1
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Veronezi GMB, Ramachandran S. Nucleation and spreading maintain Polycomb domains every cell cycle. Cell Rep 2024; 43:114090. [PMID: 38607915 PMCID: PMC11179494 DOI: 10.1016/j.celrep.2024.114090] [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: 02/08/2022] [Revised: 02/07/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Gene repression by the Polycomb pathway is essential for metazoan development. Polycomb domains, characterized by trimethylation of histone H3 lysine 27 (H3K27me3), carry the memory of repression and hence need to be maintained to counter the dilution of parental H3K27me3 with unmodified H3 during replication. Yet, how locus-specific H3K27me3 is maintained through replication is unclear. To understand H3K27me3 recovery post-replication, we first define nucleation sites within each Polycomb domain in mouse embryonic stem cells. To map dynamics of H3K27me3 domains across the cell cycle, we develop CUT&Flow (coupling cleavage under target and tagmentation with flow cytometry). We show that post-replication recovery of Polycomb domains occurs by nucleation and spreading, using the same nucleation sites used during de novo domain formation. By using Polycomb repressive complex 2 (PRC2) subunit-specific inhibitors, we find that PRC2 targets nucleation sites post-replication independent of pre-existing H3K27me3. Thus, competition between H3K27me3 deposition and nucleosome turnover drives both de novo domain formation and maintenance during every cell cycle.
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Affiliation(s)
- Giovana M B Veronezi
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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2
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Ito S, Umehara T, Koseki H. Polycomb-mediated histone modifications and gene regulation. Biochem Soc Trans 2024; 52:151-161. [PMID: 38288743 DOI: 10.1042/bst20230336] [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: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are transcriptional repressor complexes that play a fundamental role in epigenomic regulation and the cell-fate decision; these complexes are widely conserved in multicellular organisms. PRC1 is an E3 ubiquitin (ub) ligase that generates histone H2A ubiquitinated at lysine (K) 119 (H2AK119ub1), whereas PRC2 is a histone methyltransferase that specifically catalyzes tri-methylation of histone H3K27 (H3K27me3). Genome-wide analyses have confirmed that these two key epigenetic marks highly overlap across the genome and contribute to gene repression. We are now beginning to understand the molecular mechanisms that enable PRC1 and PRC2 to identify their target sites in the genome and communicate through feedback mechanisms to create Polycomb chromatin domains. Recently, it has become apparent that PRC1-induced H2AK119ub1 not only serves as a docking site for PRC2 but also affects the dynamics of the H3 tail, both of which enhance PRC2 activity, suggesting that trans-tail communication between H2A and H3 facilitates the formation of the Polycomb chromatin domain. In this review, we discuss the emerging principles that define how PRC1 and PRC2 establish the Polycomb chromatin domain and regulate gene expression in mammals.
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Affiliation(s)
- Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Umehara
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
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3
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Vijayanathan M, Trejo-Arellano MG, Mozgová I. Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective. EPIGENOMES 2022; 6:3. [PMID: 35076495 PMCID: PMC8788455 DOI: 10.3390/epigenomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
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Affiliation(s)
- Mallika Vijayanathan
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - María Guadalupe Trejo-Arellano
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - Iva Mozgová
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
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4
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Abstract
Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.
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Affiliation(s)
- Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Sandip De
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
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5
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Hugues A, Jacobs CS, Roudier F. Mitotic Inheritance of PRC2-Mediated Silencing: Mechanistic Insights and Developmental Perspectives. FRONTIERS IN PLANT SCIENCE 2020; 11:262. [PMID: 32211012 PMCID: PMC7075419 DOI: 10.3389/fpls.2020.00262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
Maintenance of gene repression by Polycomb Repressive Complex 2 (PRC2) that catalyzes the trimethylation of histone H3 at lysine 27 (H3K27me3) is integral to the orchestration of developmental programs in most multicellular eukaryotes. Faithful inheritance of H3K27me3 patterns across replication ensures the stability of PRC2-mediated transcriptional silencing over cell generations, thereby safeguarding cellular identities. In this review, we discuss the molecular and mechanistic principles that underlie H3K27me3 restoration after the passage of the replication fork, considering recent advances in different model systems. In particular, we aim at emphasizing parallels and differences between plants and other organisms, focusing on the recycling of parental histones and the replenishment of H3K27me3 patterns post-replication thanks to the remarkable properties of the PRC2 complex. We then discuss the necessity for fine-tuning this genuine epigenetic memory system so as to allow for cell fate and developmental transitions. We highlight recent insights showing that genome-wide destabilization of the H3K27me3 landscape during chromatin replication participates in achieving this flexible stability and provides a window of opportunity for subtle transcriptional reprogramming.
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Affiliation(s)
- Alice Hugues
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Université de Lyon, Lyon, France
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
| | - Chean Sern Jacobs
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Université de Lyon, Lyon, France
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Université de Lyon, Lyon, France
- *Correspondence: François Roudier,
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Yu J, Wang L, Pei P, Li X, Wu J, Qiu Z, Zhang J, Ao R, Wang S, Zhang T, Xie J. Reduced H3K27me3 leads to abnormal Hox gene expression in neural tube defects. Epigenetics Chromatin 2019; 12:76. [PMID: 31856916 PMCID: PMC6921514 DOI: 10.1186/s13072-019-0318-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
Background Neural tube defects (NTDs) are severe, common birth defects that result from failure of normal neural tube closure during early embryogenesis. Accumulating strong evidence indicates that genetic factors contribute to NTDs etiology, among them, HOX genes play a key role in neural tube closure. Although abnormal HOX gene expression can lead to NTDs, the underlying pathological mechanisms have not fully been understood. Method We detected that H3K27me3 and expression of the Hox genes in a retinoic acid (RA) induced mouse NTDs model on E8.5, E9.5 and E10.5 using RNA-sequencing and chromatin immunoprecipitation sequencing assays. Furthermore, we quantified 10 Hox genes using NanoString nCounter in brain tissue of fetuses with 39 NTDs patients including anencephaly, spina bifida, hydrocephaly and encephalocele. Results Here, our results showed differential expression in 26 genes with a > 20-fold change in the level of expression, including 10 upregulated Hox genes. RT-qPCR revealed that these 10 Hox genes were all upregulated in RA-induced mouse NTDs as well as RA-treated embryonic stem cells (ESCs). Using ChIP-seq assays, we demonstrate that a decrease in H3K27me3 level upregulates the expression of Hox cluster A–D in RA-induced mouse NTDs model on E10.5. Interestingly, RA treatment led to attenuation of H3K27me3 due to cooperate between UTX and Suz12, affecting Hox gene regulation. Further analysis, in human anencephaly cases, upregulation of 10 HOX genes was observed, along with aberrant levels of H3K27me3. Notably, HOXB4, HOXC4 and HOXD1 expression was negatively correlated with H3K27me3 levels. Conclusion Our results indicate that abnormal HOX gene expression induced by aberrant H3K27me3 levels may be a risk factor for NTDs and highlight the need for further analysis of genome-wide epigenetic modification in NTDs.
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Affiliation(s)
- Juan Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Lei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Pei Pei
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Xue Li
- School of Clinical Medical, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Jianxin Wu
- Department of Biochemistry, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Ruifang Ao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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Rodríguez-Carballo E, Lopez-Delisle L, Yakushiji-Kaminatsui N, Ullate-Agote A, Duboule D. Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol 2019; 17:55. [PMID: 31299961 PMCID: PMC6626364 DOI: 10.1186/s12915-019-0677-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases, such domains may act as coherent regulatory units, with a global on or off state. By using the HoxD gene cluster, which specifies the topology of the developing limbs via highly orchestrated regulation of gene expression, as a paradigm, we investigated how the arrangement of regulatory domains determines their activity and function. RESULTS Proximal and distal cells in the developing limb express different levels of Hoxd genes, regulated by flanking 3' and 5' TADs, respectively. We characterized the effect of large genomic rearrangements affecting these two TADs, including their fusion into a single chromatin domain. We show that, within a single hybrid TAD, the activation of both proximal and distal limb enhancers globally occurred as when both TADs are intact. However, the activity of the 3' TAD in distal cells is generally increased in the fused TAD, when compared to wild type where it is silenced. Also, target gene activity in distal cells depends on whether or not these genes had previously responded to proximal enhancers, which determines the presence or absence of H3K27me3 marks. We also show that the polycomb repressive complex 2 is mainly recruited at the Hox gene cluster and can extend its coverage to far-cis regulatory sequences as long as confined to the neighboring TAD structure. CONCLUSIONS We conclude that antagonistic limb proximal and distal enhancers can exert their specific effects when positioned into the same TAD and in the absence of their genuine target genes. We also conclude that removing these target genes reduced the coverage of a regulatory landscape by chromatin marks associated with silencing, which correlates with its prolonged activity in time.
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Affiliation(s)
- Eddie Rodríguez-Carballo
- Laboratory of Developmental Genomics, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland
| | - Nayuta Yakushiji-Kaminatsui
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland
- Present Address: Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohoma, Kanagawa, 230-0045, Japan
| | - Asier Ullate-Agote
- Laboratory of Artificial and Natural Evolution, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Denis Duboule
- Laboratory of Developmental Genomics, Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland.
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015, Lausanne, Switzerland.
- Collège de France, 75005, Paris, France.
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8
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Oksuz O, Narendra V, Lee CH, Descostes N, LeRoy G, Raviram R, Blumenberg L, Karch K, Rocha PP, Garcia BA, Skok JA, Reinberg D. Capturing the Onset of PRC2-Mediated Repressive Domain Formation. Mol Cell 2019; 70:1149-1162.e5. [PMID: 29932905 DOI: 10.1016/j.molcel.2018.05.023] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/10/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022]
Abstract
Polycomb repressive complex 2 (PRC2) maintains gene silencing by catalyzing methylation of histone H3 at lysine 27 (H3K27me2/3) within chromatin. By designing a system whereby PRC2-mediated repressive domains were collapsed and then reconstructed in an inducible fashion in vivo, a two-step mechanism of H3K27me2/3 domain formation became evident. First, PRC2 is stably recruited by the actions of JARID2 and MTF2 to a limited number of spatially interacting "nucleation sites," creating H3K27me3-forming Polycomb foci within the nucleus. Second, PRC2 is allosterically activated via its binding to H3K27me3 and rapidly spreads H3K27me2/3 both in cis and in far-cis via long-range contacts. As PRC2 proceeds further from the nucleation sites, its stability on chromatin decreases such that domains of H3K27me3 remain proximal, and those of H3K27me2 distal, to the nucleation sites. This study demonstrates the principles of de novo establishment of PRC2-mediated repressive domains across the genome.
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Affiliation(s)
- Ozgur Oksuz
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Varun Narendra
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Chul-Hwan Lee
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Nicolas Descostes
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ramya Raviram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lili Blumenberg
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly Karch
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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Abstract
Polycomb repressive complex 2 (PRC2) and its methylation of histone 3 at lysine 27 (H3K27me3) play a crucial role in epigenetic regulation of normal development and malignancy. Several factors regulate the recruitment of PRC2 and affects its chromatin modification function. Over the past years, emerging discoveries have portrayed the association of RNA (protein-coding and non-coding) with PRC2 as a critical factor in understanding PRC2 function. With PRC2 being a macromolecular complex of interest in development and diseases, further studies are needed to relate the rapidly evolving PRC2:RNA biology in that scenario. In this review, we summarize the current understanding of different modes of RNA binding by PRC2, and further discuss perspectives, key questions and therapeutic applications of PRC2 binding to RNAs.
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Affiliation(s)
- Junli Yan
- a Cancer Science Institute of Singapore , National University of Singapore , Singapore , Singapore
| | - Bibek Dutta
- b Department of Medicine , Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore
| | - Yan Ting Hee
- c Lee Kong Chian School of Medicine , Nanyang Technological University , Singapore , Singapore
| | - Wee-Joo Chng
- a Cancer Science Institute of Singapore , National University of Singapore , Singapore , Singapore.,b Department of Medicine , Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore.,d Department of Hematology-Oncology , National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS) , Singapore , Singapore
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10
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Abstract
Epigenetic mechanisms, including DNA and histone modifications, are pivotal for normal brain development and functions by modulating spatial and temporal gene expression. Dysregulation of the epigenetic machinery can serve as a causal role in numerous brain disorders. Proper mammalian brain development and functions depend on the precise expression of neuronal-specific genes, transcription factors and epigenetic modifications. Antagonistic polycomb and trithorax proteins form multimeric complexes and play important roles in these processes by epigenetically controlling gene repression or activation through various molecular mechanisms. Aberrant expression or disruption of either protein group can contribute to neurodegenerative diseases. This review focus on the current progress of Polycomb and Trithorax complexes in brain development and disease, and provides a future outlook of the field.
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11
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Du J, Kirk B, Zeng J, Ma J, Wang Q. Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes. Nucleic Acids Res 2018; 46:8848-8864. [PMID: 29992232 PMCID: PMC6158500 DOI: 10.1093/nar/gky595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are essential for maintaining epigenetic memory in both embryonic stem cells and differentiated cells. To date, how they are localized to hundreds of specific target genes within a vertebrate genome had remained elusive. Here, by focusing on short cis-acting DNA elements of single functions, we discovered three classes of response elements in human genome: Polycomb response elements (PREs), Trithorax response elements (TREs) and Polycomb/Trithorax response elements (P/TREs). In particular, the four PREs (PRE14, 29, 39 and 48) are the first set of, to our knowledge, bona fide vertebrate PREs ever discovered, while many previously reported Drosophila or vertebrate PREs are likely P/TREs. We further demonstrated that YY1 and CpG islands are specifically enriched in the four TREs (PRE30, 41, 44 and 55), but not in the PREs. The three classes of response elements as unraveled in this study should guide further global investigation and open new doors for a deeper understanding of PcG and TrxG mechanisms in vertebrates.
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Affiliation(s)
- Junqing Du
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Brian Kirk
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jia Zeng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jianpeng Ma
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Qinghua Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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12
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Cameron SR, Nandi S, Kahn TG, Barrasa JI, Stenberg P, Schwartz YB. PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 ( CCND2) oncogene. J Biol Chem 2018; 293:14342-14358. [PMID: 30068546 DOI: 10.1074/jbc.ra118.005010] [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] [Received: 07/24/2018] [Indexed: 11/06/2022] Open
Abstract
Polycomb group proteins are essential epigenetic repressors. They form multiple protein complexes of which two kinds, PRC1 and PRC2, are indispensable for repression. Although much is known about their biochemical properties, how mammalian PRC1 and PRC2 are targeted to specific genes is poorly understood. Here, we establish the cyclin D2 (CCND2) oncogene as a simple model to address this question. We provide the evidence that the targeting of PRC1 to CCND2 involves a dedicated PRC1-targeting element (PTE). The PTE appears to act in concert with an adjacent cytosine-phosphate-guanine (CpG) island to arrange for the robust binding of PRC1 and PRC2 to repressed CCND2 Our findings pave the way to identify sequence-specific DNA-binding proteins implicated in the targeting of mammalian PRC1 complexes and provide novel link between polycomb repression and cancer.
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Affiliation(s)
| | - Soumyadeep Nandi
- From the Department of Molecular Biology and.,the Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden and
| | | | | | - Per Stenberg
- From the Department of Molecular Biology and.,the Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden and.,the Division of Chemical, Biological, Radioactive and Nuclear (CBRN) Security and Defence, FOI-Swedish Defence Research Agency, 906 21 Umeå Sweden
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13
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A novel role of metal response element binding transcription factor 2 at the Hox gene cluster in the regulation of H3K27me3 by polycomb repressive complex 2. Oncotarget 2018; 9:26572-26585. [PMID: 29899877 PMCID: PMC5995182 DOI: 10.18632/oncotarget.25505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/07/2018] [Indexed: 11/25/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is known to play an important role in the regulation of early embryonic development, differentiation, and cellular proliferation by introducing methyl groups onto lysine 27 of histone H3 (H3K27me3). PRC2 is tightly associated with silencing of Hox gene clusters and their sequential activation, leading to normal development and differentiation. To investigate epigenetic changes induced by PRC2 during differentiation, deposition of PRC2 components and levels of H3K27me3 were extensively examined using mouse F9 cells as a model system. Contrary to positive correlation between PRC2 deposition and H3K27me3 level, down-regulation of PRC2 components by shRNA and inhibition of EZH1/2 resulted in unexpected elevation of H3K27me3 level at the Hox gene cluster despite its global decrease. We found that metal response element binding transcriptional factor 2 (MTF2), one of sub-stoichiometric components of PRC2, was stably bound to Hox genes. Its binding capability was dependent on other core PRC2 components. A high level of H3K27me3 at Hox genes in Suz12-knock out cells was reversed by knockdown of Mtf2.This shows that MTF2 is necessary to consolidate PRC2-mediated histone methylation. Taken together, our results indicate that expression of Hox gene clusters during differentiation is strictly modulated by the activity of PRC2 secured by MTF2.
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15
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Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell 2017; 169:930-944.e22. [PMID: 28525758 PMCID: PMC5538188 DOI: 10.1016/j.cell.2017.05.004] [Citation(s) in RCA: 1037] [Impact Index Per Article: 148.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 01/17/2023]
Abstract
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Johan H Gibcus
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Alec Uebersohn
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Nezar Abdennur
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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van Arensbergen J, Dussaud S, Pardanaud-Glavieux C, García-Hurtado J, Sauty C, Guerci A, Ferrer J, Ravassard P. A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element. PLoS One 2017; 12:e0171508. [PMID: 28225770 PMCID: PMC5321433 DOI: 10.1371/journal.pone.0171508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/02/2017] [Indexed: 12/11/2022] Open
Abstract
Lineage-selective expression of developmental genes is dependent on the interplay between activating and repressive mechanisms. Gene activation is dependent on cell-specific transcription factors that recognize transcriptional enhancer sequences. Gene repression often depends on the recruitment of Polycomb group (PcG) proteins, although the sequences that underlie the recruitment of PcG proteins, also known as Polycomb response elements (PREs), remain poorly understood in vertebrates. While distal PREs have been identified in mammals, a role for positive-acting enhancers in PcG-mediated repression has not been described. Here we have used a highly efficient procedure based on lentiviral-mediated transgenesis to carry out in vivo fine-mapping of, cis-regulatory sequences that control lineage-specific activation of Neurog3, a master regulator of pancreatic endocrine differentiation. Our findings reveal an enhancer region that is sufficient to drive correct spacio-temporal expression of Neurog3 and demonstrate that this same region serves as a PRE in alternative lineages where Neurog3 is inactive.
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Affiliation(s)
- Joris van Arensbergen
- Genomic Programming of Beta-Cells Laboratory, IDIBAPS, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas, Barcelona, Spain
| | - Sebastien Dussaud
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du cerveau et de la moelle (ICM)–Hôpital Pitié-Salpêtrière, Boulevard de l’Hôpital, Paris, France
| | - Corinne Pardanaud-Glavieux
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du cerveau et de la moelle (ICM)–Hôpital Pitié-Salpêtrière, Boulevard de l’Hôpital, Paris, France
| | - Javier García-Hurtado
- Genomic Programming of Beta-Cells Laboratory, IDIBAPS, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas, Barcelona, Spain
| | - Claire Sauty
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du cerveau et de la moelle (ICM)–Hôpital Pitié-Salpêtrière, Boulevard de l’Hôpital, Paris, France
| | - Aline Guerci
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du cerveau et de la moelle (ICM)–Hôpital Pitié-Salpêtrière, Boulevard de l’Hôpital, Paris, France
| | - Jorge Ferrer
- Genomic Programming of Beta-Cells Laboratory, IDIBAPS, Barcelona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas, Barcelona, Spain
- Department of Medicine, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, United Kingdom
- * E-mail: (PR); (JF)
| | - Philippe Ravassard
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, Institut du cerveau et de la moelle (ICM)–Hôpital Pitié-Salpêtrière, Boulevard de l’Hôpital, Paris, France
- * E-mail: (PR); (JF)
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Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet 2016; 12:e1006200. [PMID: 27466807 PMCID: PMC4965088 DOI: 10.1371/journal.pgen.1006200] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
Polycomb group response elements (PREs) in Drosophila are DNA-elements that recruit Polycomb proteins (PcG) to chromatin and regulate gene expression. PREs are easily recognizable in the Drosophila genome as strong peaks of PcG-protein binding over discrete DNA fragments; many small but statistically significant PcG peaks are also observed in PcG domains. Surprisingly, in vivo deletion of the four characterized strong PREs from the PcG regulated invected-engrailed (inv-en) gene complex did not disrupt the formation of the H3K27me3 domain and did not affect inv-en expression in embryos or larvae suggesting the presence of redundant PcG recruitment mechanism. Further, the 3D-structure of the inv-en domain was only minimally altered by the deletion of the strong PREs. A reporter construct containing a 7.5kb en fragment that contains three weak peaks but no large PcG peaks forms an H3K27me3 domain and is PcG-regulated. Our data suggests a model for the recruitment of PcG-complexes to Drosophila genes via interactions with multiple, weak PREs spread throughout an H3K27me3 domain.
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Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis and phenotypes. Acta Neuropathol 2015; 130:815-27. [PMID: 26399631 PMCID: PMC4654747 DOI: 10.1007/s00401-015-1478-0] [Citation(s) in RCA: 430] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 01/15/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG) is the most severe paediatric solid tumour, with no significant therapeutic progress made in the past 50 years. Recent studies suggest that diffuse midline glioma, H3-K27M mutant, may comprise more than one biological entity. The aim of the study was to determine the clinical and biological variables that most impact their prognosis. Ninety-one patients with classically defined DIPG underwent a systematic stereotactic biopsy and were included in this observational retrospective study. Histone H3 genes mutations were assessed by immunochemistry and direct sequencing, whilst global gene expression profiling and chromosomal imbalances were determined by microarrays. A full description of the MRI findings at diagnosis and at relapse was integrated with the molecular profiling data and clinical outcome. All DIPG but one were found to harbour either a somatic H3-K27M mutation and/or loss of H3K27 trimethylation. We also discovered a novel K27M mutation in HIST2H3C, and a lysine-to-isoleucine substitution (K27I) in H3F3A, also creating a loss of trimethylation. Patients with tumours harbouring a K27M mutation in H3.3 (H3F3A) did not respond clinically to radiotherapy as well, relapsed significantly earlier and exhibited more metastatic recurrences than those in H3.1 (HIST1H3B/C). H3.3-K27M-mutated DIPG have a proneural/oligodendroglial phenotype and a pro-metastatic gene expression signature with PDGFRA activation, while H3.1-K27M-mutated tumours exhibit a mesenchymal/astrocytic phenotype and a pro-angiogenic/hypoxic signature supported by expression profiling and radiological findings. H3K27 alterations appear as the founding event in DIPG and the mutations in the two main histone H3 variants drive two distinct oncogenic programmes with potential specific therapeutic targets.
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The quest for mammalian Polycomb response elements: are we there yet? Chromosoma 2015; 125:471-96. [PMID: 26453572 PMCID: PMC4901126 DOI: 10.1007/s00412-015-0539-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
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20
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Srivastava S, Dhawan J, Mishra RK. Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters. Mech Dev 2015; 138 Pt 2:160-169. [PMID: 26254900 DOI: 10.1016/j.mod.2015.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 01/07/2023]
Abstract
Hox gene expression imparts segment identity to body structures along the anterior-posterior axis and is tightly governed by higher order chromatin mechanisms. Chromatin regulatory features of the homeotic complex are best defined in Drosophila melanogaster, where multiple cis-regulatory elements have been identified that ensure collinear Hox gene expression patterns in accordance with their genomic organization. Recent studies focused on delineating the epigenetic features of the vertebrate Hox clusters have helped reveal their dynamic chromatin organization and its impact on gene expression. Enrichment for the 'activating' H3K4me3 and 'repressive' H3K27me3 histone modifications is a particularly strong read-out for transcriptional status and correlates well with the evidence for chromatin loop domain structures and stage specific topological changes at these loci. However, it is not clear how such distinct domains are imposed and regulated independent of each other. Comparative analysis of the chromatin structure and organization of the homeotic gene clusters in fly and mammals is increasingly revealing the functional conservation of chromatin mediated mechanisms. Here we discuss the case for interspersed boundary elements existing within mammalian Hox clusters along with their possible roles and mechanisms of action. Recent studies suggest a role for factors other than the well characterized vertebrate boundary factor CTCF, such as the GAGA binding factor (GAF), in maintaining chromatin domains at the Hox loci. We also present data demonstrating how such regulatory elements may be involved in organizing higher order structure and demarcating active domains of gene expression at the mammalian Hox clusters.
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Affiliation(s)
- Surabhi Srivastava
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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21
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Svoboda LK, Harris A, Bailey NJ, Schwentner R, Tomazou E, von Levetzow C, Magnuson B, Ljungman M, Kovar H, Lawlor ER. Overexpression of HOX genes is prevalent in Ewing sarcoma and is associated with altered epigenetic regulation of developmental transcription programs. Epigenetics 2015; 9:1613-25. [PMID: 25625846 DOI: 10.4161/15592294.2014.988048] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The polycomb proteins BMI-1 and EZH2 are highly overexpressed by Ewing sarcoma (ES), a tumor of stem cell origin that is driven by EWS-ETS fusion oncogenes, most commonly EWS-FLI1. In the current study we analyzed expression of transcription programs that are controlled by polycomb proteins during embryonic development to determine if they are abnormal in ES. Our results show that polycomb target gene expression in ES deviates from normal tissues and stem cells and that, as expected, most targets are relatively repressed. However, we also discovered a paradoxical up regulation of numerous polycomb targets and these were highly enriched for homeobox (HOX) genes. Comparison of HOX profiles between malignant and non-malignant tissues revealed a distinctive HOX profile in ES, which was characterized by overexpression of posterior HOXD genes. In addition, ectopic expression of EWS-FLI1 during stem cell differentiation led to aberrant up regulation of posterior HOXD genes. Mechanistically, this up regulation was associated with altered epigenetic regulation. Specifically, ES and EWS-FLI1+ stem cells displayed a relative loss of polycomb-dependent H3K27me3 and gain of trithorax-dependent H3K4me3 at the promoters of posterior HOXD genes and also at the HOXD11.12 polycomb response element. In addition, a striking correlation was evident between HOXD13 and other genes whose regulation is coordinately regulated during embryonic development by distal enhancer elements. Together, these studies demonstrate that epigenetic regulation of polycomb target genes, in particular HOXD genes, is altered in ES and that these changes are mediated downstream of EWS-FLI1.
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Key Words
- ARMS, alveolar rhabdomyosarcoma
- BM-MSC, adult bone marrow-derived mesenchymal stem cells
- ChIP, chromatin immunoprecipitation
- ChIP-seq, chromatin immunoprecipitation/high throughput sequencing
- ERMS, embryonal rhabdomyosarcoma
- ES, Ewing sarcoma
- Ewing sarcoma
- GCR, global control region
- HOX
- HOX, homeobox
- MSC, mesenchymal stem cells
- NC-MSC, neural crest stem cell-derived mesenchymal stem cells
- NCSC, neural crest stem cells
- OS, osteosarcoma
- PCA, principal components analysis
- PRE, polycomb response element
- RT-PCR, reverse transcriptase polymerase chain reaction
- epigenetic
- hESC, human embryonic stem cells
- polycomb
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Laurie K Svoboda
- a Translational Oncology Program and the Departments of Pediatric and Communicable Diseases; University of Michigan ; Ann Arbor , MI USA
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Ma RG, Zhang Y, Sun TT, Cheng B. Epigenetic regulation by polycomb group complexes: focus on roles of CBX proteins. J Zhejiang Univ Sci B 2015; 15:412-28. [PMID: 24793759 DOI: 10.1631/jzus.b1400077] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Polycomb group (PcG) complexes are epigenetic regulatory complexes that conduct transcriptional repression of target genes via modifying the chromatin. The two best characterized forms of PcG complexes, polycomb repressive complexes 1 and 2 (PRC1 and PRC2), are required for maintaining the stemness of embryonic stem cells and many types of adult stem cells. The spectra of target genes for PRCs are dynamically changing with cell differentiation, which is essential for proper decisions on cell fate during developmental processes. Chromobox (CBX) family proteins are canonical components in PRC1, responsible for targeting PRC1 to the chromatin. Recent studies highlight the function specifications among CBX family members in undifferentiated and differentiated stem cells, which reveal the interplay between compositional diversity and functional specificity of PRC1. In this review, we summarize the current knowledge about targeting and functional mechanisms of PRCs, emphasizing the recent breakthroughs related to CBX proteins under a number of physiological and pathological conditions.
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Affiliation(s)
- Rong-gang Ma
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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23
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Kumar S, Duester G. Retinoic acid controls body axis extension by directly repressing Fgf8 transcription. Development 2014; 141:2972-7. [PMID: 25053430 DOI: 10.1242/dev.112367] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinoic acid (RA) generated in the mesoderm of vertebrate embryos controls body axis extension by downregulating Fgf8 expression in cells exiting the caudal progenitor zone. RA activates transcription by binding to nuclear RA receptors (RARs) at RA response elements (RAREs), but it is unknown whether RA can directly repress transcription. Here, we analyzed a conserved RARE upstream of Fgf8 that binds RAR isoforms in mouse embryos. Transgenic embryos carrying Fgf8 fused to lacZ exhibited expression similar to caudal Fgf8, but deletion of the RARE resulted in ectopic trunk expression extending into somites and neuroectoderm. Epigenetic analysis using chromatin immunoprecipitation of trunk tissues from E8.25 wild-type and Raldh2(-/-) embryos lacking RA synthesis revealed RA-dependent recruitment of the repressive histone marker H3K27me3 and polycomb repressive complex 2 (PRC2) near the Fgf8 RARE. The co-regulator RERE, the loss of which results in ectopic Fgf8 expression and somite defects, was recruited near the RARb RARE by RA, but was released from the Fgf8 RARE by RA. Our findings demonstrate that RA directly represses Fgf8 through a RARE-mediated mechanism that promotes repressive chromatin, thus providing valuable insight into the mechanism of RA-FGF antagonism during progenitor cell differentiation.
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Affiliation(s)
- Sandeep Kumar
- Development, Aging, and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Gregg Duester
- Development, Aging, and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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Günther T, Schreiner S, Dobner T, Tessmer U, Grundhoff A. Influence of ND10 components on epigenetic determinants of early KSHV latency establishment. PLoS Pathog 2014; 10:e1004274. [PMID: 25033267 PMCID: PMC4102598 DOI: 10.1371/journal.ppat.1004274] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/05/2014] [Indexed: 12/15/2022] Open
Abstract
We have previously demonstrated that acquisition of intricate patterns of activating (H3K4me3, H3K9/K14ac) and repressive (H3K27me3) histone modifications is a hallmark of KSHV latency establishment. The precise molecular mechanisms that shape the latent histone modification landscape, however, remain unknown. Promyelocytic leukemia nuclear bodies (PML-NB), also called nuclear domain 10 (ND10), have emerged as mediators of innate immune responses that can limit viral gene expression via chromatin based mechanisms. Consequently, although ND10 functions thus far have been almost exclusively investigated in models of productive herpesvirus infection, it has been proposed that they also may contribute to the establishment of viral latency. Here, we report the first systematic study of the role of ND10 during KSHV latency establishment, and link alterations in the subcellular distribution of ND10 components to a temporal analysis of histone modification acquisition and host cell gene expression during the early infection phase. Our study demonstrates that KSHV infection results in a transient interferon response that leads to induction of the ND10 components PML and Sp100, but that repression by ND10 bodies is unlikely to contribute to KSHV latency establishment. Instead, we uncover an unexpected role for soluble Sp100 protein, which is efficiently and permanently relocalized from nucleoplasmic and chromatin-associated fractions into the insoluble matrix. We show that LANA expression is sufficient to induce Sp100 relocalization, likely via mediating SUMOylation of Sp100. Furthermore, we demonstrate that depletion of soluble Sp100 occurs precisely when repressive H3K27me3 marks first accumulate on viral genomes, and that knock-down of Sp100 (but not PML or Daxx) facilitates H3K27me3 acquisition. Collectively, our data support a model in which non-ND10 resident Sp100 acts as a negative regulator of polycomb repressive complex-2 (PRC2) recruitment, and suggest that KSHV may actively escape ND10 silencing mechanisms to promote establishment of latent chromatin.
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Affiliation(s)
- Thomas Günther
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabrina Schreiner
- Research Unit Viral Transformation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Thomas Dobner
- Research Unit Viral Transformation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Uwe Tessmer
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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Kong KA, Lee JY, Oh JH, Lee Y, Kim MH. Akt1 mediates the posterior Hoxc gene expression through epigenetic modifications in mouse embryonic fibroblasts. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:793-9. [PMID: 24955524 DOI: 10.1016/j.bbagrm.2014.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 05/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
The evolutionarily conserved Hox genes are organized in clusters and expressed colinearly to specify body patterning during embryonic development. Previously, Akt1 has been identified as a putative Hox gene regulator through in silico analysis. Substantial upregulation of consecutive 5' Hoxc genes has been observed when Akt1 is absent in mouse embryonic fibroblast (MEF) cells. In this study, we provide evidence that Akt1 regulates the 5' Hoxc gene expression by epigenetic modifications. Enrichment of histone H3K9 acetylation and a low level of the H3K27me3 mark were detected at the posterior 5' Hoxc loci when Akt1 is absent. A histone deacetylase (HDAC) inhibitor de-repressed 5' Hoxc gene expression when Akt1 is present, and a DNA demethylating reagent synergistically upregulated HDAC-induced 5' Hoxc gene expression. A knockdown study revealed that Hdac6 is mediated in the Hoxc12 repression through direct binding to the transcription start site (TSS) in the presence of Akt1. Co-immunoprecipitation analysis revealed that endogenous Akt1 directly interacted with Hdac6. Furthermore, exogenous Akt1 was enriched at the promoter region of the posterior Hoxc genes such as Hoxc11 and Hoxc12, not the Akt1-independent Hoxc5 and Hoxd10 loci. The regulation of the H3K27me3 mark by Ezh2 and Kdm6b at the 5' Hoxc gene promoter turned out to be Akt1 dependent. Taken together, these results suggest that Akt1 mediates the posterior 5' Hoxc gene expression through epigenetic modification such as histone methylation and acetylation, and partly through a direct binding to the promoter region of the 5' Hoxc genes and/or Hdac6 in mouse embryonic fibroblast cells.
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Affiliation(s)
- Kyoung-Ah Kong
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Oh
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Youra Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea.
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26
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Hox gene regulation and timing in embryogenesis. Semin Cell Dev Biol 2014; 34:76-84. [PMID: 24930771 DOI: 10.1016/j.semcdb.2014.06.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/15/2014] [Accepted: 06/05/2014] [Indexed: 11/22/2022]
Abstract
Hox genes are critical regulators of embryonic development in bilaterian animals. They exhibit a unique mode of transcriptional regulation where the position of the genes along the chromosome corresponds to the time and place of their expression during development. The sequential temporal activation of these genes in the primitive streak helps determining their subsequent pattern of expression along the anterior-posterior axis of the embryo, yet the precise correspondence between these two collinear processes is not fully understood. In addition, vertebrate Hox genes evolved similar modes of regulation along secondary body axes, such as the developing limbs. We review the current understanding of the mechanisms operating during activation, maintenance and silencing of Hox gene expression in these various contexts, and discuss the evolutionary significance of their genomic organization.
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Roselló-Díez A, Arques CG, Delgado I, Giovinazzo G, Torres M. Diffusible signals and epigenetic timing cooperate in late proximo-distal limb patterning. Development 2014; 141:1534-43. [DOI: 10.1242/dev.106831] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Developing vertebrate limbs initiate proximo-distal patterning by interpreting opposing gradients of diffusible signaling molecules. We report two thresholds of proximo-distal signals in the limb bud: a higher threshold that establishes the upper-arm to forearm transition; and a lower one that positions a later transition from forearm to hand. For this last transition to happen, however, the signal environment seems to be insufficient, and we show that a timing mechanism dependent on histone acetylation status is also necessary. Therefore, as a consequence of the time dependence, the lower signaling threshold remains cryptic until the timing mechanism reveals it. We propose that this timing mechanism prevents the distal transition from happening too early, so that the prospective forearm has enough time to expand and form a properly sized segment. Importantly, the gene expression changes provoked by the first transition further regulate proximo-distal signal distribution, thereby coordinating the positioning of the two thresholds, which ensures robustness. This model is compatible with the most recent genetic analyses and underscores the importance of growth during the time-dependent patterning phase, providing a new mechanistic framework for understanding congenital limb defects.
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Affiliation(s)
- Alberto Roselló-Díez
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, c/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Carlos G. Arques
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, c/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Irene Delgado
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, c/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Giovanna Giovinazzo
- Unidad de Tecnología de Células Pluripotentes, Centro Nacional de Investigaciones Cardiovasculares, CNIC, c/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Miguel Torres
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares, CNIC, c/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
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