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Jung J, Buisman SC, Weersing E, Dethmers-Ausema A, Zwart E, Schepers H, Dekker MR, Lazare SS, Hammerl F, Skokova Y, Kooistra SM, Klauke K, Poot RA, Bystrykh LV, de Haan G. CBX7 Induces Self-Renewal of Human Normal and Malignant Hematopoietic Stem and Progenitor Cells by Canonical and Non-canonical Interactions. Cell Rep 2020; 26:1906-1918.e8. [PMID: 30759399 DOI: 10.1016/j.celrep.2019.01.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 12/19/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022] Open
Abstract
In this study, we demonstrate that, among all five CBX Polycomb proteins, only CBX7 possesses the ability to control self-renewal of human hematopoietic stem and progenitor cells (HSPCs). Xenotransplantation of CBX7-overexpressing HSPCs resulted in increased multi-lineage long-term engraftment and myelopoiesis. Gene expression and chromatin analyses revealed perturbations in genes involved in differentiation, DNA and chromatin maintenance, and cell cycle control. CBX7 is upregulated in acute myeloid leukemia (AML), and its genetic or pharmacological repression in AML cells inhibited proliferation and induced differentiation. Mass spectrometry analysis revealed several non-histone protein interactions between CBX7 and the H3K9 methyltransferases SETDB1, EHMT1, and EHMT2. These CBX7-binding proteins possess a trimethylated lysine peptide motif highly similar to the canonical CBX7 target H3K27me3. Depletion of SETDB1 in AML cells phenocopied repression of CBX7. We identify CBX7 as an important regulator of self-renewal and uncover non-canonical crosstalk between distinct pathways, revealing therapeutic opportunities for leukemia.
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Affiliation(s)
- Johannes Jung
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sonja C Buisman
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ellen Weersing
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Albertina Dethmers-Ausema
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Erik Zwart
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Hein Schepers
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Mike R Dekker
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Seka S Lazare
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Franziska Hammerl
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Susanne M Kooistra
- Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Karin Klauke
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Raymond A Poot
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Leonid V Bystrykh
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Gerald de Haan
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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Zepeda-Martinez JA, Pribitzer C, Wang J, Bsteh D, Golumbeanu S, Zhao Q, Burkard TR, Reichholf B, Rhie SK, Jude J, Moussa HF, Zuber J, Bell O. Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells. SCIENCE ADVANCES 2020; 6:eaax5692. [PMID: 32270030 PMCID: PMC7112768 DOI: 10.1126/sciadv.aax5692] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/09/2020] [Indexed: 05/29/2023]
Abstract
The transcriptional repressors Polycomb repressive complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyze distinct histone modifications, establishing repressive chromatin at shared targets. How PRC1, which consists of canonical PRC1 (cPRC1) and variant PRC1 (vPRC1) complexes, and PRC2 cooperate to silence genes and support mouse embryonic stem cell (mESC) self-renewal is unclear. Using combinatorial genetic perturbations, we show that independent pathways of cPRC1 and vPRC1 are responsible for maintenance of H2A monoubiquitylation and silencing of shared target genes. Individual loss of PRC2-dependent cPRC1 or PRC2-independent vPRC1 disrupts only one pathway and does not impair mESC self-renewal capacity. However, loss of both pathways leads to mESC differentiation and activation of a subset of lineage-specific genes co-occupied by relatively high levels of PRC1/PRC2. Thus, parallel pathways explain the differential requirements for PRC1 and PRC2 and provide robust silencing of lineage-specific genes.
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Affiliation(s)
- J. A. Zepeda-Martinez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - C. Pribitzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - J. Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - D. Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - S. Golumbeanu
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Q. Zhao
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - T. R. Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - B. Reichholf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - S. K. Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J. Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - H. F. Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - J. Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - O. Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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RYBP/YAF2-PRC1 complexes and histone H1-dependent chromatin compaction mediate propagation of H2AK119ub1 during cell division. Nat Cell Biol 2020; 22:439-452. [PMID: 32203418 DOI: 10.1038/s41556-020-0484-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/14/2020] [Indexed: 01/12/2023]
Abstract
Stable propagation of epigenetic information is important for maintaining cell identity in multicellular organisms. However, it remains largely unknown how mono-ubiquitinated histone H2A on lysine 119 (H2AK119ub1) is established and stably propagated during cell division. In this study, we found that the proteins RYBP and YAF2 each specifically bind H2AK119ub1 to recruit the RYBP-PRC1 or YAF2-PRC1 complex to catalyse the ubiquitination of H2A on neighbouring nucleosomes through a positive-feedback model. Additionally, we demonstrated that histone H1-compacted chromatin enhances the distal propagation of H2AK119ub1, thereby reinforcing the inheritance of H2AK119ub1 during cell division. Moreover, we showed that either disruption of RYBP/YAF2-PRC1 activity or impairment of histone H1-dependent chromatin compaction resulted in a significant defect of the maintenance of H2AK119ub1. Therefore, our results suggest that histone H1-dependent chromatin compaction plays a critical role in the stable propagation of H2AK119ub1 by RYBP/YAF2-PRC1 during cell division.
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54
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Dunican DS, Mjoseng HK, Duthie L, Flyamer IM, Bickmore WA, Meehan RR. Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells. BMC Biol 2020; 18:25. [PMID: 32131813 PMCID: PMC7057567 DOI: 10.1186/s12915-020-0752-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Thousands of mammalian promoters are defined by co-enrichment of the histone tail modifications H3K27me3 (repressive) and H3K4me3 (activating) and are thus termed bivalent. It was previously observed that bivalent genes in human ES cells (hESC) are frequent targets for hypermethylation in human cancers, and depletion of DNA methylation in mouse embryonic stem cells has a marked impact on H3K27me3 distribution at bivalent promoters. However, only a fraction of bivalent genes in stem cells are targets of hypermethylation in cancer, and it is currently unclear whether all bivalent promoters are equally sensitive to DNA hypomethylation and whether H3K4me3 levels play a role in the interplay between DNA methylation and H3K27me3. RESULTS We report the sub-classification of bivalent promoters into two groups-promoters with a high H3K27me3:H3K4me3 (hiBiv) ratio or promoters with a low H3K27me3:H3K4me3 ratio (loBiv). HiBiv are enriched in canonical Polycomb components, show a higher degree of local intrachromosomal contacts and are highly sensitive to DNA hypomethylation in terms of H3K27me3 depletion from broad Polycomb domains. In contrast, loBiv promoters are enriched in non-canonical Polycomb components, show lower intrachromosomal contacts and are less sensitive to DNA hypomethylation at the same genomic resolution. Multiple systems reveal that hiBiv promoters are more depleted of Polycomb complexes than loBiv promoters following a reduction in DNA methylation, and we demonstrate that H3K27me3 re-accumulates at promoters when DNA methylation is restored. In human cancer, we show that hiBiv promoters lose H3K27me3 and are more susceptible to DNA hypermethylation than loBiv promoters. CONCLUSION We conclude that bivalency as a general term to describe mammalian promoters is an over-simplification and our sub-classification has revealed novel insights into the interplay between the largely antagonistic presence of DNA methylation and Polycomb systems at bivalent promoters. This approach redefines molecular pathologies underlying disease in which global DNA methylation is aberrant or where Polycomb mutations are present.
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Affiliation(s)
- Donnchadh S. Dunican
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Heidi K. Mjoseng
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Leanne Duthie
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Ilya M. Flyamer
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Richard R. Meehan
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
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55
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ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020; 38:728-736. [PMID: 32123383 PMCID: PMC7289633 DOI: 10.1038/s41587-020-0434-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/23/2020] [Indexed: 01/05/2023]
Abstract
Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications remains to be fully characterized. Here, we use natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 a H3K27 residues. We first demonstrate their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomic distribution and histone modification–binding preference. By fusing eCRs to the biotin ligase BASU, we establish ChromID, a method for identifying the chromatin-dependent protein interactome based on proximity biotinylation, and apply it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.
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56
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Blackledge NP, Fursova NA, Kelley JR, Huseyin MK, Feldmann A, Klose RJ. PRC1 Catalytic Activity Is Central to Polycomb System Function. Mol Cell 2020; 77:857-874.e9. [PMID: 31883950 PMCID: PMC7033600 DOI: 10.1016/j.molcel.2019.12.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 12/02/2019] [Indexed: 01/01/2023]
Abstract
The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how the Polycomb system selects its target genes is poorly understood, and whether its histone-modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a conditional mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 drives Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of PRC1 catalytic activity, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling evidence that PRC1 catalysis is central to Polycomb system function and gene regulation.
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Affiliation(s)
- Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Jessica R Kelley
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK.
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57
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Ricci B, Millner TO, Pomella N, Zhang X, Guglielmi L, Badodi S, Ceric D, Gemma C, Cognolato E, Zhang Y, Brandner S, Barnes MR, Marino S. Polycomb-mediated repression of EphrinA5 promotes growth and invasion of glioblastoma. Oncogene 2020; 39:2523-2538. [PMID: 31988455 PMCID: PMC7082224 DOI: 10.1038/s41388-020-1161-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 11/22/2022]
Abstract
Glioblastoma (GBM) is the most common and most aggressive intrinsic brain tumour in adults. Integrated transcriptomic and epigenomic analyses of glioblastoma initiating cells (GIC) in a mouse model uncovered a novel epigenetic regulation of EfnA5. In this model, Bmi1 enhances H3K27me3 at the EfnA5 locus and reinforces repression of selected target genes in a cellular context-dependent fashion. EfnA5 mediates Bmi1-dependent proliferation and invasion in vitro and tumour formation in an allograft model. Importantly, we show that this novel Polycomb feed-forward loop is also active in human GIC and we provide pre-clinical evidence of druggability of the EFNA5 signalling pathway in GBM xenografts overexpressing Bmi1.
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Affiliation(s)
- Barbara Ricci
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Thomas O Millner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Loredana Guglielmi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Sara Badodi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Dario Ceric
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Carolina Gemma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Erica Cognolato
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Ying Zhang
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, WC1N 3BG, UK
| | - Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, WC1N 3BG, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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Ring 1 and YY1 Binding Protein Expressed in Murine Spermatocytes but Dispensable for Spermatogenesis. Genes (Basel) 2020; 11:genes11010084. [PMID: 31940753 PMCID: PMC7016996 DOI: 10.3390/genes11010084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/28/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023] Open
Abstract
Spermatogenesis is a complex cellular-differentiation process that relies on the precise regulation of gene expression in spermatogonia, meiotic, and postmeiotic germ cells. The Ring 1 and YY1 binding protein (Rybp) is a member of the mammalian polycomb-group (PcG) protein family that plays multifunctional roles in development. Previous findings indicate that Rybp may function as an important regulator of meiosis. However, its expression in the testes and function in spermatogenesis have not been examined. In this study, we investigated Rybp expression in postnatal mouse testes using qRT-PCR and immunohistochemistry. We also examined the function of Rybp in spermatogenesis by using a conditional-knockout approach. Results showed that the relative expression of Rybp mRNA was significantly upregulated in the testes of postnatal day (PD) 6 mice. Immunofluorescent staining revealed that Rybp was enriched in the spermatocytes. Surprisingly, a conditional deletion of Rybp in fetal germ cells did not affect the fertility or normal development of spermatogenic cells. Further analysis revealed that Rybp deletion resulted in a decreased expression of meiosis-related genes, but that meiosis progression was normal. Together, these findings suggest that Rybp expression was enriched in spermatocytes, but that it was not required for spermatogenesis.
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Evolving Role of RING1 and YY1 Binding Protein in the Regulation of Germ-Cell-Specific Transcription. Genes (Basel) 2019; 10:genes10110941. [PMID: 31752312 PMCID: PMC6895862 DOI: 10.3390/genes10110941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/07/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Separation of germline cells from somatic lineages is one of the earliest decisions of embryogenesis. Genes expressed in germline cells include apoptotic and meiotic factors, which are not transcribed in the soma normally, but a number of testis-specific genes are active in numerous cancer types. During germ cell development, germ-cell-specific genes can be regulated by specific transcription factors, retinoic acid signaling and multimeric protein complexes. Non-canonical polycomb repressive complexes, like ncPRC1.6, play a critical role in the regulation of the activity of germ-cell-specific genes. RING1 and YY1 binding protein (RYBP) is one of the core members of the ncPRC1.6. Surprisingly, the role of Rybp in germ cell differentiation has not been defined yet. This review is focusing on the possible role of Rybp in this process. By analyzing whole-genome transcriptome alterations of the Rybp-/- embryonic stem (ES) cells and correlating this data with experimentally identified binding sites of ncPRC1.6 subunits and retinoic acid receptors in ES cells, we propose a model how germ-cell-specific transcription can be governed by an RYBP centered regulatory network, underlining the possible role of RYBP in germ cell differentiation and tumorigenesis.
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60
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Yang L, Liu Y, Fan M, Zhu G, Jin H, Liang J, Liu Z, Huang Z, Zhang L. Identification and characterization of benzo[d]oxazol-2(3H)-one derivatives as the first potent and selective small-molecule inhibitors of chromodomain protein CDYL. Eur J Med Chem 2019; 182:111656. [DOI: 10.1016/j.ejmech.2019.111656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/24/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022]
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Phc2 controls hematopoietic stem and progenitor cell mobilization from bone marrow by repressing Vcam1 expression. Nat Commun 2019; 10:3496. [PMID: 31375680 PMCID: PMC6677815 DOI: 10.1038/s41467-019-11386-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/12/2019] [Indexed: 01/04/2023] Open
Abstract
The timely mobilization of hematopoietic stem and progenitor cells (HSPCs) is essential for maintaining hematopoietic and tissue leukocyte homeostasis. Understanding how HSPCs migrate between bone marrow (BM) and peripheral tissues is of great significance in the clinical setting, where therapeutic strategies for modulating their migration capacity determine the clinical outcome. Here, we identify an epigenetic regulator, Phc2, as a critical modulator of HSPC trafficking. The genetic ablation of Phc2 in mice causes a severe defect in HSPC mobilization through the derepression of Vcam1 in bone marrow stromal cells (BMSCs), ultimately leading to a systemic immunodeficiency. Moreover, the pharmacological inhibition of VCAM-1 in Phc2-deficient mice reverses the symptoms. We further determine that Phc2-dependent Vcam1 repression in BMSCs is mediated by the epigenetic regulation of H3K27me3 and H2AK119ub. Together, our data demonstrate a cell-extrinsic role for Phc2 in controlling the mobilization of HSPCs by finely tuning their bone marrow niche. Mobilization of hematopoietic stem and progenitor cells (HSPCs) into the circulation is essential for maintaining homeostasis. Here, the authors show that Phc2 in bone marrow stromal cells represses the cell adhesion molecule Vcam1 and facilitates mobilization of HSPCs through regulation of epigenetic marks.
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Gentile C, Berlivet S, Mayran A, Paquette D, Guerard-Millet F, Bajon E, Dostie J, Kmita M. PRC2-Associated Chromatin Contacts in the Developing Limb Reveal a Possible Mechanism for the Atypical Role of PRC2 in HoxA Gene Expression. Dev Cell 2019; 50:184-196.e4. [DOI: 10.1016/j.devcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/24/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
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63
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Fursova NA, Blackledge NP, Nakayama M, Ito S, Koseki Y, Farcas AM, King HW, Koseki H, Klose RJ. Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression. Mol Cell 2019; 74:1020-1036.e8. [PMID: 31029541 PMCID: PMC6561741 DOI: 10.1016/j.molcel.2019.03.024] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 03/21/2019] [Indexed: 01/30/2023]
Abstract
The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here, we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes, which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.
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Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Anca M Farcas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; AMED-CREST, Japanese Agency for Medical Research and Development, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Ben Zouari Y, Molitor AM, Sikorska N, Pancaldi V, Sexton T. ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C. Genome Biol 2019; 20:102. [PMID: 31118054 PMCID: PMC6532271 DOI: 10.1186/s13059-019-1706-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/03/2019] [Indexed: 12/19/2022] Open
Abstract
Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks.
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Affiliation(s)
- Yousra Ben Zouari
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Anne M Molitor
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Natalia Sikorska
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Vera Pancaldi
- Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM U1037, Toulouse, France
- University Paul Sabatier III, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France.
- CNRS UMR7104, Illkirch, France.
- INSERM U1258, Illkirch, France.
- University of Strasbourg, Illkirch, France.
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65
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Chan HL, Morey L. Emerging Roles for Polycomb-Group Proteins in Stem Cells and Cancer. Trends Biochem Sci 2019; 44:688-700. [PMID: 31085088 DOI: 10.1016/j.tibs.2019.04.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 02/07/2023]
Abstract
Polycomb-group (PcG) complexes are multiprotein, evolutionarily conserved epigenetic machineries that regulate stem cell fate decisions and development, and are also implicated in cancer and other maladies. The PcG machinery can be divided into two major complexes: Polycomb repressive complex 1 and 2 (PRC1 and PRC2). Traditionally, PcG complexes have been associated with maintenance of gene repression mainly via histone-modifying activities. However, during the last years, increasing evidence indicates that the PcG complexes can also positively regulate gene transcription and modify non-histone substrates in multiple biological processes, cellular stages, and cancers. In this review, we will illustrate recent findings in PcG-mediated gene regulation, with special focus on the recently described non-classical functions of PcG complexes in stem cells and cancer.
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Affiliation(s)
- Ho Lam Chan
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, USA; Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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66
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Bessonova TA, Lekontseva NV, Shvyreva US, Nikulin AD, Tutukina MN, Ozoline ON. Overproduction and purification of the Escherichia coli transcription factors "toxic" to a bacterial cell. Protein Expr Purif 2019; 161:70-77. [PMID: 31054315 DOI: 10.1016/j.pep.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/25/2019] [Accepted: 05/01/2019] [Indexed: 11/28/2022]
Abstract
Transcription factors play a crucial role in control of life of a bacterial cell, working as switchers to a different life style or pathogenicity. To reconstruct the network of regulatory events taking place in changing growth conditions, we need to know regulons of as many transcription factors as possible, and motifs recognized by them. Experimentally this can be attained via ChIP-seq in vivo, SELEX and DNAse I footprinting in vitro. All these approaches require large amounts of purified proteins. However, overproduction of transcription factors leading to their extensive binding to the regulatory elements on the DNA make them toxic to a bacterial cell thus significantly complicating production of a soluble protein. Here, on the example of three regulators from Escherichia coli, UxuR, ExuR, and LeuO, we show that stable production of toxic transcription factors in a soluble fraction can be significantly enhanced by holding the expression of a recombinant protein back at the early stages of bacterial growth. This can be achieved by cloning genes together with their regulatory regions containing repressor sites, with subsequent growth in a very rich media where activity of excessive regulators is not crucial, followed by induction with a very low concentration of an inducer. Schemes of further purification of these proteins were developed, and functional activity was confirmed.
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Affiliation(s)
- Tatiana A Bessonova
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia; Institute of Protein Research RAS, Pushchino, Moscow region, 142290, Russia; Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | - Uliana S Shvyreva
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia; Institute of Protein Research RAS, Pushchino, Moscow region, 142290, Russia
| | - Alexey D Nikulin
- Institute of Protein Research RAS, Pushchino, Moscow region, 142290, Russia
| | - Maria N Tutukina
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia; Kharkevich Institute for Information Transmission Problems RAS, Moscow, 127051, Russia
| | - Olga N Ozoline
- Institute of Cell Biophysics of RAS, Pushchino, Moscow region, 142290, Russia
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O’Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin 2019; 12:26. [PMID: 31053162 PMCID: PMC6498470 DOI: 10.1186/s13072-019-0275-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/23/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.
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Affiliation(s)
- Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Sofie L. Bates
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Sakereh S. Carter
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Karly A. Nisson
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Julian Halmai
- Department of Neurology and Stem Cell Program, University of California, Sacramento, CA 95817 USA
| | - Kyle D. Fink
- Department of Neurology and Stem Cell Program, University of California, Sacramento, CA 95817 USA
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
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Pivetti S, Fernandez-Perez D, D’Ambrosio A, Barbieri CM, Manganaro D, Rossi A, Barnabei L, Zanotti M, Scelfo A, Chiacchiera F, Pasini D. Loss of PRC1 activity in different stem cell compartments activates a common transcriptional program with cell type-dependent outcomes. SCIENCE ADVANCES 2019; 5:eaav1594. [PMID: 31106267 PMCID: PMC6520019 DOI: 10.1126/sciadv.aav1594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/02/2019] [Indexed: 05/11/2023]
Abstract
Polycomb repressive complexes are evolutionarily conserved complexes that maintain transcriptional repression during development and differentiation to establish and preserve cell identity. We recently described the fundamental role of PRC1 in preserving intestinal stem cell identity through the inhibition of non-lineage-specific transcription factors. To further elucidate the role of PRC1 in adult stem cell maintenance, we now investigated its role in LGR5+ hair follicle stem cells during regeneration. We show that PRC1 depletion severely affects hair regeneration and, different from intestinal stem cells, derepression of its targets induces the ectopic activation of an epidermal-specific program. Our data support a general role of PRC1 in preserving stem cell identity that is shared between different compartments. However, the final outcome of the ectopic activation of non-lineage-specific transcription factors observed upon loss of PRC1 is largely context-dependent and likely related to the transcription factors repertoire and specific epigenetic landscape of different cellular compartments.
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Affiliation(s)
- Silvia Pivetti
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | | | - Alessandro D’Ambrosio
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | | | - Daria Manganaro
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Alessandra Rossi
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Laura Barnabei
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Marika Zanotti
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Andrea Scelfo
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Fulvio Chiacchiera
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
- University of Trento, Department of Cellular, Computational and Integrative Biology–CIBIO, Trento, Italy
- Corresponding author. (F.C.); (D.P.)
| | - Diego Pasini
- European Institute of Oncology–IRCCS, Department of Experimental Oncology, Milan, Italy
- University of Milan, Department of Health Sciences, Milan, Italy
- Corresponding author. (F.C.); (D.P.)
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69
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Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nat Commun 2019; 10:1931. [PMID: 31036804 PMCID: PMC6488670 DOI: 10.1038/s41467-019-09628-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.
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Affiliation(s)
- Hagar F Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Daniel Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, 90089, USA
| | - Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Carina Pribitzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Karin Stecher
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Katarina Bartalska
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Luca Michetti
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Jorge A Zepeda-Martinez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Jacob I Stuckey
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA, 02142, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, 90089, USA.
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Scelfo A, Fernández-Pérez D, Tamburri S, Zanotti M, Lavarone E, Soldi M, Bonaldi T, Ferrari KJ, Pasini D. Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities. Mol Cell 2019; 74:1037-1052.e7. [PMID: 31029542 PMCID: PMC6561742 DOI: 10.1016/j.molcel.2019.04.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/22/2019] [Accepted: 03/28/2019] [Indexed: 01/24/2023]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) control cell identity by establishing facultative heterochromatin repressive domains at common sets of target genes. PRC1, which deposits H2Aub1 through the E3 ligases RING1A/B, forms six biochemically distinct subcomplexes depending on the assembled PCGF protein (PCGF1–PCGF6); however, it is yet unclear whether these subcomplexes have also specific activities. Here we show that PCGF1 and PCGF2 largely compensate for each other, while other PCGF proteins have high levels of specificity for distinct target genes. PCGF2 associates with transcription repression, whereas PCGF3 and PCGF6 associate with actively transcribed genes. Notably, PCGF3 and PCGF6 complexes can assemble and be recruited to several active sites independently of RING1A/B activity (therefore, of PRC1). For chromatin recruitment, the PCGF6 complex requires the combinatorial activities of its MGA-MAX and E2F6-DP1 subunits, while PCGF3 requires an interaction with the USF1 DNA binding transcription factor. PRC1 complexes retain high target specificity with little compensatory functions PCGF2 defines repressive signatures and PCGF3 and PCGF6 transcription active states RING1A/B is dispensable for the assembly and recruitment of PCGF3 and PCGF6 complexes PCGF3 and PCGF6 complexes bind target genes through specific DNA binding activities
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Affiliation(s)
- Andrea Scelfo
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Simone Tamburri
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Elisa Lavarone
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Monica Soldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Karin Johanna Ferrari
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Diego Pasini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy.
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SCL/TAL1 cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells. Nat Commun 2018; 9:5375. [PMID: 30560907 PMCID: PMC6299140 DOI: 10.1038/s41467-018-07787-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 11/23/2018] [Indexed: 01/03/2023] Open
Abstract
During development, it is unclear if lineage-fated cells derive from multilineage-primed progenitors and whether active mechanisms operate to restrict cell fate. Here we investigate how mesoderm specifies into blood-fated cells. We document temporally restricted co-expression of blood (Scl/Tal1), cardiac (Mesp1) and paraxial (Tbx6) lineage-affiliated transcription factors in single cells, at the onset of blood specification, supporting the existence of common progenitors. At the same time-restricted stage, absence of SCL results in expansion of cardiac/paraxial cell populations and increased cardiac/paraxial gene expression, suggesting active suppression of alternative fates. Indeed, SCL normally activates expression of co-repressor ETO2 and Polycomb-PRC1 subunits (RYBP, PCGF5) and maintains levels of Polycomb-associated histone marks (H2AK119ub/H3K27me3). Genome-wide analyses reveal ETO2 and RYBP co-occupy most SCL target genes, including cardiac/paraxial loci. Reduction of Eto2 or Rybp expression mimics Scl-null cardiac phenotype. Therefore, SCL-mediated transcriptional repression prevents mis-specification of blood-fated cells, establishing active repression as central to fate determination processes. Mechanisms that operate during embryonic development to restrict cell fate are currently under investigation. Here the authors characterise the role of SCL/TAL1 at the onset of blood specification in embryonic development using mouse EB differentiation culture as a model system.
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WDR68 is essential for the transcriptional activation of the PRC1-AUTS2 complex and neuronal differentiation of mouse embryonic stem cells. Stem Cell Res 2018; 33:206-214. [PMID: 30448639 DOI: 10.1016/j.scr.2018.10.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/11/2018] [Accepted: 10/31/2018] [Indexed: 11/22/2022] Open
Abstract
Recent studies on Polycomb repressive complexes (PRC) reveal a surprising role in transcriptional activation, yet the underlying mechanism remains poorly understood. We previously identified a type 1 PRC (PRC1) that contains Autism Susceptibility Candidate 2 (AUTS2), which positively regulates transcription of neuronal genes. However, the mechanism by which the PRC1-AUTS2 complex influences neurodevelopment is unclear. Here we demonstrate that WDR68 is not only an integral component of the PRC1-AUTS2 complex, but it is also required for PRC1-AUTS2-mediated transcription activation. Furthermore, deletion of Wdr68 in mouse embryonic stem cells leads to defects in neuronal differentiation without affecting self-renewal. Through transcriptomic analysis, we found that many genes responsible for neuronal differentiation are down-regulated in Wdr68 deficient neural progenitors. These genes include those targeted by the PRC1-AUTS2 complex. In summary, our studies uncovered a previously unknown but essential component of the active PRC1 complex and evidence of its role in regulating the expression of genes that are important for neuronal differentiation.
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73
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Goldstein BJ, Choi R, Goss GM. Multiple polycomb epigenetic regulatory proteins are active in normal and regenerating adult olfactory epithelium. Laryngoscope Investig Otolaryngol 2018; 3:337-344. [PMID: 30410986 PMCID: PMC6209616 DOI: 10.1002/lio2.180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/23/2023] Open
Abstract
Objectives To investigate epigenetic mechanisms contributing to regulation of cellular renewal and neurogenesis in adult olfactory epithelium (OE). Study Design Prospective basic science study. Methods Olfactory basal cell cultures were prepared from adult mice per established protocols. in vivo studies were performed using the mouse methimazole lesion-regeneration paradigm. Nasal tissue sections were prepared from adult mice 7 days following lesion, or from unlesioned controls. Polycomb proteins were assessed by Western blot from culture or nasal tissue lysates, and by gene expression studies from cultures. In addition, in vivo expression patterns of Polycomb proteins were examined using immunohistochemistry. Chromosome immunoprecipitation (ChIP) was performed to investigate epigenetic modifications and specific chromatin interactions for Polycomb proteins in olfactory basal cells. Results Subunits of Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2) were identified in basal cell cultures and in vivo. In regenerating OE, basal progenitor cells identified by expression of the c-KIT receptor were found to coexpress the PRC2 protein EZH2. Because multiple variants of PRC1 subunits give rise to diverse PRC1 complexes serving different functions, expression of specific PRC1 variants was further examined. We identified PRC1 components including MEL18 (PCGF2) in immature neurons, and confirm BMI1 (PCGF4) expression in mature neurons. Moreover, we identified CBX8 as a neuron-specific PRC1 subunit. ChIP assays from OE cells demonstrated binding of PRC proteins to regulatory regions of specific transcription factors, consistent with PRC-mediated epigenetic silencing mechanisms active in adult OE. Conclusions Multiple Polycomb proteins have cell type-specific expression patterns in the adult OE. Findings presented here, together with evidence from prior studies, suggest that PRC-mediated epigenetic silencing contributes to regulation of cellular renewal and tissue homeostasis in the OE. Efforts to define the mechanisms that regulate repair in the OE are essential for development of new therapeutic strategies for olfactory disorders. Level of Evidence N/A.
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Affiliation(s)
- Bradley J Goldstein
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida U.S.A.,Graduate Program in Neuroscience University of Miami Miller School of Medicine Miami Florida U.S.A.,Interdisciplinary Stem Cell Institute University of Miami Miller School of Medicine Miami Florida U.S.A
| | - Rhea Choi
- Graduate Program in Neuroscience University of Miami Miller School of Medicine Miami Florida U.S.A.,Interdisciplinary Stem Cell Institute University of Miami Miller School of Medicine Miami Florida U.S.A.,Medical Scientist Training Program University of Miami Miller School of Medicine Miami Florida U.S.A
| | - Garrett M Goss
- Department of Otolaryngology University of Miami Miller School of Medicine Miami Florida U.S.A.,Interdisciplinary Stem Cell Institute University of Miami Miller School of Medicine Miami Florida U.S.A
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74
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Epigenetic and non-epigenetic functions of the RYBP protein in development and disease. Mech Ageing Dev 2018; 174:111-120. [DOI: 10.1016/j.mad.2018.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022]
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75
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Chan HL, Beckedorff F, Zhang Y, Garcia-Huidobro J, Jiang H, Colaprico A, Bilbao D, Figueroa ME, LaCava J, Shiekhattar R, Morey L. Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms. Nat Commun 2018; 9:3377. [PMID: 30139998 PMCID: PMC6107513 DOI: 10.1038/s41467-018-05728-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/25/2018] [Indexed: 12/16/2022] Open
Abstract
Polycomb repressive complex 1 (PRC1) plays essential roles in cell fate decisions and development. However, its role in cancer is less well understood. Here, we show that RNF2, encoding RING1B, and canonical PRC1 (cPRC1) genes are overexpressed in breast cancer. We find that cPRC1 complexes functionally associate with ERα and its pioneer factor FOXA1 in ER+ breast cancer cells, and with BRD4 in triple-negative breast cancer cells (TNBC). While cPRC1 still exerts its repressive function, it is also recruited to oncogenic active enhancers. RING1B regulates enhancer activity and gene transcription not only by promoting the expression of oncogenes but also by regulating chromatin accessibility. Functionally, RING1B plays a divergent role in ER+ and TNBC metastasis. Finally, we show that concomitant recruitment of RING1B to active enhancers occurs across multiple cancers, highlighting an under-explored function of cPRC1 in regulating oncogenic transcriptional programs in cancer. The role of Polycomb Repressive Complex 1 (PRC1) is well described in development. Here, the authors investigate canonical PRC1’s regulation of transcriptional programs in breast cancer where, in addition to its repressive function, it is also recruited to oncogenic active enhancers to regulate enhancer activity and chromatin accessibility.
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Affiliation(s)
- Ho Lam Chan
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yusheng Zhang
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Jenaro Garcia-Huidobro
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Centro de Investigaciones Médicas (CIM), Núcleo Científico Multidisciplinario, Escuela de Medicina, Universidad de Talca, Avenida Lircay S/N, Talca, 3460000, Chile
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Daniel Bilbao
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA.,Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA. .,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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76
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Nakagawa M, Kitabayashi I. Oncogenic roles of enhancer of zeste homolog 1/2 in hematological malignancies. Cancer Sci 2018; 109:2342-2348. [PMID: 29845708 PMCID: PMC6113435 DOI: 10.1111/cas.13655] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/16/2018] [Accepted: 05/28/2018] [Indexed: 12/27/2022] Open
Abstract
Polycomb group (PcG) proteins regulate the expression of target genes by modulating histone modifications and are representative epigenetic regulators that maintain the stemness of embryonic and hematopoietic stem cells. Histone methyltransferases enhancer of zeste homolog 1 and 2 (EZH1/2), which are subunits of polycomb repressive complexes (PRC), are recurrently mutated or highly expressed in many hematological malignancies. EZH2 has a dual function in tumorigenesis as an oncogene and tumor suppressor gene, and targeting PRC2, in particular EZH1/2, for anticancer therapy has been extensively developed in the clinical setting. Here, we review the oncogenic function of EZH1/2 and introduce new therapeutic drugs targeting these enzymes.
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Affiliation(s)
- Makoto Nakagawa
- Division of Hematological MalignancyNational Cancer Center Research InstituteTokyoJapan
- Department of Orthopaedic SurgeryGraduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Issay Kitabayashi
- Division of Hematological MalignancyNational Cancer Center Research InstituteTokyoJapan
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77
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Li M, Zhang S, Zhao W, Hou C, Ma X, Li X, Huang B, Chen H, Chen D. RYBP modulates stability and function of Ring1B through targeting UBE3A. FASEB J 2018; 33:683-695. [DOI: 10.1096/fj.201800397r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Meng Li
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Shiqiang Zhang
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Wen Zhao
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Congcong Hou
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Xiaoli Ma
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Xuekun Li
- Institute of Translational MedicineSchool of MedicineZhejiang University Hangzhou China
| | - Bingren Huang
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Hong Chen
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
| | - Deng Chen
- Department of Biochemistry and Molecular BiologyState Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical Sciences and School of Basic MedicinePeking Union Medical College Beijing China
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78
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Gu X, Wang X, Su D, Su X, Lin L, Li S, Wu Q, Liu S, Zhang P, Zhu X, Jiang X. CBX2 Inhibits Neurite Development by Regulating Neuron-Specific Genes Expression. Front Mol Neurosci 2018. [PMID: 29541019 PMCID: PMC5835719 DOI: 10.3389/fnmol.2018.00046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Polycomb group (PcG) proteins regulate the epigenetic status of transcription regulatory states during development. Progression from pluripotency to differentiation requires the sequential activation and repression of different PcG target genes, however, the relationship between early patterning signals, PcG expression, and the development of the central nervous system is still unclear. Using various models of neuronal differentiation, we provide evidence that CBX2 is a negative regulator of neuronal differentiation. Knock-down of CBX2 expression promotes neurite development, while overexpression of CBX2 inhibits neurite development. Further, we found that CBX2 is a direct target gene of miR-124. During neuronal differentiation, CBX2 was decreased while miR-124 was increased. Mechanistically, CBX2 directly interacts with the promoter region of several neuro-associated genes and regulates their expression. We found that the neuron-specific GAP-43 gene could contribute to the stimulating effect on neurite development associated with inhibition of CBX2.
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Affiliation(s)
- Xi Gu
- Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Guangzhou, China
| | - Xuemin Wang
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Dazhuang Su
- Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Guangzhou, China
| | - Xiaohong Su
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Lifang Lin
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Shuji Li
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Qiaoqi Wu
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Shuhu Liu
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Peidong Zhang
- Department of Neurobiology, Southern Medical University, Guangzhou, China
| | - Xinhong Zhu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Xiaodan Jiang
- Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Guangzhou, China
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79
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Polycomb protein family member CBX7 regulates intrinsic axon growth and regeneration. Cell Death Differ 2018; 25:1598-1611. [PMID: 29459770 PMCID: PMC6143612 DOI: 10.1038/s41418-018-0064-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 12/25/2017] [Accepted: 01/08/2018] [Indexed: 01/28/2023] Open
Abstract
Neurons in the central nervous system (CNS) lose their intrinsic ability and fail to regenerate, but the underlying mechanisms are largely unknown. Polycomb group (PcG) proteins, which include PRC1 and PRC2 complexes function as gene repressors and are involved in many biological processes. Here we report that PRC1 components (polycomb chromobox (CBX) 2, 7, and 8) are novel regulators of axon growth and regeneration. Especially, knockdown of CBX7 in either embryonic cortical neurons or adult dorsal root ganglion (DRG) neurons enhances their axon growth ability. Two important transcription factors GATA4 and SOX11 are functional downstream targets of CBX7 in controlling axon regeneration. Moreover, knockdown of GATA4 or SOX11 in cultured DRG neurons inhibits axon regeneration response from CBX7 downregulation in DRG neurons. These findings suggest that targeting CBX signaling pathway may be a novel approach for promoting the intrinsic regenerative capacity of damaged CNS neurons.
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80
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The JAZF1-SUZ12 fusion protein disrupts PRC2 complexes and impairs chromatin repression during human endometrial stromal tumorogenesis. Oncotarget 2018; 8:4062-4078. [PMID: 27845897 PMCID: PMC5354813 DOI: 10.18632/oncotarget.13270] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/29/2016] [Indexed: 11/27/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2), which contains three core proteins EZH2, EED and SUZ12, controls chromatin compaction and transcription repression through trimethylation of lysine 27 on histone 3. The (7;17)(p15;q21) chromosomal translocation present in most cases of endometrial stromal sarcomas (ESSs) results in the in-frame fusion of the JAZF1 and SUZ12 genes. We have investigated whether and how the fusion protein JAZF1-SUZ12 functionally alters PRC2. We found that the fusion protein exists at high levels in ESS containing the t(7;17). Co-transient transfection assay indicated JAZF1-SUZ12 destabilized PRC2 components EZH2 and EED, resulting in decreased histone methyl transferase (HMT) activity, which was confirmed by in vitro studies using reconstituted PRC2 and nucleosome array substrates. We also demonstrated the PRC2 containing the fusion protein decreased the binding affinity to target chromatin loci. In addition, we found that trimethylation of H3K27 was decreased in ESS samples with the t(7;17), but there was no detectable change in H3K9 in these tissues. Moreover, re-expression of SUZ12 in Suz12 (−/−) ES cells rescued the neuronal differentiation while the fusion protein failed to restore this function and enhanced cell proliferation. In summary, our studies reveal that JAZF1-SUZ12 fusion protein disrupts the PRC2 complex, abolishes HMT activity and subsequently activates chromatin/genes normally repressed by PRC2. Such dyesfunction of PRC2 inhibits normal neural differentiation of ES cell and increases cell proliferation. Related changes induced by the JAZF-SUZ12 protein in endometrial stromal cells may explain the oncogenic effect of the t(7;17) in ESS.
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81
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From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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82
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Koh AS, Miller EL, Buenrostro JD, Moskowitz DM, Wang J, Greenleaf WJ, Chang HY, Crabtree GR. Rapid chromatin repression by Aire provides precise control of immune tolerance. Nat Immunol 2018; 19:162-172. [PMID: 29335648 PMCID: PMC6049828 DOI: 10.1038/s41590-017-0032-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/07/2017] [Indexed: 01/23/2023]
Abstract
Aire mediates the expression of tissue-specific antigens in thymic epithelial cells to promote tolerance against self-reactive T lymphocytes. However, the mechanism that allows expression of tissue-specific genes at levels that prevent harm is unknown. Here we show that Brg1 generates accessibility at tissue-specific loci to impose central tolerance. We found that Aire has an intrinsic repressive function that restricts chromatin accessibility and opposes Brg1 across the genome. Aire exerted this repressive influence within minutes after recruitment to chromatin and restrained the amplitude of active transcription. Disease-causing mutations that impair Aire-induced activation also impair the protein's repressive function, which indicates dual roles for Aire. Together, Brg1 and Aire fine-tune the expression of tissue-specific genes at levels that prevent toxicity yet promote immune tolerance.
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Affiliation(s)
- Andrew S Koh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Erik L Miller
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - David M Moskowitz
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerburg Biohub, San Francisco, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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83
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Zhan S, Wang T, Ge W, Li J. Multiple roles of Ring 1 and YY1 binding protein in physiology and disease. J Cell Mol Med 2018; 22:2046-2054. [PMID: 29383875 PMCID: PMC5867070 DOI: 10.1111/jcmm.13503] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/16/2017] [Indexed: 12/17/2022] Open
Abstract
Ring 1 and YY1 binding protein (RYBP) was first identified in 1999, and its structure includes a conserved Npl4 Zinc finger motif at the N‐terminus, a central region that is characteristically enriched with arginine and lysine residues and a C‐terminal region enriched with serine and threonine amino acids. Over nearly 20 years, multiple studies have found that RYBP functions as an organ developmental adaptor. There is also evidence that RYBP regulates the expression of different genes involved in various aspects of biological processes, via a mechanism that is dependent on interactions with components of PcG complexes and/or through binding to different transcriptional factors. In addition, RYBP interacts directly or indirectly with apoptosis‐associated proteins to mediate anti‐apoptotic or pro‐apoptotic activity in both the cytoplasm and nucleus of various cell types. Furthermore, RYBP has also been shown to act as tumour suppressor gene in different solid tumours, but as an oncogene in lymphoma and melanoma. In this review, we summarize our current understanding of the functions of this multifaceted RYBP in physiological and pathological conditions, including embryonic development, apoptosis and cancer, as well as its role as a component of polycomb repressive complex 1.
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Affiliation(s)
- Shaohua Zhan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianxiao Wang
- Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei Ge
- National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China
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84
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Stielow B, Finkernagel F, Stiewe T, Nist A, Suske G. MGA, L3MBTL2 and E2F6 determine genomic binding of the non-canonical Polycomb repressive complex PRC1.6. PLoS Genet 2018; 14:e1007193. [PMID: 29381691 PMCID: PMC5806899 DOI: 10.1371/journal.pgen.1007193] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/09/2018] [Accepted: 01/09/2018] [Indexed: 02/02/2023] Open
Abstract
Diverse Polycomb repressive complexes 1 (PRC1) play essential roles in gene regulation, differentiation and development. Six major groups of PRC1 complexes that differ in their subunit composition have been identified in mammals. How the different PRC1 complexes are recruited to specific genomic sites is poorly understood. The Polycomb Ring finger protein PCGF6, the transcription factors MGA and E2F6, and the histone-binding protein L3MBTL2 are specific components of the non-canonical PRC1.6 complex. In this study, we have investigated their role in genomic targeting of PRC1.6. ChIP-seq analysis revealed colocalization of MGA, L3MBTL2, E2F6 and PCGF6 genome-wide. Ablation of MGA in a human cell line by CRISPR/Cas resulted in complete loss of PRC1.6 binding. Rescue experiments revealed that MGA recruits PRC1.6 to specific loci both by DNA binding-dependent and by DNA binding-independent mechanisms. Depletion of L3MBTL2 and E2F6 but not of PCGF6 resulted in differential, locus-specific loss of PRC1.6 binding illustrating that different subunits mediate PRC1.6 loading to distinct sets of promoters. Mga, L3mbtl2 and Pcgf6 colocalize also in mouse embryonic stem cells, where PRC1.6 has been linked to repression of germ cell-related genes. Our findings unveil strikingly different genomic recruitment mechanisms of the non-canonical PRC1.6 complex, which specify its cell type- and context-specific regulatory functions. Polycomb group proteins assemble in two major repressive multi-subunit complexes (PRC1 and PRC2), which play important roles in many physiological processes, including stem cell maintenance, differentiation, cell cycle control and cancer. In mammals, six different groups of PRC1 complexes exist (PRC1.1 to PRC1.6), which differ in their subunit composition. The mechanisms that target the different PRC1 complexes to specific genomic sites appear diverse and are poorly understood. In this study, we have investigated the genomic targeting mechanisms of the non-canonical PRC1.6 complex. In PRC1.6, the defining subunit PCGF6 is specifically associated with several proteins including the transcription factors MGA and E2F6, and the histone-binding protein L3MBTL2. We found that MGA is absolutely essential for targeting PRC1.6. MGA executes recruitment of PRC1.6 to its target sites through two distinct functions. On the one hand it acts as a sequence-specific DNA-binding factor; on the other hand it has a scaffolding function, which is independent of its DNA binding capacity. E2F6 and L3MBTL2 are also important in genomic targeting of PRC1.6 as they promote binding of PRC1.6 to different sets of genes associated with distinct functions. Our finding that different components specify loading of PRC1.6 to distinct sets of genes could establish a paradigm for other chromatin-associated complexes.
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Affiliation(s)
- Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, Marburg, Germany
| | - Guntram Suske
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
- * E-mail:
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85
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A molecular roadmap for the emergence of early-embryonic-like cells in culture. Nat Genet 2017; 50:106-119. [PMID: 29255263 PMCID: PMC5755687 DOI: 10.1038/s41588-017-0016-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/13/2017] [Indexed: 12/24/2022]
Abstract
Unlike pluripotent cells, which generate only embryonic tissues, totipotent cells can generate a full organism, including extraembryonic annexes. A rare population of cells resembling 2-cell stage embryos arises in pluripotent embryonic stem (ES) cell cultures. These 2-cell-like-cells display molecular features of totipotency and broader developmental plasticity. However, their specific nature and the process through which they arise remain outstanding questions. Here, we identify intermediate cellular states and molecular determinants during the emergence of 2-cell-like-cells. By deploying a quantitative single cell expression approach, we identified an intermediate population characterised by the expression of the transcription factor ZSCAN4 as precursor of 2-cell-like-cells. Using an siRNA screening, we uncovered novel epigenetic regulators of 2-cell-like-cell emergence, including the non-canonical PRC1 complex PRC1.6 and Ep400/Tip60. Our data shed light on the mechanisms underlying the exit from the ES cell state towards the formation of early-embryonic-like cells in culture and identify key epigenetic pathways that promote this transition.
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86
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Rapisarda V, Borghesan M, Miguela V, Encheva V, Snijders AP, Lujambio A, O'Loghlen A. Integrin Beta 3 Regulates Cellular Senescence by Activating the TGF-β Pathway. Cell Rep 2017; 18:2480-2493. [PMID: 28273461 PMCID: PMC5357738 DOI: 10.1016/j.celrep.2017.02.012] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/06/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
Cellular senescence is an important in vivo mechanism that prevents the propagation of damaged cells. However, the precise mechanisms regulating senescence are not well characterized. Here, we find that ITGB3 (integrin beta 3 or β3) is regulated by the Polycomb protein CBX7. β3 expression accelerates the onset of senescence in human primary fibroblasts by activating the transforming growth factor β (TGF-β) pathway in a cell-autonomous and non-cell-autonomous manner. β3 levels are dynamically increased during oncogene-induced senescence (OIS) through CBX7 Polycomb regulation, and downregulation of β3 levels overrides OIS and therapy-induced senescence (TIS), independently of its ligand-binding activity. Moreover, cilengitide, an αvβ3 antagonist, has the ability to block the senescence-associated secretory phenotype (SASP) without affecting proliferation. Finally, we show an increase in β3 levels in a subset of tissues during aging. Altogether, our data show that integrin β3 subunit is a marker and regulator of senescence.
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Affiliation(s)
- Valentina Rapisarda
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Michela Borghesan
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Veronica Miguela
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Vesela Encheva
- Protein Analysis and Proteomics Group, The Francis Crick Institute, South Mimms EN6 3LD, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Group, The Francis Crick Institute, South Mimms EN6 3LD, UK
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Ana O'Loghlen
- Epigenetics & Cellular Senescence Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK.
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87
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Prokop A, Gouin E, Villiers V, Nahori MA, Vincentelli R, Duval M, Cossart P, Dussurget O. OrfX, a Nucleomodulin Required for Listeria monocytogenes Virulence. mBio 2017; 8:e01550-17. [PMID: 29089430 PMCID: PMC5666158 DOI: 10.1128/mbio.01550-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/25/2017] [Indexed: 12/11/2022] Open
Abstract
Listeria monocytogenes is a bacterial pathogen causing severe foodborne infections in humans and animals. Listeria can enter into host cells and survive and multiply therein, due to an arsenal of virulence determinants encoded in different loci on the chromosome. Several key Listeria virulence genes are clustered in Listeria pathogenicity island 1. This important locus also contains orfX (lmo0206), a gene of unknown function. Here, we found that OrfX is a small, secreted protein whose expression is positively regulated by PrfA, the major transcriptional activator of Listeria virulence genes. We provide evidence that OrfX is a virulence factor that dampens the oxidative response of infected macrophages, which contributes to intracellular survival of bacteria. OrfX is targeted to the nucleus and interacts with the regulatory protein RybP. We show that in macrophages, the expression of OrfX decreases the level of RybP, which controls cellular infection. Collectively, these data reveal that Listeria targets RybP and evades macrophage oxidative stress for efficient infection. Altogether, OrfX is after LntA, the second virulence factor acting directly in the nucleus.IMPORTANCEListeria monocytogenes is a model bacterium that has been successfully used over the last 30 years to refine our understanding of the molecular, cellular, and tissular mechanisms of microbial pathogenesis. The major virulence factors of pathogenic Listeria species are located on a single chromosomal locus. Here, we report that the last gene of this locus encodes a small secreted nucleomodulin, OrfX, that is required for bacterial survival within macrophages and in the infected host. This work demonstrates that the production of OrfX contributes to limiting the host innate immune response by dampening the oxidative response of macrophages. We also identify a target of OrfX, RybP, which is an essential pleiotropic regulatory protein of the cell, and uncover its role in host defense. Our data reinforce the view that the secretion of nucleomodulins is an important strategy used by microbial pathogens to promote infection.
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Affiliation(s)
- Andrzej Prokop
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Edith Gouin
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
| | - Véronique Villiers
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
| | - Marie-Anne Nahori
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
| | | | - Mélodie Duval
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
| | - Olivier Dussurget
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, France
- Inserm, U604, Paris, France
- INRA, USC2020, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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88
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Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE. Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Mol Cell 2017; 65:432-446.e5. [PMID: 28157505 DOI: 10.1016/j.molcel.2017.01.009] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/08/2016] [Accepted: 01/05/2017] [Indexed: 12/27/2022]
Abstract
Master regulatory genes require stable silencing by the polycomb group (PcG) to prevent misexpression during differentiation and development. Some PcG proteins covalently modify histones, which contributes to heritable repression. The role for other effects on chromatin structure is less understood. We characterized the organization of PcG target genes in ESCs and neural progenitors using 5C and super-resolution microscopy. The genomic loci of repressed PcG targets formed discrete, small (20-140 Kb) domains of tight interaction that corresponded to locations bound by canonical polycomb repressive complex 1 (PRC1). These domains changed during differentiation as PRC1 binding changed. Their formation depended upon the Polyhomeotic component of canonical PRC1 and occurred independently of PRC1-catalyzed ubiquitylation. PRC1 domains differ from topologically associating domains in size and boundary characteristics. These domains have the potential to play a key role in transmitting epigenetic silencing of PcG targets by linking PRC1 to formation of a repressive higher-order structure.
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Affiliation(s)
- Sharmistha Kundu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gaurav Jain
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Boston, MA 02115, USA; Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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89
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Beringer M, Pisano P, Di Carlo V, Blanco E, Chammas P, Vizán P, Gutiérrez A, Aranda S, Payer B, Wierer M, Di Croce L. EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells. Mol Cell 2017; 64:645-658. [PMID: 27863225 DOI: 10.1016/j.molcel.2016.10.018] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/30/2016] [Accepted: 10/14/2016] [Indexed: 11/19/2022]
Abstract
The cellular plasticity of pluripotent stem cells is thought to be sustained by genomic regions that display both active and repressive chromatin properties. These regions exhibit low levels of gene expression, yet the mechanisms controlling these levels remain unknown. Here, we describe Elongin BC as a binding factor at the promoters of bivalent sites. Biochemical and genome-wide analyses show that Elongin BC is associated with Polycomb Repressive Complex 2 (PRC2) in pluripotent stem cells. Elongin BC is recruited to chromatin by the PRC2-associated factor EPOP (Elongin BC and Polycomb Repressive Complex 2 Associated Protein, also termed C17orf96, esPRC2p48, E130012A19Rik), a protein expressed in the inner cell mass of the mouse blastocyst. Both EPOP and Elongin BC are required to maintain low levels of expression at PRC2 genomic targets. Our results indicate that keeping the balance between activating and repressive cues is a more general feature of chromatin in pluripotent stem cells than previously appreciated.
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Affiliation(s)
- Malte Beringer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paola Pisano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Valerio Di Carlo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paul Chammas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Pedro Vizán
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Arantxa Gutiérrez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Michael Wierer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain.
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90
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Simoes da Silva CJ, Fereres S, Simón R, Busturia A. Drosophila SCE/dRING E3-ligase inhibits apoptosis in a Dp53 dependent manner. Dev Biol 2017; 429:81-91. [DOI: 10.1016/j.ydbio.2017.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/22/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
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91
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Co-Expression Network and Pathway Analyses Reveal Important Modules of miRNAs Regulating Milk Yield and Component Traits. Int J Mol Sci 2017; 18:ijms18071560. [PMID: 28718798 PMCID: PMC5536048 DOI: 10.3390/ijms18071560] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 01/01/2023] Open
Abstract
Co-expression network analyses provide insights into the molecular interactions underlying complex traits and diseases. In this study, co-expression network analysis was performed to detect expression patterns (modules or clusters) of microRNAs (miRNAs) during lactation, and to identify miRNA regulatory mechanisms for milk yield and component traits (fat, protein, somatic cell count (SCC), lactose, and milk urea nitrogen (MUN)) via miRNA target gene enrichment analysis. miRNA expression (713 miRNAs), and milk yield and components (Fat%, Protein%, lactose, SCC, MUN) data of nine cows at each of six different time points (day 30 (D30), D70, D130, D170, D230 and D290) of an entire lactation curve were used. Four modules or clusters (GREEN, BLUE, RED and TURQUOISE) of miRNAs were identified as important for milk yield and component traits. The GREEN and BLUE modules were significantly correlated (|r| > 0.5) with milk yield and lactose, respectively. The RED and TURQUOISE modules were significantly correlated (|r| > 0.5) with both SCC and lactose. In the GREEN module, three abundantly expressed miRNAs (miR-148a, miR-186 and miR-200a) were most significantly correlated to milk yield, and are probably the most important miRNAs for this trait. DDR1 and DDHX1 are hub genes for miRNA regulatory networks controlling milk yield, while HHEX is an important transcription regulator for these networks. miR-18a, miR-221/222 cluster, and transcription factors HOXA7, and NOTCH 3 and 4, are important for the regulation of lactose. miR-142, miR-146a, and miR-EIA17-14144 (a novel miRNA), and transcription factors in the SMAD family and MYB, are important for the regulation of SCC. Important signaling pathways enriched for target genes of miRNAs of significant modules, included protein kinase A and PTEN signaling for milk yield, eNOS and Noth signaling for lactose, and TGF β, HIPPO, Wnt/β-catenin and cell cycle signaling for SCC. Relevant enriched gene ontology (GO)-terms related to milk and mammary gland traits included cell differentiation, G-protein coupled receptor activity, and intracellular signaling transduction. Overall, this study uncovered regulatory networks in which miRNAs interacted with each other to regulate lactation traits.
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92
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O-GlcNAcylation and chromatin remodeling in mammals: an up-to-date overview. Biochem Soc Trans 2017; 45:323-338. [PMID: 28408473 DOI: 10.1042/bst20160388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
Abstract
Post-translational modifications of histones and the dynamic DNA methylation cycle are finely regulated by a myriad of chromatin-binding factors and chromatin-modifying enzymes. Epigenetic modifications ensure local changes in the architecture of chromatin, thus controlling in fine the accessibility of the machinery of transcription, replication or DNA repair to the chromatin. Over the past decade, the nutrient-sensor enzyme O-GlcNAc transferase (OGT) has emerged as a modulator of chromatin remodeling. In mammals, OGT acts either directly through dynamic and reversible O-GlcNAcylation of histones and chromatin effectors, or in an indirect manner through its recruitment into chromatin-bound multiprotein complexes. In particular, there is an increasing amount of evidence of a cross-talk between OGT and the DNA dioxygenase ten-eleven translocation proteins that catalyze active DNA demethylation. Conversely, the stability of OGT itself can be controlled by the histone lysine-specific demethylase 2 (LSD2). Finally, a few studies have explored the role of O-GlcNAcase (OGA) in chromatin remodeling. In this review, we summarize the recent findings on the link between OGT, OGA and chromatin regulators in mammalian cellular models, and discuss their relevance in physiological and pathological conditions.
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93
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Pezic D, Weeks SL, Hadjur S. More to cohesin than meets the eye: complex diversity for fine-tuning of function. Curr Opin Genet Dev 2017; 43:93-100. [PMID: 28189962 DOI: 10.1016/j.gde.2017.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/28/2022]
Abstract
Recent years have witnessed a dramatic expansion in our understanding of gene control. It is now widely appreciated that the spatial organization of the genome and the manner in which genes and regulatory elements are embedded therein has a critical role in facilitating the regulation of gene expression. The loop structures that underlie chromosome organization are anchored by cohesin complexes. Several components of the cohesin complex have multiple paralogs, leading to different levels of cohesin complex variants in cells. Here we review the current literature around cohesin variants and their known functions. We further discuss how variation in cohesin complex composition can result in functional differences that can impact genome organization and determine cell fate.
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Affiliation(s)
- Dubravka Pezic
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Samuel L Weeks
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom.
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94
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Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW, Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T, Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose R, Koseki H. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 2017; 6:21064. [PMID: 28304275 PMCID: PMC5375644 DOI: 10.7554/elife.21064] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022] Open
Abstract
The ring finger protein PCGF6 (polycomb group ring finger 6) interacts with RING1A/B and E2F6 associated factors to form a non-canonical PRC1 (polycomb repressive complex 1) known as PCGF6-PRC1. Here, we demonstrate that PCGF6-PRC1 plays a role in repressing a subset of PRC1 target genes by recruiting RING1B and mediating downstream mono-ubiquitination of histone H2A. PCGF6-PRC1 bound loci are highly enriched for promoters of germ cell-related genes in mouse embryonic stem cells (ESCs). Conditional ablation of Pcgf6 in ESCs leads to robust de-repression of such germ cell-related genes, in turn affecting cell growth and viability. We also find a role for PCGF6 in pre- and peri-implantation mouse embryonic development. We further show that a heterodimer of the transcription factors MAX and MGA recruits PCGF6 to target loci. PCGF6 thus links sequence specific target recognition by the MAX/MGA complex to PRC1-dependent transcriptional silencing of germ cell-specific genes in pluripotent stem cells.
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Affiliation(s)
- Mitsuhiro Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Shinga
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Anca Farcas
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Kit-Wan Ma
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Tamie Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Naoko Onaga
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Benedikt M Kessler
- Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Toshio Suda
- Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Robert Klose
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
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95
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Li H, Lai P, Jia J, Song Y, Xia Q, Huang K, He N, Ping W, Chen J, Yang Z, Li J, Yao M, Dong X, Zhao J, Hou C, Esteban MA, Gao S, Pei D, Hutchins AP, Yao H. RNA Helicase DDX5 Inhibits Reprogramming to Pluripotency by miRNA-Based Repression of RYBP and its PRC1-Dependent and -Independent Functions. Cell Stem Cell 2017; 20:462-477.e6. [PMID: 28111200 DOI: 10.1016/j.stem.2016.12.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 08/08/2016] [Accepted: 12/02/2016] [Indexed: 12/24/2022]
Abstract
RNA-binding proteins (RBPs), in addition to their functions in cellular homeostasis, play important roles in lineage specification and maintaining cellular identity. Despite their diverse and essential functions, which touch on nearly all aspects of RNA metabolism, the roles of RBPs in somatic cell reprogramming are poorly understood. Here we show that the DEAD-box RBP DDX5 inhibits reprogramming by repressing the expression and function of the non-canonical polycomb complex 1 (PRC1) subunit RYBP. Disrupting Ddx5 expression improves the efficiency of iPSC generation and impedes processing of miR-125b, leading to Rybp upregulation and suppression of lineage-specific genes via RYBP-dependent ubiquitination of H2AK119. Furthermore, RYBP is required for PRC1-independent recruitment of OCT4 to the promoter of Kdm2b, a histone demethylase gene that promotes reprogramming by reactivating endogenous pluripotency genes. Together, these results reveal important functions of DDX5 in regulating reprogramming and highlight the importance of a Ddx5-miR125b-Rybp axis in controlling cell fate.
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Affiliation(s)
- Huanhuan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; GZMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Ping Lai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinping Jia
- Laboratory of Translational Genomics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qing Xia
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Kaimeng Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na He
- Department of Biology, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Wangfang Ping
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiayu Chen
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongzhou Yang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiao Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunhui Hou
- Department of Biology, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Miguel A Esteban
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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96
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Abstract
Huntington's disease (HD) is a genetic, fatal autosomal dominant neurodegenerative disorder typically occurring in midlife with symptoms ranging from chorea, to dementia, to personality disturbances (Philos Trans R Soc Lond Ser B Biol Sci 354:957-961, 1999). HD is inherited in a dominant fashion, and the underlying mutation in all cases is a CAG trinucleotide repeat expansion within exon 1 of the HD gene (Cell 72:971-983, 1993). The expanded CAG repeat, translated into a lengthened glutamine tract at the amino terminus of the huntingtin protein, affects its structural properties and functional activities. The effects are pleiotropic, as huntingtin is broadly expressed in different cellular compartments (i.e., cytosol, nucleus, mitochondria) as well as in all cell types of the body at all developmental stages, such that HD pathogenesis likely starts at conception and is a lifelong process (Front Neurosci 9:509, 2015). The rate-limiting mechanism(s) of neurodegeneration in HD still remains elusive: many different processes are commonly disrupted in HD cell lines and animal models, as well as in HD patient cells (Eur J Neurosci 27:2803-2820, 2008); however, epigenetic-chromatin deregulation, as determined by the analysis of DNA methylation, histone modifications, and noncoding RNAs, has now become a prevailing feature. Thus, the overarching goal of this chapter is to discuss the current status of the literature, reviewing how an aberrant epigenetic landscape can contribute to altered gene expression and neuronal dysfunction in HD.
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97
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Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nat Genet 2016; 49:282-288. [PMID: 27941795 DOI: 10.1038/ng.3735] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 11/01/2016] [Indexed: 12/16/2022]
Abstract
Trithorax-group proteins and their mammalian homologs, including those in BAF (mSWI/SNF) complexes, are known to oppose the activity of Polycomb repressive complexes (PRCs). This opposition underlies the tumor-suppressive role of BAF subunits and is expected to contribute to neurodevelopmental disorders. However, the mechanisms underlying opposition to Polycomb silencing are poorly understood. Here we report that recurrent disease-associated mutations in BAF subunits induce genome-wide increases in PRC deposition and activity. We show that point mutations in SMARCA4 (also known as BRG1) mapping to the ATPase domain cause loss of direct binding between BAF and PRC1 that occurs independently of chromatin. Release of this direct interaction is ATP dependent, consistent with a transient eviction mechanism. Using a new chemical-induced proximity assay, we find that BAF directly evicts Polycomb factors within minutes of its occupancy, thereby establishing a new mechanism for the widespread BAF-PRC opposition underlying development and disease.
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98
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An Unexpected Regulatory Cascade Governs a Core Function of the Drosophila PRC1 Chromatin Protein Su(z)2. Genetics 2016; 205:551-558. [PMID: 27881472 DOI: 10.1534/genetics.116.187849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 11/09/2016] [Indexed: 11/18/2022] Open
Abstract
Polycomb group (PcG) proteins are major chromatin-bound factors that can read and modify chromatin states to maintain gene silencing throughout development. Here we focus on a close homolog of the PcG protein Posterior sex combs to better understand how these proteins affect regulation. This homolog, called Suppressor 2 of zeste [Su(z)2] is composed of two regions: the N-terminal homology region (HR), which serves as a hub for protein interactions, and the C-terminal region (CTR), which is believed to harbor the core activity of compacting chromatin. Here, we describe our classical genetic studies to dissect the structure of Su(z)2 Surprisingly, we found that the CTR is dispensable for viability. Furthermore, the core activity of Su(z)2 seems to reside in the HR instead of the CTR. Remarkably, our data also suggest a regulatory cascade between CTR and HR of Su(z)2, which, in turn, may help prioritize the myriad of PcG interactions that occur with the HR.
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99
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Loubière V, Delest A, Thomas A, Bonev B, Schuettengruber B, Sati S, Martinez AM, Cavalli G. Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nat Genet 2016; 48:1436-1442. [PMID: 27643538 PMCID: PMC5407438 DOI: 10.1038/ng.3671] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
Abstract
Polycomb group proteins form two main complexes, PRC2 and PRC1, which generally coregulate their target genes. Here we show that PRC1 components act as neoplastic tumor suppressors independently of PRC2 function. By mapping the distribution of PRC1 components and trimethylation of histone H3 at Lys27 (H3K27me3) across the genome, we identify a large set of genes that acquire PRC1 in the absence of H3K27me3 in Drosophila larval tissues. These genes massively outnumber canonical targets and are mainly involved in the regulation of cell proliferation, signaling and polarity. Alterations in PRC1 components specifically deregulate this set of genes, whereas canonical targets are derepressed in both PRC1 and PRC2 mutants. In human embryonic stem cells, PRC1 components colocalize with H3K27me3 as in Drosophila embryos, whereas in differentiated cell types they are selectively recruited to a large set of proliferation and signaling-associated genes that lack H3K27me3, suggesting that the redeployment of PRC1 components during development is evolutionarily conserved.
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Affiliation(s)
- Vincent Loubière
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Anna Delest
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Aubin Thomas
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Boyan Bonev
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Satish Sati
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UPR1142 CNRS, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
- Universite de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
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100
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Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R, Kokotovic M, Grimm JB, Lavis LD, Lee J, Mejia FJ, Li Y, Yao T, Ren X. Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin. eLife 2016; 5. [PMID: 27723458 PMCID: PMC5056789 DOI: 10.7554/elife.17667] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes. DOI:http://dx.doi.org/10.7554/eLife.17667.001
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Affiliation(s)
- Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Raibatak Das
- Department of Integrative Biology, University of Colorado Denver, Denver, United States
| | - Marko Kokotovic
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jun Lee
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Frances J Mejia
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Yang Li
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, United States
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