751888 PMCID: PMC9905990 DOI: 10.1098/rsob.220305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
RING1 and YY1 binding protein (RYBP) is primarily known to function as a repressor being a core component of the non-canonical polycomb repressive complexes 1 (ncPRC1s). However, several ncPRC1-independent functions of RYBP have also been described. We previously reported that RYBP is essential for mouse embryonic development and that Rybp null mutant embryonic stem cells cannot form contractile cardiomyocytes (CMCs) in vitro. We also showed that PLAGL1, a cardiac transcription factor, which is often mutated in congenital heart diseases (CHDs), is not expressed in Rybp-null mutant CMCs. However, the underlying mechanism of how RYBP regulates Plagl1 expression was not revealed. Here, we demonstrate that RYBP cooperated with NKX2-5 to transcriptionally activate the P1 and P3 promoters of the Plagl1 gene and that this activation is ncPRC1-independent. We also show that two non-coding RNAs residing in the Plagl1 locus can also regulate the Plagl1 promoters. Finally, PLAGL1 was able to activate Tnnt2, a gene important for contractility of CMCs in transfected HEK293 cells. Our study shows that the activation of Plagl1 by RYBP is important for sarcomere development and contractility, and suggests that RYBP, via its regulatory functions, may contribute to the development of CHDs.
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Affiliation(s)
- Surya Henry
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Lilla Kokity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Melinda Katalin Pirity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary
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11
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Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
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Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.,Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
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12
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Liu J, Jiang Y, Huang H, Xu J, Wu Y, Wang Q, Zhu Y, Zheng B, Shen C, Qian W, Shen J. BMI-1 promotes breast cancer proliferation and metastasis through different mechanisms in different subtypes. Cancer Sci 2022; 114:449-462. [PMID: 36285479 PMCID: PMC9899611 DOI: 10.1111/cas.15623] [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: 05/24/2022] [Revised: 09/18/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is among the most common malignant cancers in women. B-cell-specific Moloney murine leukemia virus integration site 1 (BMI-1) is a transcriptional repressor that has been shown to be involved in tumorigenesis, the cell cycle, and stem cell maintenance. In our study, increased expression of BMI-1 was found in both human triple negative breast cancer and luminal A-type breast cancer tissues compared with adjacent tissues. We also found that knockdown of BMI-1 significantly suppressed cell proliferation and migration in vitro and in vivo. Further mechanistic research demonstrated that BMI-1 directly bound to the promoter region of CDKN2D/BRCA1 and inhibited its transcription in MCF-7/MDA-MB-231. More importantly, we discovered that knockdown of CDKN2D/BRCA1 could promote cell proliferation and migration after repression by PTC-209. Our results reveal that BMI-1 transcriptionally suppressed BRCA1 in TNBC cell lines whereas, in luminal A cell lines, CDKN2D was the target gene. This provides a reference for the precise treatment of different types of breast cancer in clinical practice.
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Affiliation(s)
- Jin‐yan Liu
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Yan‐nan Jiang
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Hai Huang
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Jin‐fu Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and EmbryologyNanjing Medical UniversityNanjingChina
| | - Ying‐hui Wu
- Department of Orthopaedic SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal HospitalSuzhouChina
| | - Qiang Wang
- Department of Orthopaedic SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal HospitalSuzhouChina
| | - Yue Zhu
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and GeneticsThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Wei‐feng Qian
- Department of Breast and Thyroid SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Jun Shen
- Department of Orthopaedic SurgeryThe Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal HospitalSuzhouChina
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13
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Wang Y, Wang W, Cheng K, Geng K, Liang J, Wang P, Zhang J, Niu S, Jia L, Zhang S, Li L, Feng X, Wang C, Wang H, Zhang H, Zhang Y. Polycomb subunit Pcgf2 mediates ovulation and fertility through transcriptional regulation progesterone receptor. Front Cell Dev Biol 2022; 10:1010601. [DOI: 10.3389/fcell.2022.1010601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Ovarian follicles are the fundamental structure to support oocyte development, which provides mature oocytes for offspring. This process requires granulosa cells (GCs) to respond to the midcycle surge of hormones, leading to GC proliferation and differentiation by a series of genes’ transcriptional expression changes. Epigenetic mediator, Polycomb Repressive Complex 1 (PRC1) has been reported to function in fetal ovarian development. However, its functional relevance to folliculogenesis and ovulation remains unknown. In this study, we demonstrated that GC-selective depletion of PCGF2, a key component of PRC1, led to the loss of follicles, ovulation defects, and a lengthened estrus cycle, resulting in subfertility in female mice. The expression of PCGF2 is in the GCs of growing follicles and increases after human chorionic gonadotropin (hCG) stimulation. PCGF2 bound to the promoter of the key ovulation gene progesterone receptor (Pgr) and upregulated the expression of Pgr by targeting the epigenetic modification of H2AK119ub1 after hCG surge. Consistently, the expression of downstream genes of Pgr also sharply decreased, which resulted in the follicular rupture failed and oocyte entrapped in corpus luteum in GC-specific Pcgf2 knockout mice. Together, our study identified that PCGF2 is essential for folliculogenesis and ovulation via modulating hormone receptor expression.
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14
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Liang Q, Wang S, Zhou X, Li Y, Xing S, Sha Y, Yang F, Huang W, Liu N, Li Z, Chen Y, Xu Y, Zhu P, Lan F, Sun N. Essential role of MESP1-RING1A complex in cardiac differentiation. Dev Cell 2022; 57:2533-2549.e7. [DOI: 10.1016/j.devcel.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/04/2022] [Accepted: 10/24/2022] [Indexed: 11/23/2022]
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15
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Kim JJ, Kingston RE. Context-specific Polycomb mechanisms in development. Nat Rev Genet 2022; 23:680-695. [PMID: 35681061 PMCID: PMC9933872 DOI: 10.1038/s41576-022-00499-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
Abstract
Polycomb group (PcG) proteins are crucial chromatin regulators that maintain repression of lineage-inappropriate genes and are therefore required for stable cell fate. Recent advances show that PcG proteins form distinct multi-protein complexes in various cellular environments, such as in early development, adult tissue maintenance and cancer. This surprising compositional diversity provides the basis for mechanistic diversity. Understanding this complexity deepens and refines the principles of PcG complex recruitment, target-gene repression and inheritance of memory. We review how the core molecular mechanism of Polycomb complexes operates in diverse developmental settings and propose that context-dependent changes in composition and mechanism are essential for proper epigenetic regulation in development.
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Affiliation(s)
- Jongmin J. Kim
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E. Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,
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16
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Li T. The functions of polycomb group proteins in T cells. CELL INSIGHT 2022; 1:100048. [PMID: 37193554 PMCID: PMC10120301 DOI: 10.1016/j.cellin.2022.100048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 05/18/2023]
Abstract
T cells are involved in many aspects of adaptive immunity, including autoimmunity, anti-tumor activity, and responses to allergenic substances and pathogens. T cells undergo comprehensive epigenome remodeling in response to signals. Polycomb group (PcG) proteins are a well-studied complex of chromatin regulators, conserved in animals, and function in various biological processes. PcG proteins are divided into two distinct complexes: PRC1 (Polycomb repressive complex 1) and PRC2. PcG is correlated with the regulation of T cell development, phenotypic transformation, and function. In contrast, PcG dysregulation is correlated with pathogenesis of immune-mediated diseases and compromised anti-tumor responses. This review discusses recent findings on the involvement of PcG proteins in T cell maturation, differentiation, and activation. In addition, we explore implications in the development of the immune system diseases and cancer immunity, which offers promising targets for various treatment protocols.
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Affiliation(s)
- Ting Li
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qixiangtai Road, Tianjin, 300070, China
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17
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Doyle EJ, Morey L, Conway E. Know when to fold 'em: Polycomb complexes in oncogenic 3D genome regulation. Front Cell Dev Biol 2022; 10:986319. [PMID: 36105358 PMCID: PMC9464936 DOI: 10.3389/fcell.2022.986319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is spatially and temporally regulated through a series of orchestrated processes resulting in the formation of 3D chromatin structures such as topologically associating domains (TADs), loops and Polycomb Bodies. These structures are closely linked to transcriptional regulation, with loss of control of these processes a frequent feature of cancer and developmental syndromes. One such oncogenic disruption of the 3D genome is through recurrent dysregulation of Polycomb Group Complex (PcG) functions either through genetic mutations, amplification or deletion of genes that encode for PcG proteins. PcG complexes are evolutionarily conserved epigenetic complexes. They are key for early development and are essential transcriptional repressors. PcG complexes include PRC1, PRC2 and PR-DUB which are responsible for the control of the histone modifications H2AK119ub1 and H3K27me3. The spatial distribution of the complexes within the nuclear environment, and their associated modifications have profound effects on the regulation of gene transcription and the 3D genome. Nevertheless, how PcG complexes regulate 3D chromatin organization is still poorly understood. Here we glean insights into the role of PcG complexes in 3D genome regulation and compaction, how these processes go awry during tumorigenesis and the therapeutic implications that result from our insights into these mechanisms.
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Affiliation(s)
- Emma J. Doyle
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Lluis Morey
- Sylvester Comprehensive Cancer Centre, Miami, FL, United States
- Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eric Conway
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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18
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Lan X, Ding S, Zhang T, Yi Y, Li C, Jin W, Chen J, Liang K, Wang H, Jiang W. PCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression. Nat Commun 2022; 13:4601. [PMID: 35933409 PMCID: PMC9357003 DOI: 10.1038/s41467-022-32295-z] [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: 09/30/2021] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Polycomb group (PcG) proteins are known to repress developmental genes during embryonic development and tissue homeostasis. Here, we report that PCGF6 controls neuroectoderm specification of human pluripotent stem cells (PSCs) by activating SOX2 gene. Human PSCs with PCGF6 depletion display impaired neuroectoderm differentiation coupled with increased mesendoderm outcomes. Transcriptome analysis reveals that de-repression of the WNT/β-catenin signaling pathway is responsible for the differentiation of PSC toward the mesendodermal lineage. Interestingly, PCGF6 and MYC directly interact and co-occupy a distal regulatory element of SOX2 to activate SOX2 expression, which likely accounts for the regulation in neuroectoderm differentiation. Supporting this notion, genomic deletion of the SOX2-regulatory element phenocopies the impaired neuroectoderm differentiation, while overexpressing SOX2 rescues the neuroectoderm phenotype caused by PCGF6-depletion. Together, our study reveals that PCGF6 can function as lineage switcher between mesendoderm and neuroectoderm in human PSCs by both suppression and activation mechanisms. Variant Polycomb complexes can have tissue-specific roles during development. Here they show that PCGF6 controls lineage-specification in human PSCs by promoting neuroectoderm differentiation and repressing mesendoderm differentiation via distinct downstream targets.
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Affiliation(s)
- Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Song Ding
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Yi
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenwen Jin
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Jian Chen
- Chinese Institute for Brain Research (Beijing), Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, 102206, Beijing, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Hengbin Wang
- Department of Internal Medicine, Division of Hematology, Oncology, and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China. .,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China.
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19
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The Epigenetic Regulatory Protein CBX2 Promotes mTORC1 Signalling and Inhibits DREAM Complex Activity to Drive Breast Cancer Cell Growth. Cancers (Basel) 2022; 14:cancers14143491. [PMID: 35884550 PMCID: PMC9321755 DOI: 10.3390/cancers14143491] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Chromobox 2 (CBX2) is a chromatin-binding component of polycomb repressive complex 1, which causes gene silencing. CBX2 expression is elevated in triple-negative breast cancer (TNBC), for which there are few therapeutic options. Here, we aimed to investigate the functional role of CBX2 in TNBC. CBX2 knockdown in TNBC models reduced cell numbers, which was rescued by ectopic expression of wild-type CBX2 but not a chromatin binding-deficient mutant. Blocking CBX2 chromatin interactions using the inhibitor SW2_152F also reduced cell growth, suggesting CBX2 chromatin binding is crucial for TNBC progression. RNA sequencing and gene set enrichment analysis of CBX2-depleted cells identified downregulation of oncogenic signalling pathways, including mTORC1 and E2F signalling. Subsequent analysis identified that CBX2 represses the expression of mTORC1 inhibitors and the tumour suppressor RBL2. RBL2 repression, in turn, inhibits DREAM complex activity. The DREAM complex inhibits E2F signalling, causing cell senescence; therefore, inhibition of the DREAM complex via CBX2 may be a key oncogenic driver. We observed similar effects in oestrogen receptor-positive breast cancer, and analysis of patient datasets suggested CBX2 inhibits RBL2 activity in other cancer types. Therapeutic inhibition of CBX2 could therefore repress mTORC1 activation and promote DREAM complex-mediated senescence in TNBC and could have similar effects in other cancer types.
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20
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Functional redundancy among Polycomb complexes in maintaining the pluripotent state of embryonic stem cells. Stem Cell Reports 2022; 17:1198-1214. [PMID: 35364009 PMCID: PMC9120860 DOI: 10.1016/j.stemcr.2022.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb group proteins assemble into multi-protein complexes, known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2), that guide cell fate decisions during embryonic development. PRC1 forms an array of biochemically distinct canonical PRC1 (cPRC1) or non-canonical PRC1 (ncPRC1) complexes characterized by the mutually exclusive presence of PCGF (PCGF1-PCGF6) paralog subunit; however, whether each one of these subcomplexes fulfills a distinct role remains largely controversial. Here, by performing a CRISPR-based loss-of-function screen in embryonic stem cells (ESCs), we uncovered a previously unappreciated functional redundancy among PRC1 subcomplexes. Disruption of ncPRC1, but not cPRC1, displayed severe defects in ESC pluripotency. Remarkably, coablation of non-canonical and canonical PRC1 in ESCs resulted in exacerbation of the phenotype observed in the non-canonical PRC1-null ESCs, highlighting the importance of functional redundancy among PRC1 subcomplexes. Together, our studies demonstrate that PRC1 subcomplexes act redundantly to silence lineage-specific genes and ensure robust maintenance of ESC identity. cPRC1 complexes are not the key determinant of self-renewal and pluripotency in ESCs ncPRC1 complexes play a fundamental and redundant role in maintaining pluripotency in ESCs cPRC1 and ncPRC1 act redundantly to suppress lineage-specific genes and preserve ESC identity
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21
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Parreno V, Martinez AM, Cavalli G. Mechanisms of Polycomb group protein function in cancer. Cell Res 2022; 32:231-253. [PMID: 35046519 PMCID: PMC8888700 DOI: 10.1038/s41422-021-00606-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/10/2021] [Indexed: 02/01/2023] Open
Abstract
AbstractCancer arises from a multitude of disorders resulting in loss of differentiation and a stem cell-like phenotype characterized by uncontrolled growth. Polycomb Group (PcG) proteins are members of multiprotein complexes that are highly conserved throughout evolution. Historically, they have been described as essential for maintaining epigenetic cellular memory by locking homeotic genes in a transcriptionally repressed state. What was initially thought to be a function restricted to a few target genes, subsequently turned out to be of much broader relevance, since the main role of PcG complexes is to ensure a dynamically choregraphed spatio-temporal regulation of their numerous target genes during development. Their ability to modify chromatin landscapes and refine the expression of master genes controlling major switches in cellular decisions under physiological conditions is often misregulated in tumors. Surprisingly, their functional implication in the initiation and progression of cancer may be either dependent on Polycomb complexes, or specific for a subunit that acts independently of other PcG members. In this review, we describe how misregulated Polycomb proteins play a pleiotropic role in cancer by altering a broad spectrum of biological processes such as the proliferation-differentiation balance, metabolism and the immune response, all of which are crucial in tumor progression. We also illustrate how interfering with PcG functions can provide a powerful strategy to counter tumor progression.
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22
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Yakushiji-Kaminatsui N, Kondo T, Ohinata Y, Takano J, Koseki H. Genetic, Genomic, and Imaging Approaches to Dissect the Role of Polycomb Group Epigenetic Regulators in Mice. Methods Mol Biol 2022; 2529:207-228. [PMID: 35733017 DOI: 10.1007/978-1-0716-2481-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Among the most important histone methyltransferases for metazoan development are EZH1/2 and their homologs, which methylate histone H3 lysine 27 and act as part of a highly conserved set of chromatin regulators called Polycomb Group (PcG) proteins. Reaching a precise understanding of the roles of PcG proteins in the orchestration of differentiation and the maintenance of cell identity requires a variety of genetic and molecular approaches. Here, we present a full suite of methods for the study of PcG proteins in early murine development, including mutant strain generation, embryonic stem cell derivation, epigenomic profiling, and immunofluorescence and in situ hybridization.
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Affiliation(s)
- Nayuta Yakushiji-Kaminatsui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan.
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan
| | - Yasuhide Ohinata
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Junichiro Takano
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan.
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan.
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23
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Blackledge NP, Klose RJ. The molecular principles of gene regulation by Polycomb repressive complexes. Nat Rev Mol Cell Biol 2021; 22:815-833. [PMID: 34400841 PMCID: PMC7612013 DOI: 10.1038/s41580-021-00398-y] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Precise control of gene expression is fundamental to cell function and development. Although ultimately gene expression relies on DNA-binding transcription factors to guide the activity of the transcription machinery to genes, it has also become clear that chromatin and histone post-translational modification have fundamental roles in gene regulation. Polycomb repressive complexes represent a paradigm of chromatin-based gene regulation in animals. The Polycomb repressive system comprises two central protein complexes, Polycomb repressive complex 1 (PRC1) and PRC2, which are essential for normal gene regulation and development. Our early understanding of Polycomb function relied on studies in simple model organisms, but more recently it has become apparent that this system has expanded and diverged in mammals. Detailed studies are now uncovering the molecular mechanisms that enable mammalian PRC1 and PRC2 to identify their target sites in the genome, communicate through feedback mechanisms to create Polycomb chromatin domains and control transcription to regulate gene expression. In this Review, we discuss and contextualize the emerging principles that define how this fascinating chromatin-based system regulates gene expression in mammals.
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Affiliation(s)
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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24
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Ercoskun P, Yuce Kahraman C, Adanur Saglam K, Kanjee M, Tatar A. A new case of Turnpenny-Fry syndrome. Am J Med Genet A 2021; 188:688-691. [PMID: 34750959 DOI: 10.1002/ajmg.a.62560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 11/07/2022]
Abstract
Turnpenny-Fry syndrome is a very rare genetic disorder characterized by intellectual disability, developmental delay, facial dysmorphism, and skeletal abnormalities. Mutations of the PCGF2 gene are responsible for Turnpenny-Fry syndrome. This gene encodes the polycomb group ring finger 2 protein that is broadly expressed in various human tissues. To date, only 13 patients with Turnpenny-Fry syndrome have been reported. Our patient was referred to our clinic for neuromotor retardation and dysmorphic features. Whole exome sequencing (WES) was performed from the peripheral blood sample of the patient. WES revealed a heterozygous mutation in the PCGF2 gene. To the best of our knowledge, we reported the 14th patient with Turnpenny-Fry syndrome and the first from Turkey, who had new findings.
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Affiliation(s)
- Pelin Ercoskun
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Cigdem Yuce Kahraman
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Kübra Adanur Saglam
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Momen Kanjee
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Abdulgani Tatar
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, Turkey
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25
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Wang S, C Ordonez-Rubiano S, Dhiman A, Jiao G, Strohmier BP, Krusemark CJ, Dykhuizen EC. Polycomb group proteins in cancer: multifaceted functions and strategies for modulation. NAR Cancer 2021; 3:zcab039. [PMID: 34617019 PMCID: PMC8489530 DOI: 10.1093/narcan/zcab039] [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: 04/09/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/12/2022] Open
Abstract
Polycomb repressive complexes (PRCs) are a heterogenous collection of dozens, if not hundreds, of protein complexes composed of various combinations of subunits. PRCs are transcriptional repressors important for cell-type specificity during development, and as such, are commonly mis-regulated in cancer. PRCs are broadly characterized as PRC1 with histone ubiquitin ligase activity, or PRC2 with histone methyltransferase activity; however, the mechanism by which individual PRCs, particularly the highly diverse set of PRC1s, alter gene expression has not always been clear. Here we review the current understanding of how PRCs act, both individually and together, to establish and maintain gene repression, the biochemical contribution of individual PRC subunits, the mis-regulation of PRC function in different cancers, and the current strategies for modulating PRC activity. Increased mechanistic understanding of PRC function, as well as cancer-specific roles for individual PRC subunits, will uncover better targets and strategies for cancer therapies.
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Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University and Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907 USA
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26
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Blanco E, González-Ramírez M, Di Croce L. Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. Sci Rep 2021; 11:19545. [PMID: 34599234 PMCID: PMC8486768 DOI: 10.1038/s41598-021-98889-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu, and the source code is freely distributed at https://github.com/eblancoga/seqcode.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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27
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Dobrinić P, Szczurek AT, Klose RJ. PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency. Nat Struct Mol Biol 2021; 28:811-824. [PMID: 34608337 PMCID: PMC7612713 DOI: 10.1038/s41594-021-00661-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 08/10/2021] [Indexed: 12/15/2022]
Abstract
The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The inter-relatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics, we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.
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Affiliation(s)
- Paula Dobrinić
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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28
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Flora P, Dalal G, Cohen I, Ezhkova E. Polycomb Repressive Complex(es) and Their Role in Adult Stem Cells. Genes (Basel) 2021; 12:1485. [PMID: 34680880 PMCID: PMC8535826 DOI: 10.3390/genes12101485] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/31/2022] Open
Abstract
Populations of resident stem cells (SCs) are responsible for maintaining, repairing, and regenerating adult tissues. In addition to having the capacity to generate all the differentiated cell types of the tissue, adult SCs undergo long periods of quiescence within the niche to maintain themselves. The process of SC renewal and differentiation is tightly regulated for proper tissue regeneration throughout an organisms' lifetime. Epigenetic regulators, such as the polycomb group (PcG) of proteins have been implicated in modulating gene expression in adult SCs to maintain homeostatic and regenerative balances in adult tissues. In this review, we summarize the recent findings that elucidate the composition and function of the polycomb repressive complex machinery and highlight their role in diverse adult stem cell compartments.
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Affiliation(s)
- Pooja Flora
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
| | - Gil Dalal
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Elena Ezhkova
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
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29
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Sugishita H, Kondo T, Ito S, Nakayama M, Yakushiji-Kaminatsui N, Kawakami E, Koseki Y, Ohinata Y, Sharif J, Harachi M, Blackledge NP, Klose RJ, Koseki H. Variant PCGF1-PRC1 links PRC2 recruitment with differentiation-associated transcriptional inactivation at target genes. Nat Commun 2021; 12:5341. [PMID: 34504070 PMCID: PMC8429492 DOI: 10.1038/s41467-021-24894-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/23/2021] [Indexed: 12/21/2022] Open
Abstract
Polycomb repressive complexes-1 and -2 (PRC1 and 2) silence developmental genes in a spatiotemporal manner during embryogenesis. How Polycomb group (PcG) proteins orchestrate down-regulation of target genes upon differentiation, however, remains elusive. Here, by differentiating embryonic stem cells into embryoid bodies, we reveal a crucial role for the PCGF1-containing variant PRC1 complex (PCGF1-PRC1) to mediate differentiation-associated down-regulation of a group of genes. Upon differentiation cues, transcription is down-regulated at these genes, in association with PCGF1-PRC1-mediated deposition of histone H2AK119 mono-ubiquitination (H2AK119ub1) and PRC2 recruitment. In the absence of PCGF1-PRC1, both H2AK119ub1 deposition and PRC2 recruitment are disrupted, leading to aberrant expression of target genes. PCGF1-PRC1 is, therefore, required for initiation and consolidation of PcG-mediated gene repression during differentiation. Polycomb repressive complexes (PRC1 and PRC2) repress genes that are crucial for development via epigenetic modifications; however, their role in differentiation is not well known. Here the authors reveal that a PCGF1-containing PRC1 variant facilitates exit from pluripotency by downregulating target genes and recruiting PRC2.
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Affiliation(s)
- Hiroki Sugishita
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan.,International Research Center for Neurointelligence (IRCN), Institutes for Advanced Study, The University of Tokyo, Bunkyo-ku, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | | | - Eiryo Kawakami
- Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Healthcare and Medical Data Driven AI based Predictive Reasoning Development Unit, RIKEN Medical Sciences Innovation Hub Program, Yokohama, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yasuhide Ohinata
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mio Harachi
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan.
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30
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Wang S, Alpsoy A, Sood S, Ordonez-Rubiano SC, Dhiman A, Sun Y, Jiao G, Krusemark CJ, Dykhuizen EC. A Potent, Selective CBX2 Chromodomain Ligand and Its Cellular Activity During Prostate Cancer Neuroendocrine Differentiation. Chembiochem 2021; 22:2335-2344. [PMID: 33950564 PMCID: PMC8358665 DOI: 10.1002/cbic.202100118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/04/2021] [Indexed: 12/16/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic regulators that facilitate both embryonic development and cancer progression. PcG proteins form Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). PRC2 trimethylates histone H3 lysine 27 (H3K27me3), a histone mark recognized by the N-terminal chromodomain (ChD) of the CBX subunit of canonical PRC1. There are five PcG CBX paralogs in humans. CBX2 in particular is upregulated in a variety of cancers, particularly in advanced prostate cancers. Using CBX2 inhibitors to understand and target CBX2 in prostate cancer is highly desirable; however, high structural similarity among the CBX ChDs has been challenging for developing selective CBX ChD inhibitors. Here, we utilize selections of focused DNA encoded libraries (DELs) for the discovery of a selective CBX2 chromodomain probe, SW2_152F. SW2_152F binds to CBX2 ChD with a Kd of 80 nM and displays 24-1000-fold selectivity for CBX2 ChD over other CBX paralogs in vitro. SW2_152F is cell permeable, selectively inhibits CBX2 chromatin binding in cells, and blocks neuroendocrine differentiation of prostate cancer cell lines in response to androgen deprivation.
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Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Life Science Interdisciplinary Graduate Program, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Life Science Interdisciplinary Graduate Program, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Sandra Carolina Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Yixing Sun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Center for Cancer Research, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Emily C. Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Center for Cancer Research, 201 S. University St. West Lafayette, IN, 47907 USA
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31
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Liu J, Liu S, Han L, Sheng Y, Zhang Y, Kim IM, Wan J, Yang L. LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells. Development 2021; 148:268341. [PMID: 34027990 PMCID: PMC8276986 DOI: 10.1242/dev.199628] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
Polycomb repressive complex 2 (PRC2) deposits H3K27me3 on chromatin to silence transcription. PRC2 broadly interacts with RNAs. Currently, the role of the RNA-PRC2 interaction in human cardiogenesis remains elusive. Here, we found that human-specific heart brake lncRNA 1 (HBL1) interacted with two PRC2 subunits, JARID2 and EED, in human pluripotent stem cells (hPSCs). Loss of JARID2, EED or HBL1 significantly enhanced cardiac differentiation from hPSCs. HBL1 depletion disrupted genome-wide PRC2 occupancy and H3K27me3 chromatin modification on essential cardiogenic genes, and broadly enhanced cardiogenic gene transcription in undifferentiated hPSCs and later-on differentiation. In addition, ChIP-seq revealed reduced EED occupancy on 62 overlapped cardiogenic genes in HBL1−/− and JARID2−/− hPSCs, indicating that the epigenetic state of cardiogenic genes was determined by HBL1 and JARID2 at pluripotency stage. Furthermore, after cardiac development occurs, the cytosolic and nuclear fractions of HBL1 could crosstalk via a conserved ‘microRNA-1-JARID2’ axis to modulate cardiogenic gene transcription. Overall, our findings delineate the indispensable role of HBL1 in guiding PRC2 function during early human cardiogenesis, and expand the mechanistic scope of lncRNA(s) that cytosolic and nuclear portions of HBL1 could coordinate to orchestrate human cardiogenesis. Summary: This study reveals the indispensable role of the lncRNA HBL1 in guiding PRC2 function during early human cardiogenesis, and uncovers the crosstalk of the cytosolic and nuclear regions of HBL1 to orchestrate human cardiac development.
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Affiliation(s)
- Juli Liu
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lei Han
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yi Sheng
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yucheng Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Il-Man Kim
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lei Yang
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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32
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PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Nat Commun 2021; 12:2829. [PMID: 33990559 PMCID: PMC8121881 DOI: 10.1038/s41467-021-22871-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/03/2021] [Indexed: 12/13/2022] Open
Abstract
Polycomb group (PcG) proteins maintain cell identity by repressing gene expression during development. Surprisingly, emerging studies have recently reported that a number of PcG proteins directly activate gene expression during cell fate determination process. However, the mechanisms by which they direct gene activation in pluripotency remain poorly understood. Here, we show that Phc1, a subunit of canonical polycomb repressive complex 1 (cPRC1), can exert its function in pluripotency maintenance via a PRC1-independent activation of Nanog. Ablation of Phc1 reduces the expression of Nanog and overexpression of Nanog partially rescues impaired pluripotency caused by Phc1 depletion. We find that Phc1 interacts with Nanog and activates Nanog transcription by stabilizing the genome-wide chromatin interactions of the Nanog locus. This adds to the already known canonical function of PRC1 in pluripotency maintenance via a PRC1-dependent repression of differentiation genes. Overall, our study reveals a function of Phc1 to activate Nanog transcription through regulating chromatin architecture and proposes a paradigm for PcG proteins to maintain pluripotency. Phc1 is a subunit of the polycomb repressive complex 1 (PRC1), which represses gene expression during development. Here the authors show that Phc1 acts independently from PRC1 to activate Nanog transcription by stabilizing genome-wide chromatin interactions of the Nanog locus, and in turn stabilize pluripotency.
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33
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Fursova NA, Turberfield AH, Blackledge NP, Findlater EL, Lastuvkova A, Huseyin MK, Dobrinić P, Klose RJ. BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome. Genes Dev 2021; 35:749-770. [PMID: 33888563 PMCID: PMC8091973 DOI: 10.1101/gad.347005.120] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification.
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Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anne H Turberfield
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Emma L Findlater
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Paula Dobrinić
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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34
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Maat H, Atsma TJ, Hogeling SM, Rodríguez López A, Jaques J, Olthuis M, de Vries MP, Gravesteijn C, Brouwers-Vos AZ, van der Meer N, Datema S, Salzbrunn J, Huls G, Baas R, Martens JHA, van den Boom V, Schuringa JJ. The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia. iScience 2021; 24:102435. [PMID: 34113809 PMCID: PMC8169803 DOI: 10.1016/j.isci.2021.102435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/05/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
In an attempt to unravel functionality of the non-canonical PRC1.1 Polycomb complex in human leukemogenesis, we show that USP7 and TRIM27 are integral components of PRC1.1. USP7 interactome analyses show that PRC1.1 is the predominant Polycomb complex co-precipitating with USP7. USP7 inhibition results in PRC1.1 disassembly and loss of chromatin binding, coinciding with reduced H2AK119ub and H3K27ac levels and diminished gene transcription of active PRC1.1-controlled loci, whereas H2AK119ub marks are also lost at PRC1 loci. TRIM27 and USP7 are reciprocally required for incorporation into PRC1.1, and TRIM27 knockdown partially rescues USP7 inhibitor sensitivity. USP7 inhibitors effectively impair proliferation in AML cells in vitro, also independent of the USP7-MDM2-TP53 axis, and MLL-AF9-induced leukemia is delayed in vivo in human leukemia xenografts. We propose a model where USP7 counteracts TRIM27 E3 ligase activity, thereby maintaining PRC1.1 integrity and function. Moreover, USP7 inhibition may be a promising new strategy to treat AML patients. We identify USP7 and TRIM27 as integral components of non-canonical PRC1.1 USP7 inhibition results in PRC1.1 disassembly and loss of chromatin binding TRIM27 and USP7 are reciprocally required for incorporation into PRC1.1 USP7 inhibitors effectively impair AML proliferation, also independent of TP53
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Affiliation(s)
- Henny Maat
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Tjerk Jan Atsma
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Shanna M Hogeling
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Aida Rodríguez López
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Jennifer Jaques
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Mirjam Olthuis
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Pharmacy, Interfaculty Mass Spectrometry Center, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Department of Pediatrics, Center for Liver, Digestive, and Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Chantal Gravesteijn
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Annet Z Brouwers-Vos
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nisha van der Meer
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Suzan Datema
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Jonas Salzbrunn
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Gerwin Huls
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Roy Baas
- Division of Biochemistry and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - Vincent van den Boom
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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35
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Yu J, Wu Y, Li H, Zhou H, Shen C, Gao T, Lin M, Dai X, Ou J, Liu M, Huang X, Zheng B, Sun F. BMI1 Drives Steroidogenesis Through Epigenetically Repressing the p38 MAPK Pathway. Front Cell Dev Biol 2021; 9:665089. [PMID: 33928089 PMCID: PMC8076678 DOI: 10.3389/fcell.2021.665089] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/22/2021] [Indexed: 11/18/2022] Open
Abstract
Testosterone biosynthesis progressively decreases in aging males primarily as a result of functional changes to Leydig cells. Despite this, the mechanisms underlying steroidogenesis remain largely unclear. Using gene knock-out approaches, we and others have recently identified Bmi1 as an anti-aging gene. Herein, we investigate the role of BMI1 in steroidogenesis using mouse MLTC-1 and primary Leydig cells. We show that BMI1 can positively regulate testosterone production. Mechanistically, in addition to its known role in antioxidant activity, we also report that p38 mitogen-activated protein kinase (MAPK) signaling is activated, and testosterone levels reduced, in BMI1-deficient cells; however, the silencing of the p38 MAPK pathway restores testosterone production. Furthermore, we reveal that BMI1 directly binds to the promoter region of Map3k3, an upstream activator of p38, thereby modulating its chromatin status and repressing its expression. Consequently, this results in the inhibition of the p38 MAPK pathway and the promotion of steroidogenesis. Our study uncovered a novel epigenetic mechanism in steroidogenesis involving BMI1-mediated gene silencing and provides potential therapeutic targets for the treatment of hypogonadism.
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Affiliation(s)
- Jun Yu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, China
| | - Yibo Wu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Hong Li
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Hui Zhou
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Tingting Gao
- Center of Clinical Reproductive Medicine, The Affiliated Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University, Changzhou, China
| | - Meng Lin
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Xiuliang Dai
- Center of Clinical Reproductive Medicine, The Affiliated Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University, Changzhou, China
| | - Jian Ou
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
| | - Meiling Liu
- National Health Commission Key Laboratory of Male Reproductive Health, National Research Institute for Family Planning, Beijing, China
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China.,National Health Commission Key Laboratory of Male Reproductive Health, National Research Institute for Family Planning, Beijing, China
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, China
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36
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AKT-mediated regulation of chromatin ubiquitylation and tumorigenesis through Mel18 phosphorylation. Oncogene 2021; 40:2422-2436. [PMID: 33664452 DOI: 10.1038/s41388-020-01602-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 01/31/2023]
Abstract
Polycomb repressor complex 1 (PRC1) is linked to the regulation of gene expression and histone ubiquitylation conformation, which contributes to carcinogenesis. However, the upstream regulators of PRC1 biogenesis machinery remain obscure. Here, we report that the polycomb group-related mammalian gene Mel18 is a target of the protein kinase AKT. AKT phosphorylates Mel18 at T334 to disrupt the interaction between Mel18 and other PRC1 members, leading to attenuated PRC1-dependent ubiquitylation of histone H2A at Lys119. As such, PRC1 target genes, many of which are known oncogenes, are derepressed upon T334-Mel18 phosphorylation, which promotes malignant behaviours, including cell proliferation, tumour formation, migration and invasion, bone and brain metastatic lesion formation. Notably, a positive correlation between AKT activity and pT334-Mel18 is observed, and prognostic models based on p-AKT and pT334-Mel18 that predicted overall survival and distant metastasis-free survival in breast cancer patients are established. These findings have implications for understanding the role of AKT and its associated proteins in chromatin ubiquitylation, and also indicate the AKT-Mel18-H2AK119ub axis as a novel prognostic biomarker and therapeutic target for cancer patients.
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37
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The Role of Polycomb Group Protein BMI1 in DNA Repair and Genomic Stability. Int J Mol Sci 2021; 22:ijms22062976. [PMID: 33804165 PMCID: PMC7998361 DOI: 10.3390/ijms22062976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/31/2022] Open
Abstract
The polycomb group (PcG) proteins are a class of transcriptional repressors that mediate gene silencing through histone post-translational modifications. They are involved in the maintenance of stem cell self-renewal and proliferation, processes that are often dysregulated in cancer. Apart from their canonical functions in epigenetic gene silencing, several studies have uncovered a function for PcG proteins in DNA damage signaling and repair. In particular, members of the poly-comb group complexes (PRC) 1 and 2 have been shown to recruit to sites of DNA damage and mediate DNA double-strand break repair. Here, we review current understanding of the PRCs and their roles in cancer development. We then focus on the PRC1 member BMI1, discussing the current state of knowledge of its role in DNA repair and genome integrity, and outline how it can be targeted pharmacologically.
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38
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He J, Babarinde IA, Sun L, Xu S, Chen R, Shi J, Wei Y, Li Y, Ma G, Zhuang Q, Hutchins AP, Chen J. Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE. Nat Commun 2021; 12:1456. [PMID: 33674594 PMCID: PMC7935913 DOI: 10.1038/s41467-021-21808-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) make up a majority of a typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity. How transposable elements (TE) contribute to cell fate changes is unclear. Here, the authors generate a pipeline to quantify TE expression from single cell data. They show the dynamic expression of TEs from gastrulation to somatic cell reprogramming and human disease
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Affiliation(s)
- Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Isaac A Babarinde
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Li Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Shuyang Xu
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruhai Chen
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junjie Shi
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanjie Wei
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yuhao Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Gang Ma
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Qiang Zhuang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China. .,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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39
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Youmans DT, Gooding AR, Dowell RD, Cech TR. Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells. Mol Cell 2021; 81:488-501.e9. [PMID: 33338397 PMCID: PMC7867654 DOI: 10.1016/j.molcel.2020.11.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) silences expression of developmental transcription factors in pluripotent stem cells by methylating lysine 27 on histone H3. Two mutually exclusive subcomplexes, PRC2.1 and PRC2.2, are defined by the set of accessory proteins bound to the core PRC2 subunits. Here we introduce separation-of-function mutations into the SUZ12 subunit of PRC2 to drive it into a PRC2.1 or 2.2 subcomplex in human induced pluripotent stem cells (iPSCs). We find that PRC2.2 occupies polycomb target genes at low levels and that homeobox transcription factors are upregulated when this complex is exclusively present. In contrast with previous studies, we find that chromatin occupancy of PRC2 increases drastically when it is forced to form PRC2.1. Additionally, several cancer-associated mutations also coerce formation of PRC2.1. We suggest that PRC2 chromatin occupancy can be altered in the context of disease or development by tuning the ratio of PRC2.1 to PRC2.2.
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Affiliation(s)
- Daniel T Youmans
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; Medical Scientist Training Program, University of Colorado School of Medicine, Aurora, CO 80045, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Anne R Gooding
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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40
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Elsherbiny A, Dobreva G. Epigenetic memory of cell fate commitment. Curr Opin Cell Biol 2021; 69:80-87. [PMID: 33535129 DOI: 10.1016/j.ceb.2020.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
During development, discrete cell fates are established in precise spatiotemporal order guided by morphogen signals. These signals converge in the nucleus to induce transcriptional and epigenetic programming that determines cell fate. Once cell identity is established, cell programs have to be accurately sustained through multiple rounds of cell division, during which DNA replication serves as a window of opportunity for altering cell fate. In this review, we summarize recent advances in understanding the molecular players that underlie epigenetic memory of cell fate decisions, with a particular focus on histone modifications and mitotic bookmarking factors. We also discuss the different mechanisms of inheritance of repressed and active chromatin states.
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Affiliation(s)
- Adel Elsherbiny
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany.
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41
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Li X, Ji G, Zhou J, Du J, Li X, Shi W, Hu Y, Zhou W, Hao A. Pcgf1 Regulates Early Neural Tube Development Through Histone Methylation in Zebrafish. Front Cell Dev Biol 2021; 8:581636. [PMID: 33575252 PMCID: PMC7870693 DOI: 10.3389/fcell.2020.581636] [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: 07/09/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
The neural induction constitutes the initial step in the generation of the neural tube. Pcgf1, as one of six Pcgf paralogs, is a maternally expressed gene, but its role and mechanism in early neural induction during neural tube development have not yet been explored. In this study, we found that zebrafish embryos exhibited a small head and reduced or even absence of telencephalon after inhibiting the expression of Pcgf1. Moreover, the neural induction process of zebrafish embryos was abnormally activated, and the subsequent NSC self-renewal was inhibited after injecting the Pcgf1 MO. The results of in vitro also showed that knockdown of Pcgf1 increased the expression levels of the neural markers Pax6, Pou3f1, and Zfp521, but decreased the expression levels of the pluripotent markers Oct4, Hes1, and Nanog, which further confirmed that Pcgf1 was indispensable for maintaining the pluripotency of P19 cells. To gain a better understanding of the role of Pcgf1 in early development, we analyzed mRNA profiles from Pcgf1-deficient P19 cells using RNA-seq. We found that the differentially expressed genes were enriched in many functional categories, which related to the development phenotype, and knockdown of Pcgf1 increased the expression of histone demethylases. Finally, our results showed that Pcgf1 loss-of-function decreased the levels of transcriptional repression mark H3K27me3 at the promoters of Ngn1 and Otx2, and the levels of transcriptional activation mark H3K4me3 at the promoters of Pou5f3 and Nanog. Together, our findings reveal that Pcgf1 might function as both a facilitator for pluripotent maintenance and a repressor for neural induction.
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Affiliation(s)
- Xinyue Li
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guangyu Ji
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Juan Zhou
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jingyi Du
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xian Li
- Department of Foot and Ankle Surgery, Cheeloo College of Medicine, The Second Hospital, Shandong University, Jinan, China
| | - Wei Shi
- Department of Blood Transfusion, Qilu Hospital of Shandong University, Jinan, China
| | - Yong Hu
- Department of Foot and Ankle Surgery, Cheeloo College of Medicine, The Second Hospital, Shandong University, Jinan, China
| | - Wenjuan Zhou
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Aijun Hao
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
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42
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Guo Y, Zhao S, Wang GG. Polycomb Gene Silencing Mechanisms: PRC2 Chromatin Targeting, H3K27me3 'Readout', and Phase Separation-Based Compaction. Trends Genet 2021; 37:547-565. [PMID: 33494958 DOI: 10.1016/j.tig.2020.12.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022]
Abstract
Modulation of chromatin structure and/or modification by Polycomb repressive complexes (PRCs) provides an important means to partition the genome into functionally distinct subdomains and to regulate the activity of the underlying genes. Both the enzymatic activity of PRC2 and its chromatin recruitment, spreading, and eviction are exquisitely regulated via interactions with cofactors and DNA elements (such as unmethylated CpG islands), histones, RNA (nascent mRNA and long noncoding RNA), and R-loops. PRC2-catalyzed histone H3 lysine 27 trimethylation (H3K27me3) is recognized by distinct classes of effectors such as canonical PRC1 and BAH module-containing proteins (notably BAHCC1 in human). These effectors mediate gene silencing by different mechanisms including phase separation-related chromatin compaction and histone deacetylation. We discuss recent advances in understanding the structural architecture of PRC2, the regulation of its activity and chromatin recruitment, and the molecular mechanisms underlying Polycomb-mediated gene silencing. Because PRC deregulation is intimately associated with the development of diseases, a better appreciation of Polycomb-based (epi)genomic regulation will have far-reaching implications in biology and medicine.
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Affiliation(s)
- Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
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Feng Y, Pauklin S. Revisiting 3D chromatin architecture in cancer development and progression. Nucleic Acids Res 2020; 48:10632-10647. [PMID: 32941624 PMCID: PMC7641747 DOI: 10.1093/nar/gkaa747] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/21/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Cancer development and progression are demarcated by transcriptional dysregulation, which is largely attributed to aberrant chromatin architecture. Recent transformative technologies have enabled researchers to examine the genome organization at an unprecedented dimension and precision. In particular, increasing evidence supports the essential roles of 3D chromatin architecture in transcriptional homeostasis and proposes its alterations as prominent causes of human cancer. In this article, we will discuss the recent findings on enhancers, enhancer-promoter interaction, chromatin topology, phase separation and explore their potential mechanisms in shaping transcriptional dysregulation in cancer progression. In addition, we will propose our views on how to employ state-of-the-art technologies to decode the unanswered questions in this field. Overall, this article motivates the study of 3D chromatin architecture in cancer, which allows for a better understanding of its pathogenesis and develop novel approaches for diagnosis and treatment of cancer.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford OX3 7LD, U.K
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford OX3 7LD, U.K
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Balakrishnan I, Danis E, Pierce A, Madhavan K, Wang D, Dahl N, Sanford B, Birks DK, Davidson N, Metselaar DS, Meel MH, Lemma R, Donson A, Vijmasi T, Katagi H, Sola I, Fosmire S, Alimova I, Steiner J, Gilani A, Hulleman E, Serkova NJ, Hashizume R, Hawkins C, Carcaboso AM, Gupta N, Monje M, Jabado N, Jones K, Foreman N, Green A, Vibhakar R, Venkataraman S. Senescence Induced by BMI1 Inhibition Is a Therapeutic Vulnerability in H3K27M-Mutant DIPG. Cell Rep 2020; 33:108286. [PMID: 33086074 PMCID: PMC7574900 DOI: 10.1016/j.celrep.2020.108286] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/05/2020] [Accepted: 09/25/2020] [Indexed: 01/19/2023] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an incurable brain tumor of childhood characterized by histone mutations at lysine 27, which results in epigenomic dysregulation. There has been a failure to develop effective treatment for this tumor. Using a combined RNAi and chemical screen targeting epigenomic regulators, we identify the polycomb repressive complex 1 (PRC1) component BMI1 as a critical factor for DIPG tumor maintenance in vivo. BMI1 chromatin occupancy is enriched at genes associated with differentiation and tumor suppressors in DIPG cells. Inhibition of BMI1 decreases cell self-renewal and attenuates tumor growth due to induction of senescence. Prolonged BMI1 inhibition induces a senescence-associated secretory phenotype, which promotes tumor recurrence. Clearance of senescent cells using BH3 protein mimetics co-operates with BMI1 inhibition to enhance tumor cell killing in vivo.
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Affiliation(s)
- Ilango Balakrishnan
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Etienne Danis
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Angela Pierce
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Krishna Madhavan
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Dong Wang
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nathan Dahl
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Bridget Sanford
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Diane K Birks
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nate Davidson
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis S Metselaar
- Princess Máxima Center for Pediatric Oncology, Utrecht and Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Michaël Hananja Meel
- Princess Máxima Center for Pediatric Oncology, Utrecht and Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rakeb Lemma
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Donson
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Trinka Vijmasi
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Hiroaki Katagi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ismail Sola
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Fosmire
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Irina Alimova
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Jenna Steiner
- Departments of Radiology, Radiation Oncology, and Anesthesiology, Colorado Animal Imaging Shared Resource (AISR), University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ahmed Gilani
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht and Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Natalie J Serkova
- Departments of Radiology, Radiation Oncology, and Anesthesiology, Colorado Animal Imaging Shared Resource (AISR), University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rintaro Hashizume
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Cynthia Hawkins
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Angel M Carcaboso
- Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona 08950, Spain
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle Monje
- Departments of Neurology, Neurosurgery, Pediatrics, and Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada
| | - Kenneth Jones
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Nicholas Foreman
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Adam Green
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
| | - Rajeev Vibhakar
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
| | - Sujatha Venkataraman
- Department of Pediatrics and Section of Pediatric Hematology/Oncology/BMT, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA; The Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA.
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The genetic basis for PRC1 complex diversity emerged early in animal evolution. Proc Natl Acad Sci U S A 2020; 117:22880-22889. [PMID: 32868440 DOI: 10.1073/pnas.2005136117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Polycomb group proteins are essential regulators of developmental processes across animals. Despite their importance, studies on Polycomb are often restricted to classical model systems and, as such, little is known about the evolution of these important chromatin regulators. Here we focus on Polycomb Repressive Complex 1 (PRC1) and trace the evolution of core components of canonical and non-canonical PRC1 complexes in animals. Previous work suggested that a major expansion in the number of PRC1 complexes occurred in the vertebrate lineage. We show that the expansion of the Polycomb Group RING Finger (PCGF) protein family, an essential step for the establishment of the large diversity of PRC1 complexes found in vertebrates, predates the bilaterian-cnidarian ancestor. This means that the genetic repertoire necessary to form all major vertebrate PRC1 complexes emerged early in animal evolution, over 550 million years ago. We further show that PCGF5, a gene conserved in cnidarians and vertebrates but lost in all other studied groups, is expressed in the nervous system in the sea anemone Nematostella vectensis, similar to its mammalian counterpart. Together this work provides a framework for understanding the evolution of PRC1 complex diversity and it establishes Nematostella as a promising model system in which the functional ramifications of this diversification can be further explored.
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Giner-Laguarda N, Vidal M. Functions of Polycomb Proteins on Active Targets. EPIGENOMES 2020; 4:17. [PMID: 34968290 PMCID: PMC8594714 DOI: 10.3390/epigenomes4030017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Chromatin regulators of the Polycomb group of genes are well-known by their activities as transcriptional repressors. Characteristically, their presence at genomic sites occurs with specific histone modifications and sometimes high-order chromatin structures correlated with silencing of genes involved in cell differentiation. However, evidence gathered in recent years, on flies and mammals, shows that in addition to these sites, Polycomb products bind to a large number of active regulatory regions. Occupied sites include promoters and also intergenic regions, containing enhancers and super-enhancers. Contrasting with occupancies at repressed targets, characteristic histone modifications are low or undetectable. Functions on active targets are dual, restraining gene expression at some targets while promoting activity at others. Our aim here is to summarize the evidence available and discuss the convenience of broadening the scope of research to include Polycomb functions on active targets.
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Affiliation(s)
| | - Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain;
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Gentile C, Kmita M. Polycomb Repressive Complexes in Hox Gene Regulation: Silencing and Beyond: The Functional Dynamics of Polycomb Repressive Complexes in Hox Gene Regulation. Bioessays 2020; 42:e1900249. [PMID: 32743818 DOI: 10.1002/bies.201900249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/17/2020] [Indexed: 11/10/2022]
Abstract
The coordinated expression of the Hox gene family encoding transcription factors is critical for proper embryonic development and patterning. Major efforts have thus been dedicated to understanding mechanisms controlling Hox expression. In addition to the temporal and spatial sequential activation of Hox genes, proper embryonic development requires that Hox genes get differentially silenced in a cell-type specific manner as development proceeds. Factors contributing to Hox silencing include the polycomb repressive complexes (PRCs), which control gene expression through epigenetic modifications. This review focuses on PRC-dependent regulation of the Hox genes and is aimed at integrating the growing complexity of PRC functional properties in the context of Hox regulation. In particular, mechanisms underlying PRC binding dynamics as well as a series of studies that have revealed the impact of PRC on the 3D organization of the genome is discussed, which has a significant role on Hox regulation during development.
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Affiliation(s)
- Claudia Gentile
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Département de Médecine, Université de Montréal, Montréal, Quebec, H3C 3J7, Canada
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48
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Henry S, Szabó V, Sutus E, Pirity MK. RYBP is important for cardiac progenitor cell development and sarcomere formation. PLoS One 2020; 15:e0235922. [PMID: 32673370 PMCID: PMC7365410 DOI: 10.1371/journal.pone.0235922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/24/2020] [Indexed: 12/28/2022] Open
Abstract
We have previously established that epigenetic regulator RING1 and YY1 binding protein (RYBP) is required for the contractility of embryonic stem (ES) cell derived cardiomyocytes (CMCs), suggesting its essential role in contractility. In order to investigate the underlying molecular events of this phenotype, we compared the transcriptomic profile of the wild type and Rybp null mutant ES cells and CMCs differentiated from these cell lines. We identified genes related to ion homeostasis, cell adhesion and sarcomeric organization affected in the Rybp null mutant CMCs, by using hierarchical gene clustering and Gene Ontology analysis. We have also demonstrated that the amount of RYBP is drastically reduced in the terminally differentiated wild type CMCs whilst it is broadly expressed in the early phase of differentiation when progenitors form. We also describe that RYBP is important for the proper expression of key cardiac transcription factors including Mesp1, Shh and Mef2c. These findings identify Rybp as a gene important for both early cardiac gene transcription and consequent sarcomere formation necessary for contractility. Since impairment of sarcomeric function and contractility plays a central role in reduced cardiac pump function leading to heart failures in human, current results might be relevant to the pathophysiology of cardiomyopathies.
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Affiliation(s)
- Surya Henry
- Biological Research Centre, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Viktória Szabó
- Biological Research Centre, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Enikő Sutus
- Biological Research Centre, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
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49
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Zhang Y, Chan HL, Garcia-Martinez L, Karl DL, Weich N, Slingerland JM, Verdun RE, Morey L. Estrogen induces dynamic ERα and RING1B recruitment to control gene and enhancer activities in luminal breast cancer. SCIENCE ADVANCES 2020; 6:eaaz7249. [PMID: 32548262 PMCID: PMC7274770 DOI: 10.1126/sciadv.aaz7249] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/02/2020] [Indexed: 05/04/2023]
Abstract
RING1B, a core Polycomb repressive complex 1 subunit, is a histone H2A ubiquitin ligase essential for development. RING1B is overexpressed in patients with luminal breast cancer (BC) and recruited to actively transcribed genes and enhancers co-occupied by the estrogen receptor α (ERα). Whether ERα-induced transcriptional programs are mediated by RING1B is not understood. We show that prolonged estrogen administration induces transcriptional output and chromatin landscape fluctuations. RING1B loss impairs full estrogen-mediated gene expression and chromatin accessibility for key BC transcription factors. These effects were mediated, in part, by RING1B enzymatic activity and nucleosome binding functions. RING1B is recruited in a cyclic manner to ERα, FOXA1, and GRHL2 cobound sites and regulates estrogen-induced enhancers and ERα recruitment. Last, ChIP exo revealed multiple binding events of these factors at single-nucleotide resolution, including RING1B occupancy approximately 10 base pairs around ERα bound sites. We propose RING1B as a key regulator of the dynamic, liganded-ERα transcriptional regulatory circuit in luminal BC.
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Affiliation(s)
- Yusheng Zhang
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Ho Lam Chan
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Liliana Garcia-Martinez
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Daniel L. Karl
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Natalia Weich
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joyce M. Slingerland
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Braman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ramiro E. Verdun
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA
- Corresponding author.
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50
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The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells. Commun Biol 2020; 3:262. [PMID: 32451438 PMCID: PMC7248108 DOI: 10.1038/s42003-020-0984-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/01/2020] [Indexed: 01/05/2023] Open
Abstract
Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. Human embryonic stem cells (hESCs) have a unique chromatin architecture characterized by low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess the link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of the ubiquitin-conjugating enzyme UBE2K. Loss of UBE2K upregulates the trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Besides H3K9 trimethylation, UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates histone H3 levels and H3K9 trimethylation in Caenorhabditis elegans germ cells. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells. Azra Fatima et al. show that ubiquitin-conjugating enzyme UBE2K regulates neurogenic potential through its target histone H3 in human embryonic stem cells. This study suggests that UBE2K promotes histone H3 degradation, reducing the H3K9me3 repressive marks in immortal cells of both worms and humans.
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