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Guan S, Tang J, Ma X, Miao R, Cheng B. CBX7C⋅PHC2 interaction facilitates PRC1 assembly and modulates its phase separation properties. iScience 2024; 27:109548. [PMID: 38600974 PMCID: PMC11004992 DOI: 10.1016/j.isci.2024.109548] [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: 08/06/2023] [Revised: 02/04/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
CBX7 is a key component of PRC1 complex. Cbx7C is an uncharacterized Cbx7 splicing isoform specifically expressed in mouse embryonic stem cells (mESCs). We demonstrate that CBX7C functions as an epigenetic repressor at the classic PRC1 targets in mESCs, and its preferential interaction to PHC2 facilitates PRC1 assembly. Both Cbx7C and Phc2 are significantly upregulated during cell differentiation, and knockdown of Cbx7C abolishes the differentiation of mESCs to embryoid bodies. Interestingly, CBX7C⋅PHC2 interaction at low levels efficiently undergoes the formation of functional Polycomb bodies with high mobility, whereas the coordination of the two factors at high doses results in the formation of large, low-mobility, chromatin-free aggregates. Overall, these findings uncover the unique roles and molecular basis of the CBX7C⋅PHC2 interaction in PRC1 assembly on chromatin and Pc body formation and open a new avenue of controlling PRC1 activities via modulation of its phase separation properties.
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Affiliation(s)
- Shanli Guan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Jiajia Tang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Ruidong Miao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Bo Cheng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
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Song YL, Yang MH, Zhang S, Wang H, Kai KL, Yao CX, Dai FF, Zhou MJ, Li JB, Wei ZR, Yin Z, Zhu WG, Xue L, Zang MX. A GRIP-1-EZH2 switch binding to GATA-4 is linked to the genesis of rhabdomyosarcoma through miR-29a. Oncogene 2022; 41:5223-5237. [PMID: 36309571 DOI: 10.1038/s41388-022-02521-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 12/14/2022]
Abstract
Terminal differentiation failure is an important cause of rhabdomyosarcoma genesis, however, little is known about the epigenetic regulation of aberrant myogenic differentiation. Here, we show that GATA-4 recruits polycomb group proteins such as EZH2 to negatively regulate miR-29a in undifferentiated C2C12 myoblast cells, whereas recruitment of GRIP-1 to GATA-4 proteins displaces EZH2, resulting in the activation of miR-29a during myogenic differentiation of C2C12 cells. Moreover, in poorly differentiated rhabdomyosarcoma cells, EZH2 still binds to the miR-29a promoter with GATA-4 to mediate transcriptional repression of miR-29a. Interestingly, once re-differentiation of rhabdomyosarcoma cells toward skeletal muscle, EZH2 was dispelled from miR-29a promoter which is similar to that in myogenic differentiation of C2C12 cells. Eventually, this expression of miR-29a results in limited rhabdomyosarcoma cell proliferation and promotes myogenic differentiation. We thus establish that GATA-4 can function as a molecular switch in the up- and downregulation of miR-29a expression. We also demonstrate that GATA-4 acts as a tumor suppressor in rhabdomyosarcoma partly via miR-29a, which thus provides a potential therapeutic target for rhabdomyosarcoma.
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Affiliation(s)
- Yang-Liu Song
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ming-Hui Yang
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Si Zhang
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hao Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Kun-Lun Kai
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chun-Xia Yao
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Fei-Fei Dai
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Meng-Jiao Zhou
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jin-Biao Li
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhi-Ru Wei
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhongnan Yin
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Lixiang Xue
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China.
- Cancer Center of Peking University Third Hospital, Peking University Third Hospital, Beijing, 100191, China.
| | - Ming-Xi Zang
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
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Hu FF, Chen H, Duan Y, Lan B, Liu CJ, Hu H, Dong X, Zhang Q, Cheng YM, Liu M, Guo AY, Xuan C. CBX2 and EZH2 cooperatively promote the growth and metastasis of lung adenocarcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:670-684. [PMID: 35070495 PMCID: PMC8760531 DOI: 10.1016/j.omtn.2021.12.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022]
Abstract
The disruption of epigenetic regulation is common in tumors; the abnormal expression of epigenetic factors leads to cancer occurrence and development. In this study, to investigate the potential function of histone methylation regulators in lung adenocarcinoma (LUAD), we performed differential expression analysis using RNA-seq data downloaded from The Cancer Genome Atlas (TCGA) database, and identified CBX2 and EZH2 as obviously upregulated histone methylation regulators. CBX2 knockdown significantly inhibited LUAD cell growth and metastasis in vitro and in vivo. The combined high expression of CBX2 and EZH2 was an indicator of poor prognosis in LUAD. The inhibition of both CBX2 and EZH2 exerted cooperative suppressive effects on the growth and metastasis of LUAD cells. Mechanistically, we revealed that CBX2 and EZH2 downregulated several PPAR signaling pathway genes and tumor suppressor genes through binding to their promoter cooperatively or separately. Furthermore, knockdown of CBX2 improved the therapeutic efficiency of EZH2 inhibitor on A549 cells. Our study reveals the cooperative oncogenic role of CBX2 and EZH2 in promoting LUAD progression, thereby providing potential targets for LUAD diagnosis and therapy.
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Affiliation(s)
- Fei-Fei Hu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.,Brain Science and Advanced Technology Institute, School of medicine, Wuhan University of Science & Technology, Wuhan, Hubei 430065, China.,Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hao Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yang Duan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.,Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong 261041, China
| | - Bei Lan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Chun-Jie Liu
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hui Hu
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xu Dong
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Qiong Zhang
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yi-Ming Cheng
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Min Liu
- Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Shandong 250014, China
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chenghao Xuan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
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Kang SJ, Chun T. Structural heterogeneity of the mammalian polycomb repressor complex in immune regulation. Exp Mol Med 2020; 52:1004-1015. [PMID: 32636442 PMCID: PMC8080698 DOI: 10.1038/s12276-020-0462-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/21/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
Epigenetic regulation is mainly mediated by enzymes that can modify the structure of chromatin by altering the structure of DNA or histones. Proteins involved in epigenetic processes have been identified to study the detailed molecular mechanisms involved in the regulation of specific mRNA expression. Evolutionarily well-conserved polycomb group (PcG) proteins can function as transcriptional repressors by the trimethylation of histone H3 at the lysine 27 residue (H3K27me3) and the monoubiquitination of histone H2A at the lysine 119 residue (H2AK119ub). PcG proteins form two functionally distinct protein complexes: polycomb repressor complex 1 (PRC1) and PRC2. In mammals, the structural heterogeneity of each PRC complex is dramatically increased by several paralogs of its subunit proteins. Genetic studies with transgenic mice along with RNA-seq and chromatin immunoprecipitation (ChIP)-seq analyses might be helpful for defining the cell-specific functions of paralogs of PcG proteins. Here, we summarize current knowledge about the immune regulatory role of PcG proteins related to the compositional diversity of each PRC complex and introduce therapeutic drugs that target PcG proteins in hematopoietic malignancy. Protein complexes that suppress gene activity by remodeling chromatin, the substance that contains most of a cell’s DNA, play a critical role in regulating the immune system and provide a therapeutic target for treating blood cancers. Seok-Jin Kang and Taehoon Chun from Korea University in Seoul, South Korea, review how polycomb group proteins, best known for their function in embryonic development, also contribute to the formation of immune cells from blood stem cell precursors. Studies with stem cells and cancer cells have begun to reveal many targets of these proteins, and drug companies are evaluating candidate agents directed against some polycomb group proteins in patients with lymphoma and other cancers. More comprehensive profiling of protein function across a broad range of immune cell types could reveal new targets for additional diseases associated with immune dysfunction.
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Affiliation(s)
- Seok-Jin Kang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Taehoon Chun
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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5
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Cohen I, Bar C, Ezhkova E. Activity of PRC1 and Histone H2AK119 Monoubiquitination: Revising Popular Misconceptions. Bioessays 2020; 42:e1900192. [PMID: 32196702 PMCID: PMC7585675 DOI: 10.1002/bies.201900192] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/12/2020] [Indexed: 12/21/2022]
Abstract
Polycomb group proteins are evolutionary conserved chromatin-modifying complexes, essential for the regulation of developmental and cell-identity genes. Polycomb-mediated transcriptional regulation is provided by two multi-protein complexes known as Polycomb repressive complex 1 (PRC1) and 2 (PRC2). Recent studies positioned PRC1 as a foremost executer of Polycomb-mediated transcriptional control. Mammalian PRC1 complexes can form multiple sub-complexes that vary in their core and accessory subunit composition, leading to fascinating and diverse transcriptional regulatory mechanisms employed by PRC1 complexes. These mechanisms include PRC1-catalytic activity toward monoubiquitination of histone H2AK119, a well-established hallmark of PRC1 complexes, whose importance has been long debated. In this review, the central roles that PRC1-catalytic activity plays in transcriptional repression are emphasized and the recent evidence supporting a role for PRC1 complexes in gene activation is discussed.
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Affiliation(s)
- Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
- These authors contributed equally to this work
| | - Carmit Bar
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology; Icahn School of Medicine at Mount Sinai; 1 Gustave L. Levy Place, New York, NY 10029; USA
- These authors contributed equally to this work
| | - Elena Ezhkova
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
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6
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Ramirez-Prado JS, Latrasse D, Rodriguez-Granados NY, Huang Y, Manza-Mianza D, Brik-Chaouche R, Jaouannet M, Citerne S, Bendahmane A, Hirt H, Raynaud C, Benhamed M. The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1118-1131. [PMID: 31437321 DOI: 10.1111/tpj.14502] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Polycomb repressive complexes (PRCs) have been traditionally associated with the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional upregulation. Consistently, increased expression of these two transcription factors leads to the misregulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019, and ANAC055 overexpressers in several of their phenotypes, including increased aphid resistance, abscisic acid (ABA) sensitivity and drought tolerance. In addition, like the MYC2 and ANAC overexpressers, lhp1 displays reduced salicylic acid (SA) content caused by a deregulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress-responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine tuning the complex balance between developmental and stress-responsive processes.
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Affiliation(s)
- Juan Sebastian Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Maelle Jaouannet
- CNRS, INRA, Université Nice Sophia Antipolis, UMR 1355-7254, Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Heribert Hirt
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Cecile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
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7
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Günther T, Fröhlich J, Herrde C, Ohno S, Burkhardt L, Adler H, Grundhoff A. A comparative epigenome analysis of gammaherpesviruses suggests cis-acting sequence features as critical mediators of rapid polycomb recruitment. PLoS Pathog 2019; 15:e1007838. [PMID: 31671162 PMCID: PMC6932816 DOI: 10.1371/journal.ppat.1007838] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 12/26/2019] [Accepted: 09/18/2019] [Indexed: 12/23/2022] Open
Abstract
Latent Kaposi sarcoma-associated herpesvirus (KSHV) genomes rapidly acquire distinct patterns of the activating histone modification H3K4-me3 as well as repressive H3K27-me3 marks, a modification linked to transcriptional silencing by polycomb repressive complexes (PRC). Interestingly, PRCs have recently been reported to restrict viral gene expression in a number of other viral systems, suggesting they may play a broader role in controlling viral chromatin. If so, it is an intriguing possibility that latency establishment may result from viral subversion of polycomb-mediated host responses to exogenous DNA. To investigate such scenarios we sought to establish whether rapid repression by PRC constitutes a general hallmark of herpesvirus latency. For this purpose, we performed a comparative epigenome analysis of KSHV and the related murine gammaherpesvirus 68 (MHV-68). We demonstrate that, while latently replicating MHV-68 genomes readily acquire distinct patterns of activation-associated histone modifications upon de novo infection, they fundamentally differ in their ability to efficiently attract H3K27-me3 marks. Statistical analyses of ChIP-seq data from in vitro infected cells as well as in vivo latency reservoirs furthermore suggest that, whereas KSHV rapidly attracts PRCs in a genome-wide manner, H3K27-me3 acquisition by MHV-68 genomes may require spreading from initial seed sites to which PRC are recruited as the result of an inefficient or stochastic recruitment, and that immune pressure may be needed to select for latency pools harboring PRC-silenced episomes in vivo. Using co-infection experiments and recombinant viruses, we also show that KSHV's ability to rapidly and efficiently acquire H3K27-me3 marks does not depend on the host cell environment or unique properties of the KSHV-encoded LANA protein, but rather requires specific cis-acting sequence features. We show that the non-canonical PRC1.1 component KDM2B, a factor which binds to unmethylated CpG motifs, is efficiently recruited to KSHV genomes, indicating that CpG island characteristics may constitute these features. In accord with the fact that, compared to MHV-68, KSHV genomes exhibit a fundamentally higher density of CpG motifs, we furthermore demonstrate efficient acquisition of H2AK119-ub by KSHV and H3K36-me2 by MHV-68 (but not vice versa), furthermore supporting the notion that KSHV genomes rapidly attract PRC1.1 complexes in a genome-wide fashion. Collectively, our results suggest that rapid PRC silencing is not a universal feature of viral latency, but that some viruses may rather have adopted distinct genomic features to specifically exploit default host pathways that repress epigenetically naive, CpG-rich DNA.
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Affiliation(s)
- Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jacqueline Fröhlich
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Christina Herrde
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Shinji Ohno
- Comprehensive Pneumology Center, Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Lia Burkhardt
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Heiko Adler
- Comprehensive Pneumology Center, Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Munich, Germany
- German Center of Lung Research (DZL), Giessen, Germany
- * E-mail: (HA); (AG)
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail: (HA); (AG)
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8
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Abstract
Though genetic data suggest that Polycomb group proteins (PcGs) are central chromatin modifiers and repressors that have been implicated in control of embryonic stem cell (ESC) pluripotency, the precise mechanism of PcG complex recruitment remains elusive, especially in mammals. We now report that the first and second MBT repeats of L3mbtl2 are important structural and functional features that are necessary and sufficient for L3mbtl2-mediated recruitment of PRC1.6 complex to target promoters. Interestingly, this region of L3mbtl2 harbors the evolutionarily conserved Pho-binding pocket also present in Drosophila Sfmbt, and mutation of the critical residues within this pocket completely abolishes its interaction with target promoters. Additionally, decreased PRC1.6 chromatin occupancy was observed following loss of individual components (L3mbtl2, Pcgf6, and Max) of the complex. Our findings suggest that the recruitment of noncanonical PRC1.6 complex in ESCs might be the result of L3mbtl2's interaction with multiple components of the complex.
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9
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A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention. J Virol 2019; 93:JVI.02143-18. [PMID: 30814291 DOI: 10.1128/jvi.02143-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/07/2019] [Indexed: 12/14/2022] Open
Abstract
Chromatin-based modifications of herpesviral genomes play a crucial role in dictating the outcome of infection. Consistent with this, host cell multiprotein complexes, such as polycomb repressive complexes (PRCs), were proposed to act as epigenetic regulators of herpesviral latency. In particular, PRC2 has recently been shown to contribute to the silencing of human cytomegalovirus (HCMV) genomes. Here, we identify a novel proviral role of PRC1 and PRC2, the two main polycomb repressive complexes, during productive HCMV infection. Western blot analyses revealed strong HCMV-mediated upregulation of RING finger protein 1B (RING1B) and B lymphoma Moloney murine leukemia virus insertion region 1 homolog (BMI1) as well as of enhancer of zeste homolog 2 (EZH2), suppressor of zeste 12 (SUZ12), and embryonic ectoderm development (EED), which constitute the core components of PRC1 and PRC2, respectively. Furthermore, we observed a relocalization of PRC components to viral replication compartments, whereas histone modifications conferred by the respective PRCs were specifically excluded from these sites. Depletion of individual PRC1/PRC2 proteins by RNA interference resulted in a significant reduction of newly synthesized viral genomes and, in consequence, a decreased release of viral particles. Furthermore, accelerated native isolation of protein on nascent DNA (aniPOND) revealed a physical association of EZH2 and BMI1 with nascent HCMV DNA, suggesting a direct contribution of PRC proteins to viral DNA replication. Strikingly, substances solely inhibiting the enzymatic activity of PRC1/2 did not exert antiviral effects, while drugs affecting the abundance of PRC core components strongly compromised HCMV genome synthesis and particle release. Taken together, our data reveal an enzymatically independent, noncanonical function of both PRC1 and PRC2 during HCMV DNA replication, which may serve as a novel cellular target for antiviral therapy.IMPORTANCE Polycomb group (PcG) proteins are primarily known as transcriptional repressors that modify chromatin and contribute to the establishment and maintenance of cell fates. Furthermore, emerging evidence indicates that overexpression of PcG proteins in various types of cancers contributes to the dysregulation of cellular proliferation. Consequently, several inhibitors targeting PcG proteins are presently undergoing preclinical and clinical evaluation. Here, we show that infection with human cytomegalovirus also induces a strong upregulation of several PcG proteins. Our data suggest that viral DNA replication depends on a noncanonical function of polycomb repressor complexes which is independent of the so-far-described enzymatic activities of individual PcG factors. Importantly, we observe that a subclass of inhibitory drugs that affect the abundance of PcG proteins strongly interferes with viral replication. This principle may serve as a novel promising target for antiviral treatment.
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10
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Brand M, Nakka K, Zhu J, Dilworth FJ. Polycomb/Trithorax Antagonism: Cellular Memory in Stem Cell Fate and Function. Cell Stem Cell 2019; 24:518-533. [PMID: 30951661 PMCID: PMC6866673 DOI: 10.1016/j.stem.2019.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stem cells are continuously challenged with the decision to either self-renew or adopt a new fate. Self-renewal is regulated by a system of cellular memory, which must be bypassed for differentiation. Previous studies have identified Polycomb group (PcG) and Trithorax group (TrxG) proteins as key modulators of cellular memory. In this Perspective, we draw from embryonic and adult stem cell studies to discuss the complex roles played by PcG and TrxG in maintaining cell identity while allowing for microenvironment-mediated alterations in cell fate. Finally, we discuss the potential for targeting these proteins as a therapeutic approach in cancer.
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Affiliation(s)
- Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6.
| | - Kiran Nakka
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6
| | - Jiayu Zhu
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6.
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11
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Lebedeva LA, Yakovlev KV, Kozlov EN, Schedl P, Deshpande G, Shidlovskii YV. Transcriptional quiescence in primordial germ cells. Crit Rev Biochem Mol Biol 2018; 53:579-595. [PMID: 30280955 DOI: 10.1080/10409238.2018.1506733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In most animal species, newly formed primordial germ cells (PGCs) acquire the special characteristics that distinguish them from the surrounding somatic cells. Proper fate specification of the PGCs is coupled with transcriptional quiescence, whether they are segregated by determinative or inductive mechanisms. Inappropriate differentiation of PGCs into somatic cells is thought to be prevented due to repression of RNA polymerase (Pol) II-dependent transcription. In the case of a determinative mode of PGC formation (Drosophila, Caenorhabditis elegans, etc.), there is a broad downregulation of Pol II activity. By contrast, PGCs display only gene-specific repression in organisms that rely on inductive signaling-based mechanism (e.g., mice). In addition to the global block of Pol II activity in PGCs, gene expression can be suppressed in other ways, such as chromatin remodeling and Piwi-mediated RNAi. Here, we discuss the mechanisms responsible for the transcriptionally silent state of PGCs in common experimental animals, such as Drosophila, C. elegans, Danio rerio, Xenopus, and mouse. While a PGC-specific downregulation of transcription is a common feature among these organisms, the diverse nature of underlying mechanisms suggests that this functional trait likely evolved independently on several instances. We discuss the possible biological relevance of these silencing mechanisms vis-a-vis fate determination of PGCs.
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Affiliation(s)
- Lyubov A Lebedeva
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia
| | - Konstantin V Yakovlev
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,b Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia
| | - Eugene N Kozlov
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia
| | - Paul Schedl
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,c Department of Molecular Biology , Princeton University , Princeton , USA
| | - Girish Deshpande
- c Department of Molecular Biology , Princeton University , Princeton , USA
| | - Yulii V Shidlovskii
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,d Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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12
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Zhao W, Liu M, Ji H, Zhu Y, Wang C, Huang Y, Ma X, Xing G, Xia Y, Jiang Q, Qin J. The polycomb group protein Yaf2 regulates the pluripotency of embryonic stem cells in a phosphorylation-dependent manner. J Biol Chem 2018; 293:12793-12804. [PMID: 29959227 DOI: 10.1074/jbc.ra118.003299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/25/2018] [Indexed: 01/04/2023] Open
Abstract
The polycomb group (PcG) proteins are key epigenetic regulators in stem cell maintenance. PcG proteins have been thought to act through one of two polycomb repressive complexes (PRCs), but more recent biochemical analyses have challenged this model in the identification of noncanonical PRC1 (nc-PRC1) complexes characterized by the presence of Rybp or Yaf2 in place of the canonical Chromobox proteins. However, the biological significance of these nc-PRC1s and the potential mechanisms by which they mediate gene repression are largely unknown. Here, we explore the functional consequences of Yaf2 disruption on stem cell regulation. We show that deletion of Yaf2 results in compromised proliferation and abnormal differentiation of mouse embryonic stem cells (mESCs). Genome-wide profiling indicates Yaf2 functions primarily as a transcriptional repressor, particularly impacting genes associated with ectoderm cell fate in a manner distinct from Rybp. We confirm that Yaf2 assembles into a noncanonical PRC complex, with deletion analysis identifying the region encompassing amino acid residues 102-150 as required for this assembly. Furthermore, we identified serine 166 as a Yaf2 phosphorylation site, and we demonstrate that mutation of this site to alanine (S166A) compromises Ring1B-mediated H2A monoubiquitination and in turn its ability to repress target gene expression. We therefore propose that Yaf2 and its phosphorylation status serve as dual regulators to maintain the pluripotent state in mESCs.
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Affiliation(s)
- Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Mengjie Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Haijing Ji
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095
| | - Yaru Zhu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Yikai Huang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Xiaoqi Ma
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Guangdong Xing
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014
| | - Yin Xia
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong
| | - Qing Jiang
- Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing 210008, China
| | - Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032.
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13
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Botchkarev VA. Second International Symposium-Epigenetic Regulation of Skin Regeneration and Aging: From Chromatin Biology towards the Understanding of Epigenetic Basis of Skin Diseases. J Invest Dermatol 2017; 137:1604-1608. [PMID: 28583676 DOI: 10.1016/j.jid.2017.01.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Vladimir A Botchkarev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK; Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA.
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14
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Botchkarev VA, Mardaryev AN. Repressing the Keratinocyte Genome: How the Polycomb Complex Subunits Operate in Concert to Control Skin and Hair Follicle Development. J Invest Dermatol 2017; 136:1538-1540. [PMID: 27450498 DOI: 10.1016/j.jid.2016.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 04/27/2016] [Indexed: 01/10/2023]
Abstract
The Polycomb group proteins are transcriptional repressors that are critically important in the control of stem cell activity and maintenance of the identity of differentiated cells. Polycomb proteins interact with each other to form chromatin-associated repressive complexes (Polycomb repressive complexes 1 and 2) leading to chromatin compaction and gene silencing. However, the roles of the distinct components of the Polycomb repressive complex 2 in the control of skin development and keratinocyte differentiation remain obscure. Dauber et al. demonstrate the conditional ablations of three essential Polycomb repressive complex 2 subunits (EED, Suz12, or Ezh1/2) in the epidermal progenitors result in quite similar skin phenotypes including premature acquisition of a functional epidermal barrier, formation of ectopic Merkel cells, and defective postnatal hair follicle development. The reported data demonstrate that in skin epithelia, EED, Suz12, and Ezh1/2 function largely as subunits of the Polycomb repressive complex 2, which is important in the context of data demonstrating their independent activities in other cell types. The report provides an important platform for further analyses of the role of distinct Polycomb components in the control of gene expression programs in the disorders of epidermal differentiation, such as psoriasis and epidermal cancer.
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Affiliation(s)
- Vladimir A Botchkarev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK; Department of Dermatology, Boston University School of Medicine, Boston, USA.
| | - Andrei N Mardaryev
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
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15
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Connelly KE, Dykhuizen EC. Compositional and functional diversity of canonical PRC1 complexes in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:233-245. [PMID: 28007606 DOI: 10.1016/j.bbagrm.2016.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/17/2022]
Abstract
The compositional complexity of Polycomb Repressive Complex 1 (PRC1) increased dramatically during vertebrate evolution. What is considered the "canonical" PRC1 complex consists of four subunits originally identified as regulators of body segmentation in Drosophila. In mammals, each of these four canonical subunits consists of two to six paralogs that associate in a combinatorial manner to produce over a hundred possible distinct PRC1 complexes with unknown function. Genetic studies have begun to define the phenotypic roles for different PRC1 paralogs; however, relating these phenotypes to unique biochemical and transcriptional function for the different paralogs has been challenging. In this review, we attempt to address how the compositional diversity of canonical PRC1 complexes relates to unique roles for individual PRC1 paralogs in transcriptional regulation. This review focuses primarily on PRC1 complex composition, genome targeting, and biochemical function.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907, USA.
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16
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Xiao J, Lee US, Wagner D. Tug of war: adding and removing histone lysine methylation in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:41-53. [PMID: 27614255 DOI: 10.1016/j.pbi.2016.08.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 05/17/2023]
Abstract
Histone lysine methylation plays a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes, including plants. It shapes plant developmental and growth programs as well as responses to the environment. The methylation status of certain amino-acids, in particular of the histone 3 (H3) lysine tails, is dynamically controlled by opposite acting histone methyltransferase 'writers' and histone demethylase 'erasers'. The methylation status is interpreted by a third set of proteins, the histone modification 'readers', which specifically bind to a methylated amino-acid on the H3 tail. Histone methylation writers, readers, and erasers themselves are regulated by intrinsic or extrinsic stimuli; this forms a feedback loop that contributes to development and environmental adaptation in Arabidopsis and other plants. Recent studies have expanded our knowledge regarding the biological roles and dynamic regulation of histone methylation. In this review, we will discuss recent advances in understanding the regulation and roles of histone methylation in plants and animals.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Un-Sa Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Kahn TG, Dorafshan E, Schultheis D, Zare A, Stenberg P, Reim I, Pirrotta V, Schwartz YB. Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements. Nucleic Acids Res 2016; 44:10132-10149. [PMID: 27557709 PMCID: PMC5137424 DOI: 10.1093/nar/gkw701] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The targeting of PRC1 and PRC2 is poorly understood and was proposed to be hierarchical and involve tri-methylation of histone H3 (H3K27me3) and/or monoubiquitylation of histone H2A (H2AK118ub). Here, we present a strict test of this hypothesis using the Drosophila model. We discover that neither H3K27me3 nor H2AK118ub is required for targeting PRC complexes to Polycomb Response Elements (PREs). We find that PRC1 can bind PREs in the absence of PRC2 but at many PREs PRC2 requires PRC1 to be targeted. We show that one role of H3K27me3 is to allow PcG complexes anchored at PREs to interact with surrounding chromatin. In contrast, the bulk of H2AK118ub is unrelated to PcG repression. These findings radically change our view of how PcG repression is targeted and suggest that PRC1 and PRC2 can communicate independently of histone modifications.
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Affiliation(s)
- Tatyana G Kahn
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Dorothea Schultheis
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Erlangen, D-91058, Germany
| | - Aman Zare
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden.,Division of CBRN Defense and Security, Swedish Defense Research Agency, FOI, Umeå, 906 21, Sweden
| | - Ingolf Reim
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Erlangen, D-91058, Germany
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
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18
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Veluchamy A, Jégu T, Ariel F, Latrasse D, Mariappan KG, Kim SK, Crespi M, Hirt H, Bergounioux C, Raynaud C, Benhamed M. LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PLoS One 2016; 11:e0158936. [PMID: 27410265 PMCID: PMC4943711 DOI: 10.1371/journal.pone.0158936] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/24/2016] [Indexed: 11/18/2022] Open
Abstract
Precise expression patterns of genes in time and space are essential for proper development of multicellular organisms. Dynamic chromatin conformation and spatial organization of the genome constitute a major step in this regulation to modulate developmental outputs. Polycomb repressive complexes (PRCs) mediate stable or flexible gene repression in response to internal and environmental cues. In Arabidopsis thaliana, LHP1 co-localizes with H3K27me3 epigenetic marks throughout the genome and interacts with PRC1 and PRC2 members as well as with a long noncoding RNA. Here, we show that LHP1 is responsible for the spreading of H3K27me3 towards the 3' end of the gene body. We also identified a subset of LHP1-activated genes and demonstrated that LHP1 shapes local chromatin topology in order to control transcriptional co-regulation. Our work reveals a general role of LHP1 from local to higher conformation levels of chromatin configuration to determine its accessibility to define gene expression patterns.
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Affiliation(s)
- Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Teddy Jégu
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Federico Ariel
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Kiruthiga Gayathri Mariappan
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Heribert Hirt
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
- * E-mail:
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19
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Mardaryev AN, Liu B, Rapisarda V, Poterlowicz K, Malashchuk I, Rudolf J, Sharov AA, Jahoda CA, Fessing MY, Benitah SA, Xu GL, Botchkarev VA. Cbx4 maintains the epithelial lineage identity and cell proliferation in the developing stratified epithelium. J Cell Biol 2015; 212:77-89. [PMID: 26711500 PMCID: PMC4700479 DOI: 10.1083/jcb.201506065] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 11/17/2015] [Indexed: 11/23/2022] Open
Abstract
Polycomb complex member Cbx4 represses nonepidermal lineage and cell cycle inhibitor genes in the epidermal keratinocytes and operates as a direct p63 target, maintaining epithelial identity and proliferative activity in the developing epidermis. During development, multipotent progenitor cells establish lineage-specific programmers of gene activation and silencing underlying their differentiation into specialized cell types. We show that the Polycomb component Cbx4 serves as a critical determinant that maintains the epithelial identity in the developing epidermis by repressing nonepidermal gene expression programs. Cbx4 ablation in mice results in a marked decrease of the epidermal thickness and keratinocyte (KC) proliferation associated with activation of numerous neuronal genes and genes encoding cyclin-dependent kinase inhibitors (p16/p19 and p57). Furthermore, the chromodomain- and SUMO E3 ligase–dependent Cbx4 activities differentially regulate proliferation, differentiation, and expression of nonepidermal genes in KCs. Finally, Cbx4 expression in KCs is directly regulated by p63 transcription factor, whereas Cbx4 overexpression is capable of partially rescuing the effects of p63 ablation on epidermal development. These data demonstrate that Cbx4 plays a crucial role in the p63-regulated program of epidermal differentiation, maintaining the epithelial identity and proliferative activity in KCs via repression of the selected nonepidermal lineage and cell cycle inhibitor genes.
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Affiliation(s)
- Andrei N Mardaryev
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK
| | - Bo Liu
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Valentina Rapisarda
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK
| | - Krzysztof Poterlowicz
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK
| | - Igor Malashchuk
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK
| | - Jana Rudolf
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK
| | - Andrey A Sharov
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118
| | - Colin A Jahoda
- School of Biological Sciences, University of Durham, Durham DH1 3LE, England, UK
| | - Michael Y Fessing
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK
| | - Salvador A Benitah
- Institute for Research in Biomedicine, 08028 Barcelona, Spain Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain
| | - Guo-Liang Xu
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Vladimir A Botchkarev
- Centre for Skin Sciences, School of Life Sciences, University of Bradford, Yorkshire BD7 1DP, England, UK Department of Dermatology, Boston University School of Medicine, Boston, MA 02118
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20
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Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation. Sci Rep 2015; 5:16567. [PMID: 26568260 PMCID: PMC4645096 DOI: 10.1038/srep16567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 11/09/2022] Open
Abstract
In mouse embryonic stem (mES) cells, ubiquitylation of histone H2A lysine 119 represses a large number of developmental genes and maintains mES cell pluripotency. It has been suggested that a number of H2A ubiquitin ligases as well as deubiquitylases and related peptide fragments contribute to a delicate balance between self-renewal and multi-lineage differentiation in mES cells. Here, we tested whether known H2A ubiquitin ligases and deubiquitylases are involved in mES cell regulation and discovered that Dzip3, the E3 ligase of H2AK119, represses differentiation-inducible genes, as does Ring1B. The two sets of target genes partially overlapped but had different spectra. We found that Dzip3 represses gene expression by orchestrating changes in 3D organization, in addition to regulating ubiquitylation of H2A. Our results shed light on the epigenetic mechanism of transcriptional regulation, which depends on 3D chromatin reorganization to regulate mES cell differentiation.
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21
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Kanellopoulou C, Gilpatrick T, Kilaru G, Burr P, Nguyen CK, Morawski A, Lenardo MJ, Muljo SA. Reprogramming of Polycomb-Mediated Gene Silencing in Embryonic Stem Cells by the miR-290 Family and the Methyltransferase Ash1l. Stem Cell Reports 2015; 5:971-978. [PMID: 26549848 PMCID: PMC4682067 DOI: 10.1016/j.stemcr.2015.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 11/17/2022] Open
Abstract
Members of the miR-290 family are the most abundantly expressed microRNAs (miRNAs) in mouse embryonic stem cells (ESCs). They regulate aspects of differentiation, pluripotency, and proliferation of ESCs, but the molecular program that they control has not been fully delineated. In the absence of Dicer, ESCs fail to express mature miR-290 miRNAs and have selective aberrant overexpression of Hoxa, Hoxb, Hoxc, and Hoxd genes essential for body plan patterning during embryogenesis, but they do not undergo a full differentiation program. Introduction of mature miR-291 into DCR−/− ESCs restores Hox gene silencing. This was attributed to the unexpected regulation of Polycomb-mediated gene targeting by miR-291. We identified the methyltransferase Ash1l as a pivotal target of miR-291 mediating this effect. Collectively, our data shed light on the role of Dicer in ESC homeostasis by revealing a facet of molecular regulation by the miR-290 family. Silencing of Hox genes in ESCs is defective in the absence of Dicer A member of the miR-290 family is sufficient to rescue the Hox gene-silencing defect There is widespread Polycomb deregulation in Dicer-deficient ESCs miR-290 can restore Polycomb localization by regulating Ash1l
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Affiliation(s)
- Chryssa Kanellopoulou
- Molecular Development of the Immune System Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Timothy Gilpatrick
- Molecular Development of the Immune System Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gokhul Kilaru
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Patrick Burr
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cuong K Nguyen
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Aaron Morawski
- Molecular Development of the Immune System Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
| | - Stefan A Muljo
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Halsall JA, Turan N, Wiersma M, Turner BM. Cells adapt to the epigenomic disruption caused by histone deacetylase inhibitors through a coordinated, chromatin-mediated transcriptional response. Epigenetics Chromatin 2015; 8:29. [PMID: 26380582 PMCID: PMC4572612 DOI: 10.1186/s13072-015-0021-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The genome-wide hyperacetylation of chromatin caused by histone deacetylase inhibitors (HDACi) is surprisingly well tolerated by most eukaryotic cells. The homeostatic mechanisms that underlie this tolerance are unknown. Here we identify the transcriptional and epigenomic changes that constitute the earliest response of human lymphoblastoid cells to two HDACi, valproic acid and suberoylanilide hydroxamic acid (Vorinostat), both in widespread clinical use. RESULTS Dynamic changes in transcript levels over the first 2 h of exposure to HDACi were assayed on High Density microarrays. There was a consistent response to the two different inhibitors at several concentrations. Strikingly, components of all known lysine acetyltransferase (KAT) complexes were down-regulated, as were genes required for growth and maintenance of the lymphoid phenotype. Up-regulated gene clusters were enriched in regulators of transcription, development and phenotypic change. In untreated cells, HDACi-responsive genes, whether up- or down-regulated, were packaged in highly acetylated chromatin. This was essentially unaffected by HDACi. In contrast, HDACi induced a strong increase in H3K27me3 at transcription start sites, irrespective of their transcriptional response. Inhibition of the H3K27 methylating enzymes, EZH1/2, altered the transcriptional response to HDACi, confirming the functional significance of H3K27 methylation for specific genes. CONCLUSIONS We propose that the observed transcriptional changes constitute an inbuilt adaptive response to HDACi that promotes cell survival by minimising protein hyperacetylation, slowing growth and re-balancing patterns of gene expression. The transcriptional response to HDACi is mediated by a precisely timed increase in H3K27me3 at transcription start sites. In contrast, histone acetylation, at least at the three lysine residues tested, seems to play no direct role. Instead, it may provide a stable chromatin environment that allows transcriptional change to be induced by other factors, possibly acetylated non-histone proteins.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Maaike Wiersma
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Bryan M Turner
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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Context-dependent actions of Polycomb repressors in cancer. Oncogene 2015; 35:1341-52. [DOI: 10.1038/onc.2015.195] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/15/2015] [Accepted: 05/05/2015] [Indexed: 12/21/2022]
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PcG and trxG in plants - friends or foes. Trends Genet 2015; 31:252-62. [PMID: 25858128 DOI: 10.1016/j.tig.2015.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.
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Abstract
Correct expression of specific sets of genes in time and space ensures the establishment and maintenance of cell identity, which is required for proper development of multicellular organisms. Polycomb and Trithorax group proteins form multisubunit complexes that antagonistically act in epigenetic gene repression and activation, respectively. The traditional view of Polycomb repressive complexes (PRCs) as executors of long-lasting and stable gene repression is being extended by evidence of flexible repression in response to developmental and environmental cues, increasing the complexity of mechanisms that ensure selective and properly timed PRC targeting and release of Polycomb repression. Here, we review advances in understanding of the composition, mechanisms of targeting, and function of plant PRCs and discuss the parallels and differences between plant and animal models.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; ,
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