1
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Thor S. Indirect neurogenesis in space and time. Nat Rev Neurosci 2024:10.1038/s41583-024-00833-x. [PMID: 38951687 DOI: 10.1038/s41583-024-00833-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2024] [Indexed: 07/03/2024]
Abstract
During central nervous system (CNS) development, neural progenitor cells (NPCs) generate neurons and glia in two different ways. In direct neurogenesis, daughter cells differentiate directly into neurons or glia, whereas in indirect neurogenesis, neurons or glia are generated after one or more daughter cell divisions. Intriguingly, indirect neurogenesis is not stochastically deployed and plays instructive roles during CNS development: increased generation of cells from specific lineages; increased generation of early or late-born cell types within a lineage; and increased cell diversification. Increased indirect neurogenesis might contribute to the anterior CNS expansion evident throughout the Bilateria and help to modify brain-region size without requiring increased NPC numbers or extended neurogenesis. Increased indirect neurogenesis could be an evolutionary driver of the gyrencephalic (that is, folded) cortex that emerged during mammalian evolution and might even have increased during hominid evolution. Thus, selection of indirect versus direct neurogenesis provides a powerful developmental and evolutionary instrument that drives not only the evolution of CNS complexity but also brain expansion and modulation of brain-region size, and thereby the evolution of increasingly advanced cognitive abilities. This Review describes indirect neurogenesis in several model species and humans, and highlights some of the molecular genetic mechanisms that control this important process.
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Affiliation(s)
- Stefan Thor
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland, Australia.
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2
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Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo. Nat Commun 2022; 13:4295. [PMID: 35879318 PMCID: PMC9314430 DOI: 10.1038/s41467-022-32057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/13/2022] [Indexed: 11/08/2022] Open
Abstract
Parents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype. Parents transmit both genetic and epigenetic information to their offspring, with maternal effect genes being critical regulators of the offspring epigenome. Here they show that maternally deposited SMCHD1 has long-lasting effects on Hox gene expression and vertebral patterning during post-implantation development.
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3
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Yaghmaeian Salmani B, Balderson B, Bauer S, Ekman H, Starkenberg A, Perlmann T, Piper M, Bodén M, Thor S. Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes. Development 2022; 149:274592. [PMID: 35245348 PMCID: PMC8959139 DOI: 10.1242/dev.200076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/18/2022] [Indexed: 11/20/2022]
Abstract
The hypothalamus displays staggering cellular diversity, chiefly established during embryogenesis by the interplay of several signalling pathways and a battery of transcription factors. However, the contribution of epigenetic cues to hypothalamus development remains unclear. We mutated the polycomb repressor complex 2 gene Eed in the developing mouse hypothalamus, which resulted in the loss of H3K27me3, a fundamental epigenetic repressor mark. This triggered ectopic expression of posteriorly expressed regulators (e.g. Hox homeotic genes), upregulation of cell cycle inhibitors and reduced proliferation. Surprisingly, despite these effects, single cell transcriptomic analysis revealed that most neuronal subtypes were still generated in Eed mutants. However, we observed an increase in glutamatergic/GABAergic double-positive cells, as well as loss/reduction of dopamine, hypocretin and Tac2-Pax6 neurons. These findings indicate that many aspects of the hypothalamic gene regulatory flow can proceed without the key H3K27me3 epigenetic repressor mark, but points to a unique sensitivity of particular neuronal subtypes to a disrupted epigenomic landscape. Summary: Polycomb repressor complex 2 inactivation results in selective effects on mouse hypothalamic development, increasing glutamatergic/GABA cells, while reducing dopamine, Hcrt and Tac2-Pax6 cells.
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Affiliation(s)
- Behzad Yaghmaeian Salmani
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
- Department of Cell and Molecular Biology, Karolinska Institute, SE-17177 Stockholm, Sweden
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Susanne Bauer
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
| | - Helen Ekman
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
| | - Annika Starkenberg
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institute, SE-17177 Stockholm, Sweden
| | - Michael Piper
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD 4072, Australia
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4
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Desai D, Pethe P. Polycomb repressive complex 1: Regulators of neurogenesis from embryonic to adult stage. J Cell Physiol 2020; 235:4031-4045. [PMID: 31608994 DOI: 10.1002/jcp.29299] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/27/2019] [Indexed: 02/05/2023]
Abstract
Development of vertebrate nervous system is a complex process which involves differential gene expression and disruptions in this process or in the mature brain, may lead to neurological disorders and diseases. Extensive work that spanned several decades using rodent models and recent work on stem cells have helped uncover the intricate process of neuronal differentiation and maturation. There are various morphological changes, genetic and epigenetic modifications which occur during normal mammalian neural development, one of the chromatin modifications that controls vital gene expression are the posttranslational modifications on histone proteins, that controls accessibility of translational machinery. Among the histone modifiers, polycomb group proteins (PcGs), such as Ezh2, Eed and Suz12 form large protein complexes-polycomb repressive complex 2 (PRC2); while Ring1b and Bmi1 proteins form core of PRC1 along with accessory proteins such as Cbx, Hph, Rybp and Pcgfs catalyse histone modifications such as H3K27me3 and H2AK119ub1. PRC1 proteins are known to play critical role in X chromosome inactivation in females but they also repress the expression of key developmental genes and tightly regulate the mammalian neuronal development. In this review we have discussed the signalling pathways, morphogens and nuclear factors that initiate, regulate and maintain cells of the nervous system. Further, we have extensively reviewed the recent literature on the role of Ring1b and Bmi1 in mammalian neuronal development and differentiation; as well as highlighted questions that are still unanswered.
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Affiliation(s)
- Divya Desai
- Department of Biological Sciences, Sunandan Divatia School of Science (SDSOS), Narsee Monjee Institute of Management Studies (NMIMS) deemed-to-be University, Mumbai, India
| | - Prasad Pethe
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International University (SIU), Pune, India
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5
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Curt JR, Yaghmaeian Salmani B, Thor S. Anterior CNS expansion driven by brain transcription factors. eLife 2019; 8:45274. [PMID: 31271353 PMCID: PMC6634974 DOI: 10.7554/elife.45274] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023] Open
Abstract
During CNS development, there is prominent expansion of the anterior region, the brain. In Drosophila, anterior CNS expansion emerges from three rostral features: (1) increased progenitor cell generation, (2) extended progenitor cell proliferation, (3) more proliferative daughters. We find that tailless (mouse Nr2E1/Tlx), otp/Rx/hbn (Otp/Arx/Rax) and Doc1/2/3 (Tbx2/3/6) are important for brain progenitor generation. These genes, and earmuff (FezF1/2), are also important for subsequent progenitor and/or daughter cell proliferation in the brain. Brain TF co-misexpression can drive brain-profile proliferation in the nerve cord, and can reprogram developing wing discs into brain neural progenitors. Brain TF expression is promoted by the PRC2 complex, acting to keep the brain free of anti-proliferative and repressive action of Hox homeotic genes. Hence, anterior expansion of the Drosophila CNS is mediated by brain TF driven ‘super-generation’ of progenitors, as well as ‘hyper-proliferation’ of progenitor and daughter cells, promoted by PRC2-mediated repression of Hox activity.
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Affiliation(s)
- Jesús Rodriguez Curt
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | | | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden.,School of Biomedical Sciences, University of Queensland, Saint Lucia, Australia
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6
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Katoh-Fukui Y, Baba T, Sato T, Otake H, Nagakui-Noguchi Y, Shindo M, Suyama M, Ohkawa Y, Tsumura H, Morohashi KI, Fukami M. Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones. Bone 2019; 120:219-231. [PMID: 30389610 DOI: 10.1016/j.bone.2018.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/29/2022]
Abstract
A set of key developmental genes is essential for skeletal growth from multipotent progenitor cells at weaning. Polycomb group proteins, which regulate such genes contributes to the cell lineage commitment and subsequent differentiation via epigenetic chromatin modification and remodeling. However, it is unclear which cell lineage and gene sets are targeted by polycomb proteins during skeletal growth. We now report that mice deficient in a polycomb group gene Cbx2cterm/cterm exhibited skeletal hypoplasia in the tibia, femur, and cranium. Long bone cavities in these mice contained fewer multipotent mesenchymal stromal cells. RNA-sequencing of bone marrow cells showed downregulation and upregulation of osteoblastic and adipogenic genes, respectively. Furthermore, the expression levels of genes specifically expressed in B-cell precursors were decreased. Forced expression of Cbx2 in Cbx2cterm/cterm bone marrow stromal cell recovered fibroblastic colony formation and suppressed adipogenic differentiation. Collectively, our results suggest that Cbx2 controls the maintenance and adipogenic differentiation of mesenchymal stromal cells in the bone marrow.
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Affiliation(s)
- Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute of Child Health and Development, Tokyo 157-8535, Japan.
| | - Takashi Baba
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Sato
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan; Division of Bioinformatics, Kyushu University, Fukuoka, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, Japan
| | - Hiroyuki Otake
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Miyuki Shindo
- Department of Experimental Animals, National Research Institute of Child Health and Development, Tokyo, Japan
| | - Mikita Suyama
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan; Division of Bioinformatics, Kyushu University, Fukuoka, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, Japan; Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hideki Tsumura
- Department of Experimental Animals, National Research Institute of Child Health and Development, Tokyo, Japan
| | - Ken-Ichirou Morohashi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute of Child Health and Development, Tokyo 157-8535, Japan
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7
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Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters. Nat Struct Mol Biol 2018; 25:766-777. [PMID: 30127357 DOI: 10.1038/s41594-018-0111-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022]
Abstract
The regulation of higher-order chromatin structure is complex and dynamic, and a full understanding of the suite of mechanisms governing this architecture is lacking. Here, we reveal the noncanonical SMC protein Smchd1 to be a novel regulator of long-range chromatin interactions in mice, and we add Smchd1 to the canon of epigenetic proteins required for Hox-gene regulation. The effect of losing Smchd1-dependent chromatin interactions has varying outcomes that depend on chromatin context. At autosomal targets transcriptionally sensitive to Smchd1 deletion, we found increased short-range interactions and ectopic enhancer activation. In contrast, the inactive X chromosome was transcriptionally refractive to Smchd1 ablation, despite chromosome-wide increases in short-range interactions. In the inactive X, we observed spreading of trimethylated histone H3 K27 (H3K27me3) domains into regions not normally decorated by this mark. Together, these data suggest that Smchd1 is able to insulate chromatin, thereby limiting access to other chromatin-modifying proteins.
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8
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An Z, Akily B, Sabalic M, Zong G, Chai Y, Sharpe PT. Regulation of Mesenchymal Stem to Transit-Amplifying Cell Transition in the Continuously Growing Mouse Incisor. Cell Rep 2018; 23:3102-3111. [PMID: 29874594 PMCID: PMC6383149 DOI: 10.1016/j.celrep.2018.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/22/2018] [Accepted: 04/25/2018] [Indexed: 12/25/2022] Open
Abstract
In adult tissues and organs with high turnover rates, the generation of transit-amplifying cell (TAC) populations from self-renewing stem cells drives cell replacement. The role of stem cells is to provide a renewable source of cells that give rise to TACs to provide the cell numbers that are necessary for cell differentiation. Regulation of the formation of TACs is thus fundamental to controlling cell replacement. Here, we analyze the properties of a population of mesenchymal TACs in the continuously growing mouse incisor to identify key components of the molecular regulation that drives proliferation. We show that the polycomb repressive complex 1 acts as a global regulator of the TAC phenotype by its direct action on the expression of key cell-cycle regulatory genes and by regulating Wnt/β-catenin-signaling activity. We also identify an essential requirement for TACs in maintaining mesenchymal stem cells, which is indicative of a positive feedback mechanism.
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Affiliation(s)
- Zhengwen An
- Centre for Craniofacial and Regenerative Biology, Dental Institute, Kings College, London, UK
| | - Basem Akily
- Centre for Craniofacial and Regenerative Biology, Dental Institute, Kings College, London, UK
| | - Maja Sabalic
- Centre for Craniofacial and Regenerative Biology, Dental Institute, Kings College, London, UK
| | - Guo Zong
- Centre for Craniofacial and Regenerative Biology, Dental Institute, Kings College, London, UK
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Paul T Sharpe
- Centre for Craniofacial and Regenerative Biology, Dental Institute, Kings College, London, UK.
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9
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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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10
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Yaghmaeian Salmani B, Monedero Cobeta I, Rakar J, Bauer S, Curt JR, Starkenberg A, Thor S. Evolutionarily conserved anterior expansion of the central nervous system promoted by a common PcG-Hox program. Development 2018. [DOI: 10.1242/dev.160747] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A conserved feature of the central nervous system (CNS) is the prominent expansion of anterior regions (brain) when compared to posterior (nerve cord). The cellular and regulatory processes driving anterior CNS expansion are not well understood in any bilaterian species. Here, we address this expansion in Drosophila and mouse. We find that when compared to the nerve cord the brain, in both Drosophila and mouse, displays extended progenitor proliferation, more elaborate daughter cell proliferation and more rapid cell cycle speed. These features contribute to anterior CNS expansion in both species. With respect to genetic control, enhanced brain proliferation is severely reduced by ectopic Hox gene expression, by either Hox misexpression or by loss of Polycomb Group (PcG) function. Strikingly, in PcG mutants, early CNS proliferation appears unaffected, whereas subsequently, brain proliferation is severely reduced. Hence, a conserved PcG-Hox program promotes the anterior expansion of the CNS. The profound differences in proliferation and in the underlying genetic mechanisms between brain and nerve cord lend support to the emerging concept of separate evolutionary origins of these two CNS regions.
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Affiliation(s)
| | - Ignacio Monedero Cobeta
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Jonathan Rakar
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Susanne Bauer
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Jesús Rodriguez Curt
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Annika Starkenberg
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Stefan Thor
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
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11
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PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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12
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Liu S, Jiang M, Wang W, Liu W, Song X, Ma Z, Zhang S, Liu L, Liu Y, Cao X. Nuclear RNF2 inhibits interferon function by promoting K33-linked STAT1 disassociation from DNA. Nat Immunol 2017; 19:41-52. [DOI: 10.1038/s41590-017-0003-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
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13
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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: 69] [Impact Index Per Article: 9.9] [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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14
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Sheikh BN, Metcalf D, Voss AK, Thomas T. MOZ and BMI1 act synergistically to maintain hematopoietic stem cells. Exp Hematol 2017; 47:83-97.e8. [DOI: 10.1016/j.exphem.2016.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 11/25/2022]
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15
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Dupret B, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Group Protein Pcgf1 Is Dispensable in Zebrafish but Involved in Early Growth and Aging. PLoS One 2016; 11:e0158700. [PMID: 27442247 PMCID: PMC4956247 DOI: 10.1371/journal.pone.0158700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/19/2016] [Indexed: 12/31/2022] Open
Abstract
Polycomb Repressive Complex (PRC) 1 regulates the control of gene expression programs via chromatin structure reorganization. Through mutual exclusion, different PCGF members generate a variety of PRC1 complexes with potentially distinct cellular functions. In this context, the molecular function of each of the PCGF family members remains elusive. The study of PCGF family member expression in zebrafish development and during caudal fin regeneration reveals that the zebrafish pcgf genes are subjected to different regulations and that all PRC1 complexes in terms of Pcgf subunit composition are not always present in the same tissues. To unveil the function of Pcgf1 in zebrafish, a mutant line was generated using the TALEN technology. Mutant pcgf1-/- fish are viable and fertile, but the growth rate at early developmental stages is reduced in absence of pcgf1 gene function and a significant number of pcgf1-/- fish show signs of premature aging. This first vertebrate model lacking Pcgf1 function shows that this Polycomb Group protein is involved in cell proliferation during early embryogenesis and establishes a link between epigenetics and aging.
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Affiliation(s)
- Barbara Dupret
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
| | - Pamela Völkel
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
- CNRS, Lille, France
| | - Xuefen Le Bourhis
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
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16
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Grijzenhout A, Godwin J, Koseki H, Gdula MR, Szumska D, McGouran JF, Bhattacharya S, Kessler BM, Brockdorff N, Cooper S. Functional analysis of AEBP2, a PRC2 Polycomb protein, reveals a Trithorax phenotype in embryonic development and in ESCs. Development 2016; 143:2716-23. [PMID: 27317809 PMCID: PMC5004903 DOI: 10.1242/dev.123935] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/07/2016] [Indexed: 01/02/2023]
Abstract
The Polycomb repressive complexes PRC1 and PRC2 are key mediators of heritable gene silencing in multicellular organisms. Here, we characterise AEBP2, a known PRC2 co-factor which, in vitro, has been shown to stimulate PRC2 activity. We show that AEBP2 localises specifically to PRC2 target loci, including the inactive X chromosome. Proteomic analysis confirms that AEBP2 associates exclusively with PRC2 complexes. However, analysis of embryos homozygous for a targeted mutation of Aebp2 unexpectedly revealed a Trithorax phenotype, normally linked to antagonism of Polycomb function. Consistent with this, we observe elevated levels of PRC2-mediated histone H3K27 methylation at target loci in Aebp2 mutant embryonic stem cells (ESCs). We further demonstrate that mutant ESCs assemble atypical hybrid PRC2 subcomplexes, potentially accounting for enhancement of Polycomb activity, and suggesting that AEBP2 normally plays a role in defining the mutually exclusive composition of PRC2 subcomplexes. Highlighted article: Targeted mutation of the Polycomb protein AEBP2 in mouse provides evidence for a role for this factor in defining the composition and activity of PRC2 complexes.
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Affiliation(s)
- Anne Grijzenhout
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jonathan Godwin
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Michal Ryszard Gdula
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dorota Szumska
- Department of Cardiovascular Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Joanna F McGouran
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Shoumo Bhattacharya
- Department of Cardiovascular Medicine and Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sarah Cooper
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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17
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San B, Chrispijn ND, Wittkopp N, van Heeringen SJ, Lagendijk AK, Aben M, Bakkers J, Ketting RF, Kamminga LM. Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2. Sci Rep 2016; 6:24658. [PMID: 27145952 PMCID: PMC4857124 DOI: 10.1038/srep24658] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/29/2016] [Indexed: 11/09/2022] Open
Abstract
Polycomb group (PcG) proteins are transcriptional repressors of numerous genes, many of which regulate cell cycle progression or developmental processes. We used zebrafish to study Enhancer of zeste homolog 2 (Ezh2), the PcG protein responsible for placing the transcriptional repressive H3K27me3 mark. We identified a nonsense mutant of ezh2 and generated maternal zygotic (MZ) ezh2 mutant embryos. In contrast to knockout mice for PcG proteins, MZezh2 mutant embryos gastrulate seemingly normal, but die around 2 days post fertilization displaying pleiotropic phenotypes. Expression analyses indicated that genes important for early development are not turned off properly, revealing a regulatory role for Ezh2 during zygotic gene expression. In addition, we suggest that Ezh2 regulates maternal mRNA loading of zygotes. Analyses of tissues arising later in development, such as heart, liver, and pancreas, indicated that Ezh2 is required for maintenance of differentiated cell fates. Our data imply that the primary role of Ezh2 is to maintain tissues after tissue specification. Furthermore, our work indicates that Ezh2 is essential to sustain tissue integrity and to set up proper maternal mRNA contribution, and presents a novel and powerful tool to study how PcG proteins contribute to early vertebrate development.
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Affiliation(s)
- Bilge San
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Naomi D Chrispijn
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Nadine Wittkopp
- Hubrecht Institute, University Medical Centre Utrecht, Utrecht, The Netherlands.,Institute of Molecular Biology, Mainz, Germany
| | - Simon J van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Anne K Lagendijk
- Hubrecht Institute, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marco Aben
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute, University Medical Centre Utrecht, Utrecht, The Netherlands.,Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - René F Ketting
- Hubrecht Institute, University Medical Centre Utrecht, Utrecht, The Netherlands.,Institute of Molecular Biology, Mainz, Germany
| | - Leonie M Kamminga
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Hubrecht Institute, University Medical Centre Utrecht, Utrecht, The Netherlands
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18
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Stein C, Nötzold RR, Riedl S, Bouchard C, Bauer UM. The Arginine Methyltransferase PRMT6 Cooperates with Polycomb Proteins in Regulating HOXA Gene Expression. PLoS One 2016; 11:e0148892. [PMID: 26848759 PMCID: PMC4746130 DOI: 10.1371/journal.pone.0148892] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/25/2016] [Indexed: 01/13/2023] Open
Abstract
Protein arginine methyltransferase 6 (PRMT6) catalyses asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a), which has been shown to impede the deposition of histone H3 lysine 4 trimethylation (H3K4me3) by blocking the binding and activity of the MLL1 complex. Importantly, the genomic occurrence of H3R2me2a has been found to coincide with histone H3 lysine 27 trimethylation (H3K27me3), a repressive histone mark generated by the Polycomb repressive complex 2 (PRC2). Therefore, we investigate here a putative crosstalk between PRMT6- and PRC-mediated repression in a cellular model of neuronal differentiation. We show that PRMT6 and subunits of PRC2 as well as PRC1 are bound to the same regulatory regions of rostral HOXA genes and that they control the differentiation-associated activation of these genes. Furthermore, we find that PRMT6 interacts with subunits of PRC1 and PRC2 and that depletion of PRMT6 results in diminished PRC1/PRC2 and H3K27me3 occupancy and in increased H3K4me3 levels at these target genes. Taken together, our data uncover a novel, additional mechanism of how PRMT6 contributes to gene repression by cooperating with Polycomb proteins.
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Affiliation(s)
- Claudia Stein
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - René Reiner Nötzold
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Stefanie Riedl
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Caroline Bouchard
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Uta-Maria Bauer
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
- * E-mail:
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19
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Sowpati DT, Ramamoorthy S, Mishra RK. Expansion of the polycomb system and evolution of complexity. Mech Dev 2015; 138 Pt 2:97-112. [DOI: 10.1016/j.mod.2015.07.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 11/28/2022]
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20
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Morey L, Santanach A, Blanco E, Aloia L, Nora E, Bruneau B, Di Croce L. Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms. Cell Stem Cell 2015; 17:300-15. [DOI: 10.1016/j.stem.2015.08.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/15/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
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21
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Zhen CY, Duc HN, Kokotovic M, Phiel CJ, Ren X. Cbx2 stably associates with mitotic chromosomes via a PRC2- or PRC1-independent mechanism and is needed for recruiting PRC1 complex to mitotic chromosomes. Mol Biol Cell 2014; 25:3726-39. [PMID: 25232004 PMCID: PMC4230780 DOI: 10.1091/mbc.e14-06-1109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cbx2 is immobilized at mitotic chromosomes, and the immobilization is independent of PRC1 or PRC2. Cbx2 plays important roles in recruiting PRC1 complex to mitotic chromosomes. This study provides novel insights into the PcG epigenetic memory passing down through cell divisions. Polycomb group (PcG) proteins are epigenetic transcriptional factors that repress key developmental regulators and maintain cellular identity through mitosis via a poorly understood mechanism. Using quantitative live-cell imaging in mouse ES cells and tumor cells, we demonstrate that, although Polycomb repressive complex (PRC) 1 proteins (Cbx-family proteins, Ring1b, Mel18, and Phc1) exhibit variable capacities of association with mitotic chromosomes, Cbx2 overwhelmingly binds to mitotic chromosomes. The recruitment of Cbx2 to mitotic chromosomes is independent of PRC1 or PRC2, and Cbx2 is needed to recruit PRC1 complex to mitotic chromosomes. Quantitative fluorescence recovery after photobleaching analysis indicates that PRC1 proteins rapidly exchange at interphasic chromatin. On entry into mitosis, Cbx2, Ring1b, Mel18, and Phc1 proteins become immobilized at mitotic chromosomes, whereas other Cbx-family proteins dynamically bind to mitotic chromosomes. Depletion of PRC1 or PRC2 protein has no effect on the immobilization of Cbx2 on mitotic chromosomes. We find that the N-terminus of Cbx2 is needed for its recruitment to mitotic chromosomes, whereas the C-terminus is required for its immobilization. Thus these results provide fundamental insights into the molecular mechanisms of epigenetic inheritance.
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Affiliation(s)
- Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364
| | - Marko Kokotovic
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364
| | - Christopher J Phiel
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217-3364
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364
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22
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Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LLP, Ito S, Cooper S, Kondo K, Koseki Y, Ishikura T, Long HK, Sheahan TW, Brockdorff N, Kessler BM, Koseki H, Klose RJ. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 2014; 157:1445-1459. [PMID: 24856970 PMCID: PMC4048464 DOI: 10.1016/j.cell.2014.05.004] [Citation(s) in RCA: 533] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/10/2014] [Accepted: 05/02/2014] [Indexed: 11/30/2022]
Abstract
Chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. This activity is restricted to variant PRC1 complexes, and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for normal polycomb domain formation and mouse development. These observations provide a surprising PRC1-dependent logic for PRC2 occupancy at target sites in vivo.
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Affiliation(s)
- Neil P Blackledge
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Anca M Farcas
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Takashi Kondo
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hamish W King
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Joanna F McGouran
- Ubiquitin Proteolysis Group, Central Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN, UK
| | - Lars L P Hanssen
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sarah Cooper
- Laboratory of Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Kaori Kondo
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tomoyuki Ishikura
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hannah K Long
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Thomas W Sheahan
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Neil Brockdorff
- Laboratory of Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Benedikt M Kessler
- Ubiquitin Proteolysis Group, Central Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN, UK
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Robert J Klose
- Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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23
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Isono K, Endo TA, Ku M, Yamada D, Suzuki R, Sharif J, Ishikura T, Toyoda T, Bernstein BE, Koseki H. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev Cell 2013; 26:565-77. [PMID: 24091011 DOI: 10.1016/j.devcel.2013.08.016] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/29/2013] [Accepted: 08/19/2013] [Indexed: 01/01/2023]
Abstract
The Polycomb-group (PcG) repressive complex-1 (PRC1) forms microscopically visible clusters in nuclei; however, the impact of this cluster formation on transcriptional regulation and the underlying mechanisms that regulate this process remain obscure. Here, we report that the sterile alpha motif (SAM) domain of a PRC1 core component Phc2 plays an essential role for PRC1 clustering through head-to-tail macromolecular polymerization, which is associated with stable target binding of PRC1/PRC2 and robust gene silencing activity. We propose a role for SAM domain polymerization in this repression by two distinct mechanisms: first, through capturing and/or retaining PRC1 at the PcG targets, and second, by strengthening the interactions between PRC1 and PRC2 to stabilize transcriptional repression. Our findings reveal a regulatory mechanism mediated by SAM domain polymerization for PcG-mediated repression of developmental loci that enables a robust yet reversible gene repression program during development.
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Affiliation(s)
- Kyoichi Isono
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; CREST, Japan Science and Technology Agency, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; PREST, Japan Science and Technology Agency, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan.
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24
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Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol 2013; 20:1147-55. [PMID: 24096405 DOI: 10.1038/nsmb.2669] [Citation(s) in RCA: 646] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/12/2013] [Indexed: 12/12/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic regulators of transcription that have key roles in stem-cell identity, differentiation and disease. Mechanistically, they function within multiprotein complexes, called Polycomb repressive complexes (PRCs), which modify histones (and other proteins) and silence target genes. The dynamics of PRC1 and PRC2 components has been the focus of recent research. Here we discuss our current knowledge of the PRC complexes, how they are targeted to chromatin and how the high diversity of the PcG proteins allows these complexes to influence cell identity.
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25
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Aloia L, Di Stefano B, Di Croce L. Polycomb complexes in stem cells and embryonic development. Development 2013; 140:2525-34. [PMID: 23715546 DOI: 10.1242/dev.091553] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic modifiers involved in controlling gene repression. Organized within multiprotein complexes, they regulate developmental genes in multiple cell types and tissue contexts, including embryonic and adult stem cells, and are essential for cell fate transitions and proper development. Here, we summarize recent breakthroughs that have revealed the diversity of PcG complexes acting in different cell types and genomic contexts. Intriguingly, it appears that particular PcG proteins have specific functions in embryonic development, in pluripotent stem cells and in reprogramming somatic cells into a pluripotent-like state. Finally, we highlight recent results from analyzing PcG protein functions in multipotent stem cells, such as neural, hematopoietic and epidermal stem cells.
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Affiliation(s)
- Luigi Aloia
- Centre for Genomic Regulation (CRG), and UPF, Dr Aiguader 88, 08003 Barcelona,Spain
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26
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Völkel P, Le Faou P, Vandamme J, Pira D, Angrand PO. A human Polycomb isoform lacking the Pc box does not participate to PRC1 complexes but forms protein assemblies and represses transcription. Epigenetics 2012; 7:482-91. [PMID: 22419124 DOI: 10.4161/epi.19741] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polycomb repression controls the expression of hundreds of genes involved in development and is mediated by essentially two classes of chromatin-associated protein complexes. The Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27, an epigenetic mark that serves as a docking site for the PRC1 protein complex. Drosophila core PRC1 is composed of four subunits: Polycomb (Pc), Posterior sex combs (Psc), Polyhomeotic (Ph) and Sex combs extra (Sce). Each of these proteins has multiple orthologs in vertebrates, thus generating an enormous scope for potential combinatorial diversity. In particular, mammalian genomes encode five Pc family members: CBX2, CBX4, CBX6, CBX7 and CBX8. To complicate matters further, distinct isoforms might arise from single genes. Here, we address the functional role of the two human CBX2 isoforms. Owing to different polyadenylation sites and alternative splicing events, the human CBX2 locus produces two transcripts: a 5-exon transcript that encodes the 532-amino acid CBX2-1 isoform that contains the conserved chromodomain and Pc box and a 4-exon transcript encoding a shorter isoform, CBX2-2, lacking the Pc box but still possessing a chromodomain. Using biochemical approaches and a novel in vivo imaging assay, we show that the short CBX2-2 isoform lacking the Pc box, does not participate in PRC1 protein complexes, but self-associates in vivo and forms complexes of high molecular weight. Furthermore, the CBX2 short isoform is still able to repress transcription, suggesting that Polycomb repression might occur in the absence of PRC1 formation.
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Affiliation(s)
- Pamela Völkel
- Chromatinomics, Interdisciplinary Research Institute, CNRS USR 3078, Université de Lille 1 Sciences et Technologies, Villeneuve d'Ascq Cedex, France
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27
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Sen N, Satija YK, Das S. PGC-1α, a key modulator of p53, promotes cell survival upon metabolic stress. Mol Cell 2012; 44:621-34. [PMID: 22099309 DOI: 10.1016/j.molcel.2011.08.044] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/05/2011] [Accepted: 08/30/2011] [Indexed: 11/17/2022]
Abstract
Metabolic stress results in p53 activation, which can trigger cell-cycle arrest, ROS clearance, or apoptosis. However, what determines the p53-mediated cell fate decision upon metabolic stress is not very well understood. We show here that PGC-1α binds to p53 and modulates its transactivation function, resulting in preferential transactivation of proarrest and metabolic target genes. Thus glucose starvation results in p53-dependent cell-cycle arrest and ROS clearance, but abrogation of PGC-1α expression results in extensive apoptosis. Additionally, prolonged starvation results in PGC-1α degradation concomitant with induction of apoptosis. We have also identified RNF2, a Polycomb group (PcG) protein, as the cognate E3 ubiquitin ligase. Starvation of mice where PGC-1α expression is abrogated results in loss of p53-mediated ROS clearance, enhanced p53-dependent apoptosis, and consequent severe liver atrophy. These findings provide key insights into the role of PGC-1α in regulating p53-mediated cell fate decisions in response to metabolic stress.
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Affiliation(s)
- Nirmalya Sen
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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28
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Tan J, Jones M, Koseki H, Nakayama M, Muntean A, Maillard I, Hess JL. CBX8, a polycomb group protein, is essential for MLL-AF9-induced leukemogenesis. Cancer Cell 2011; 20:563-75. [PMID: 22094252 PMCID: PMC3220883 DOI: 10.1016/j.ccr.2011.09.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 07/21/2011] [Accepted: 09/20/2011] [Indexed: 10/15/2022]
Abstract
Chromosomal translocations involving the mixed lineage leukemia (MLL) gene lead to the development of acute leukemias. Constitutive HOX gene activation by MLL fusion proteins is required for MLL-mediated leukemogenesis; however, the underlying mechanisms remain elusive. Here, we show that chromobox homolog 8 (CBX8), a Polycomb Group protein that interacts with MLL-AF9 and TIP60, is required for MLL-AF9-induced transcriptional activation and leukemogenesis. Conversely, both CBX8 ablation and specific disruption of the CBX8 interaction by point mutations in MLL-AF9 abrogate HOX gene upregulation and abolish MLL-AF9 leukemic transformation. Surprisingly, Cbx8-deficient mice are viable and display no apparent hematopoietic defects. Together, our findings demonstrate that CBX8 plays an essential role in MLL-AF9 transcriptional regulation and leukemogenesis.
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Affiliation(s)
- Jiaying Tan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Morgan Jones
- Center for Stem Cell Biology, Life Sciences Institute, Graduate Program in Cell and Molecular Biology and MSTP, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Research Center for Allergy and Immunology, Yokohama 230-0045, Japan
| | - Manabu Nakayama
- Laboratory of Human Gene Research, Department of Human Genome Research, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Andrew Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ivan Maillard
- Center for Stem Cell Biology, Life Sciences Institute, Department of Medicine and Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jay L. Hess
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Corresponding Author: Jay L. Hess M.D., Ph.D., M5240 Medical Sciences I, 1301 Catherine Avenue, Ann Arbor, MI, 48109-0602, Phone: (734) 763-6384, Fax: (734) 763-4782,
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29
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Le Faou P, Völkel P, Angrand PO. The zebrafish genes encoding the Polycomb repressive complex (PRC) 1. Gene 2011; 475:10-21. [DOI: 10.1016/j.gene.2010.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 12/23/2010] [Indexed: 12/31/2022]
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30
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Vandamme J, Völkel P, Rosnoblet C, Le Faou P, Angrand PO. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Mol Cell Proteomics 2011; 10:M110.002642. [PMID: 21282530 DOI: 10.1074/mcp.m110.002642] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Polycomb group (PcG) proteins maintain transcriptional repression of hundreds of genes involved in development, signaling or cancer using chromatin-based epigenetic mechanisms. Biochemical studies in Drosophila have revealed that PcG proteins associate in at least two classes of protein complexes known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Drosophila core PRC1 is composed of four subunits, Polycomb (Pc), Sex combs extra (Sce), Polyhomeotic (Ph), and Posterior sex combs (Psc). Each of these proteins has multiple orthologs in vertebrates classified respectively as the CBX, RING1/RNF2, PHC, and BMI1/PCGF families. Mammalian genomes encode five CBX family members (CBX2, CBX4, CBX6, CBX7, and CBX8) that are believed to have distinct biological functions. Here, we applied a tandem affinity purification (TAP) approach coupled with tandem mass spectrometry (MS/MS) methodologies in order to identify interacting partners of CBX family proteins under the same experimental conditions. Our analysis identified with high confidence about 20 proteins co-eluted with CBX2 and CBX7 tagged proteins, about 40 with CBX4, and around 60 with CBX6 and CBX8. We provide evidences that the CBX family proteins are mutually exclusive and define distinct PRC1-like protein complexes. CBX proteins also interact with different efficiencies with the other PRC1 components. Among the novel CBX interacting partners, protein kinase 2 associates with all CBX-PRC1 protein complexes, whereas 14-3-3 proteins specifically bind to CBX4. 14-3-3 protein binding to CBX4 appears to modulate the interaction between CBX4 and the BMI1/PCGF components of PRC1, but has no effect on CBX4-RING1/RNF2 interaction. Finally, we suggest that differences in CBX protein interactions would account, at least in part, for distinct subnuclear localization of the CBX family members.
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Affiliation(s)
- Julien Vandamme
- Chromatinomics, Interdisciplinary Research Institute, Univ. Lille Nord de France, Université de Lille 1 Sciences et Technologies/CNRS USR 3078, 50 Avenue Halley, Parc Scientifique de la Haute Borne, F-59658 Villeneuve d'Ascq Cedex, France
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Regulation of the polycomb protein Ring1B by self-ubiquitination or by E6-AP may have implications to the pathogenesis of Angelman syndrome. Proc Natl Acad Sci U S A 2010; 107:6788-93. [PMID: 20351251 DOI: 10.1073/pnas.1003108107] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The polycomb repressive complex (PRC) 1 protein Ring1B is an ubiquitin ligase that modifies nucleosomal histone H2A, a modification which plays a critical role in regulation of gene expression. We have shown that self-ubiquitination of Ring1B generates multiply branched, "noncanonical" polyubiquitin chains that do not target the ligase for degradation, but rather stimulate its activity toward histone H2A. This finding implies that Ring1B is targeted by a heterologous E3. In this study, we identified E6-AP (E6-associated protein) as a ligase that targets Ring1B for "canonical" ubiquitination and subsequent degradation. We further demonstrated that both the self-ubiquitination of Ring1B and its modification by E6-AP target the same lysines, suggesting that the fate of Ring1B is tightly regulated (e.g., activation vs. degradation) by the type of chains and the ligase that catalyzes their formation. As expected, inactivation of E6-AP affects downstream effectors: Ring1B and ubiquitinated H2A levels are increased accompanied by repressed expression of HoxB9, a PRC1 target gene. Consistent with these findings, E6-AP knockout mice display an elevated level of Ring1B and ubiquitinated histone H2A in various tissues, including cerebellar Purkinje neurons, which may have implications to the pathogenesis of Angelman syndrome, a neurodevelopmental disorder caused by deficiency of E6-AP in the brain.
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Polycomb group complexes--many combinations, many functions. Trends Cell Biol 2009; 19:692-704. [PMID: 19889541 DOI: 10.1016/j.tcb.2009.10.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 10/05/2009] [Accepted: 10/05/2009] [Indexed: 11/21/2022]
Abstract
Polycomb Group (PcG) proteins are transcription regulatory proteins that control the expression of a variety of genes from early embryogenesis through birth to adulthood. PcG proteins form several complexes that are thought to collaborate to repress gene transcription. Individual PcG proteins have unique characteristics, and mutations in genes encoding different PcG proteins cause distinct phenotypes. Histone modifications have important roles in some PcG protein functions, but they are not universally required. The mechanisms of gene-specific recruitment, transcription repression, and selective derepression of genes by vertebrate PcG proteins are incompletely understood. Future studies of this enigmatic group of developmental regulators are certain to produce unanticipated discoveries.
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Additional sex combs-like 1 belongs to the enhancer of trithorax and polycomb group and genetically interacts with Cbx2 in mice. Dev Biol 2009; 337:9-15. [PMID: 19833123 DOI: 10.1016/j.ydbio.2009.10.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 09/29/2009] [Accepted: 10/03/2009] [Indexed: 01/16/2023]
Abstract
The Additional sex combs (Asx) gene of Drosophila behaves genetically as an enhancer of trithorax and polycomb (ETP) in displaying bidirectional homeotic phenotypes, suggesting that is required for maintenance of both activation and silencing of Hox genes. There are three murine homologs of Asx called Additional sex combs-like1, 2, and 3. Asxl1 is required for normal adult hematopoiesis; however, its embryonic function is unknown. We used a targeted mouse mutant line Asxl1(tm1Bc) to determine if Asxl1 is required to silence and activate Hox genes in mice during axial patterning. The mutant embryos exhibit simultaneous anterior and posterior transformations of the axial skeleton, consistent with a role for Asxl1 in activation and silencing of Hox genes. Transformations of the axial skeleton are enhanced in compound mutant embryos for the polycomb group gene M33/Cbx2. Hoxa4, Hoxa7, and Hoxc8 are derepressed in Asxl1(tm1Bc) mutants in the antero-posterior axis, but Hoxc8 expression is reduced in the brain of mutants, consistent with Asxl1 being required both for activation and repression of Hox genes. We discuss the genetic and molecular definition of ETPs, and suggest that the function of Asxl1 depends on its cellular context.
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MAPKAP kinase MK2 maintains self-renewal capacity of haematopoietic stem cells. EMBO J 2009; 28:1392-406. [PMID: 19369945 DOI: 10.1038/emboj.2009.100] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 03/24/2009] [Indexed: 11/09/2022] Open
Abstract
The structurally related MAPK-activated protein kinases (MAPKAPKs or MKs) MK2, MK3 and MK5 are involved in multiple cellular functions, including cell-cycle control and cellular differentiation. Here, we show that after deregulation of cell-cycle progression, haematopoietic stem cells (HSCs) in MK2-deficient mice are reduced in number and show an impaired ability for competitive repopulation in vivo. To understand the underlying molecular mechanism, we dissected the role of MK2 in association with the polycomb group complex (PcG) and generated a MK2 mutant, which is no longer able to bind to PcG. The reduced ability for repopulation is rescued by re-introduction of MK2, but not by the Edr2-non-binding mutant of MK2. Thus, MK2 emerges as a regulator of HSC homeostasis, which could act through chromatin remodelling by the PcG complex.
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Hibiya K, Katsumoto T, Kondo T, Kitabayashi I, Kudo A. Brpf1, a subunit of the MOZ histone acetyl transferase complex, maintains expression of anterior and posterior Hox genes for proper patterning of craniofacial and caudal skeletons. Dev Biol 2009; 329:176-90. [PMID: 19254709 DOI: 10.1016/j.ydbio.2009.02.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 01/22/2009] [Accepted: 02/18/2009] [Indexed: 11/15/2022]
Abstract
The epigenetic mechanism involving chromatin modification plays a critical role in the maintenance of the expression of Hox genes. Here, we characterize a mutant of the medaka fish, named biaxial symmetries (bis), in which brpf1, a subunit of the MOZ histone acetyl transferase (HAT) complex, is mutated. The bis mutant displayed patterning defects both in the anterior-posterior axis of the craniofacial skeleton and the dorsal-ventral axis of the caudal one. In the anterior region, the bis mutant exhibited craniofacial cartilage homeosis. The expression of Hox genes was decreased in the pharyngeal arches, suggesting that the pharyngeal segmental identities were altered in the bis mutant. In the posterior region, the bis mutant exhibited abnormal patterning of the caudal skeleton, which ectopically formed at the dorsal side of the caudal fin. The expression of Zic genes was decreased at the posterior region, suggesting that the dorsal-ventral axis formation of the posterior trunk was disrupted in the bis mutant. We also found that the MOZ-deficient mice exhibited an abnormal patterning of their craniofacial and cervical skeletons and a decrease of Hox transcripts. We propose a common role of the MOZ HAT complex in vertebrates, a complex which is required for the proper patterning for skeletal development.
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Affiliation(s)
- Kenta Hibiya
- Department of Biological Information, Tokyo Institute of Technology, 4259-B-33 Midori-ku, Nagatsuta, Yokohama 226-8501, Japan
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Miki J, Fujimura YI, Koseki H, Kamijo T. Polycomb complexes regulate cellular senescence by repression of ARF in cooperation with E2F3. Genes Cells 2008; 12:1371-82. [PMID: 18076574 DOI: 10.1111/j.1365-2443.2007.01135.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cellular senescence is a program in normal cells triggered in response to various types of stress that cells experience when they are explanted into culture. In this study, functional analyses on the role of the class II polycomb complex in cellular senescence were performed using mouse embryo fibroblasts (MEFs) with a genetically deleted member of the complex, Mel18. Mel18-null MEFs undergo typical premature senescence accompanied by the up-regulation of ARF/p53/p16(INK4a) and decrease of Ring1b/Bmi1. Our results demonstrated that ARF or p53 deletion cancels the senescence in Mel18-null MEFs, and the fact that p16(INK4a) is up-regulated in double-null MEFs suggests that the ARF/p53 pathway plays a central role in stress-induced senescence. The in vivo binding of Ring1b and E2F3b to the ARF promoter decreased progressively in senescence, and Mel18 inactivation accelerated the exfoliation of Ring1b/E2F3b from the promoter sequence, indicating the cooperation of polycombs/E2F3b on ARF expression and cellular senescence. Taken together, it seems that class II polycomb proteins and E2F3b dually control cellular senescence via the ARF/p53 pathway.
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Affiliation(s)
- Jun Miki
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
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Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation. Mol Cell Biol 2008; 28:2884-95. [PMID: 18316406 DOI: 10.1128/mcb.00949-07] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polycomb group (PcG) transcription regulatory proteins maintain cell identity by sustained repression of numerous genes. The differentiation of embryonic stem (ES) cells induces a genome-wide shift in PcG target gene expression. We investigated the effects of differentiation and protein interactions on CBX family PcG protein localization and dynamics by using fluorescence imaging. In mouse ES cells, different CBX proteins exhibited distinct distributions and mobilities. Most CBX proteins were enriched in foci known as Polycomb bodies. Focus formation did not affect CBX protein mobilities, and the foci dispersed during ES cell differentiation. The mobilities of CBX proteins increased upon the induction of differentiation and decreased as differentiation progressed. The deletion of the chromobox, which mediates interactions with RING1B, prevented the immobilization of CBX proteins. In contrast, the deletion of the chromodomain, which can bind trimethylated lysine 27 of histone H3, had little effect on CBX protein dynamics. The distributions and mobilities of most CBX proteins corresponded to those of CBX-RING1B complexes detected by using bimolecular fluorescence complementation analysis. Epigenetic reprogramming during ES cell differentiation is therefore associated with global changes in the subnuclear distributions and dynamics of CBX protein complexes.
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Wutz A. Xist function: bridging chromatin and stem cells. Trends Genet 2007; 23:457-64. [PMID: 17681633 DOI: 10.1016/j.tig.2007.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 06/06/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
In mammals, dosage compensation is achieved by transcriptional silencing of one of the two female X chromosomes. X inactivation is dynamically regulated in development. The non-coding Xist RNA localizes to the inactive X, initiates gene repression in the early embryo, and later stabilizes the inactive state. Different functions of Xist are observed depending on which epigenetic regulatory pathways are active in a given cell. Because Xist has evolved recently, with the origin of placental mammals, the underlying pathways are also important in regulating developmental control genes. This review emphasizes the opportunity that Xist provides to functionally define epigenetic transitions in development, to understand cell identity, pluripotency and stem cell differentiation.
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Affiliation(s)
- Anton Wutz
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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Leeb M, Wutz A. Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells. ACTA ACUST UNITED AC 2007; 178:219-29. [PMID: 17620408 PMCID: PMC2064442 DOI: 10.1083/jcb.200612127] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Polycomb group (PcG) gene Ring1B has been implicated in the repression of developmental control genes and X inactivation and is essential for embryogenesis. Ring1B protein contains a RING finger domain and functions as an E3 ubiquitin ligase that is crucial for the monoubiquitination of histone H2A (H2AK119ub1). Here, we study the function of Ring1B in mouse embryonic stem (ES) cells. The deletion of Ring1B causes the loss of several PcG proteins, showing an unanticipated function in the regulation of PcG protein levels. Derepression of lineage genes and an aberrant differentiation potential is observed in Ring1B-deficient ES cells. Despite a crucial function of Ring1B in establishing the chromosome-wide ubiquitination of histone H2A lysine 119 (H2AK119ub1) upon Xist expression in ES cells, the initiation of silencing by Xist is independent of Ring1B. Other chromatin marks associated with the initiation of X inactivation are not affected in Ring1B-deficient cells, suggesting compensation for the loss of Ring1B in X inactivation in contrast to the repression of lineage genes.
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Affiliation(s)
- Martin Leeb
- Research Institute of Molecular Pathology, Vienna, Austria
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Luo L, Uerlings Y, Happel N, Asli NS, Knoetgen H, Kessel M. Regulation of geminin functions by cell cycle-dependent nuclear-cytoplasmic shuttling. Mol Cell Biol 2007; 27:4737-44. [PMID: 17470552 PMCID: PMC1951490 DOI: 10.1128/mcb.00123-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 02/27/2007] [Accepted: 04/18/2007] [Indexed: 12/24/2022] Open
Abstract
The geminin protein functions both as a DNA rereplication inhibitor through association with Cdt1 and as a repressor of Hox gene transcription through the polycomb pathway. Here, we report that the functions of avian geminin are coordinated with and regulated by cell cycle-dependent nuclear-cytoplasmic shuttling. In S phase, geminin enters nuclei and inhibits both loading of the minichromosome maintenance (MCM) complex onto chromatin and Hox gene transcription. At the end of mitosis, geminin is exported from nuclei by the exportin protein Crm1 and is unavailable in the nucleus during the next G(1) phase, thus ensuring proper chromatin loading of the MCM complex and Hox gene transcription. This mechanism for regulating the functions of geminin adds to distinct mechanisms, such as protein degradation and ubiquitination, applied in other vertebrates.
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Affiliation(s)
- Lingfei Luo
- Department of Molecular Cell Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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Weston AD, Ozolins TRS, Brown NA. Thoracic skeletal defects and cardiac malformations: a common epigenetic link? ACTA ACUST UNITED AC 2007; 78:354-70. [PMID: 17315248 DOI: 10.1002/bdrc.20084] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Congenital heart defects (CHDs) are the most common birth defects in humans. In addition, cardiac malformations represent the most frequently identified anomaly in teratogenicity experiments with laboratory animals. To explore the mechanisms of these drug-induced defects, we developed a model in which pregnant rats are treated with dimethadione, resulting in a high incidence of heart malformations. Interestingly, these heart defects were accompanied by thoracic skeletal malformations (cleft sternum, fused ribs, extra or missing ribs, and/or wavy ribs), which are characteristic of anterior-posterior (A/P) homeotic transformations and/or disruptions at one or more stages in somite development. A review of other teratogenicity studies suggests that the co-occurrence of these two disparate malformations is not unique to dimethadione, rather it may be a more general phenomenon caused by various structurally unrelated agents. The coexistence of cardiac and thoracic skeletal malformations has also presented clinically, suggesting a mechanistic link between cardiogenesis and skeletal development. Evidence from genetically modified mice reveals that several genes are common to heart development and to formation of the axial skeleton. Some of these genes are important in regulating chromatin architecture, while others are tightly controlled by chromatin-modifying proteins. This review focuses on the role of these epigenetic factors in development of the heart and axial skeleton, and examines the hypothesis that posttranslational modifications of core histones may be altered by some developmental toxicants.
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MESH Headings
- Abnormalities, Drug-Induced/etiology
- Abnormalities, Drug-Induced/genetics
- Abnormalities, Drug-Induced/metabolism
- Abnormalities, Multiple/etiology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Bone and Bones/abnormalities
- Chromosomal Proteins, Non-Histone
- Epigenesis, Genetic
- Female
- Heart Defects, Congenital/etiology
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/metabolism
- Histones/metabolism
- Humans
- MicroRNAs/genetics
- Models, Biological
- Pregnancy
- Protein Processing, Post-Translational
- Ribs/abnormalities
- Sternum/abnormalities
- Teratogens/toxicity
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Andrea D Weston
- Developmental and Reproductive Toxicology Center of Emphasis, Drug Safety Research, and Development, Pfizer Global Research and Development, Groton, Connecticut 06340, USA
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Wong CK, Chen Z, So KL, Li D, Li P. Polycomb group protein RING1B is a direct substrate of Caspases-3 and -9. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:844-52. [PMID: 17379327 DOI: 10.1016/j.bbamcr.2007.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 02/06/2007] [Accepted: 02/07/2007] [Indexed: 11/30/2022]
Abstract
Both Caspase-3 and Caspase-9 play critical roles in the execution of mitochondria-mediated apoptosis. Caspase-9 binds to Apaf-1 in the presence of cytochrome c and dATP/ATP, and is activated by self-cleavage. Caspase-3 is activated by cleavage of caspase-8 and caspase-9. Over hundred direct caspase-3 substrates are identified whereas only few direct caspase-9 substrates are known. Here, we demonstrate that Ring1B, a component of polycomb protein complex that plays important roles in modulating chromatin structures, is a direct substrate of active caspase-3 and caspase-9 both in vitro and in vivo. The specific cleavage sites for caspase-3 and caspase-9 were mapped to Asp(175) and Asp(208), respectively. Importantly, cleavage of Ring1B by active caspases-3 and caspase-9 triggers the redistribution of Ring1B, from exclusive nuclear localization to even distribution throughout the entire cell. The transcriptional repression activity of Ring1B was also disrupted by caspase cleavage. Our data suggest that caspases-3 and caspase-9 play novel roles in transcription by regulating polycomb protein function through direct cleaving of Ring1B.
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Affiliation(s)
- Chung Kai Wong
- Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Breiling A, Sessa L, Orlando V. Biology of Polycomb and Trithorax Group Proteins. INTERNATIONAL REVIEW OF CYTOLOGY 2007; 258:83-136. [PMID: 17338920 DOI: 10.1016/s0074-7696(07)58002-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellular phenotypes can be ascribed to different patterns of gene expression. Epigenetic mechanisms control the generation of different phenotypes from the same genotype. Thus differentiation is basically a process driven by changes in gene activity during development, often in response to transient factors or environmental stimuli. To keep the specific characteristics of cell types, tissue-specific gene expression patterns must be transmitted stably from one cell to the daughter cells, also in the absence of the early-acting determination factors. This heritability of patterns of active and inactive genes is enabled by epigenetic mechanisms that create a layer of information on top of the DNA sequence that ensures mitotic and sometimes also meiotic transmission of expression patterns. The proteins of the Polycomb and Trithorax group comprise such a cellular memory mechanism that preserves gene expression patterns through many rounds of cell division. This review provides an overview of the genetics and molecular biology of these maintenance proteins, concentrating mainly on mechanisms of Polycomb group-mediated repression.
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Affiliation(s)
- Achim Breiling
- Dulbecco Telethon Institute, Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy
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Wang S, He F, Xiong W, Gu S, Liu H, Zhang T, Yu X, Chen Y. Polycomblike-2-deficient mice exhibit normal left–right asymmetry. Dev Dyn 2007; 236:853-61. [PMID: 17266133 DOI: 10.1002/dvdy.21070] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Polycomb group (PcG) proteins are required for maintaining the repressed state of developmentally important genes such as homeotic genes. Polycomblike (Pcl), a member of PcG genes with two characteristic PHD finger motifs, was shown to strongly enhance the effects of PcG genes in Drosophila. Three Pcl genes exist in the mouse genome, with their function largely unknown. Our previous studies demonstrate that the chick Pcl2 is essential for the left-right asymmetry by silencing Shh expression in the right side of the node (Wang et al., [2004b] Development 131:4381-4391). To elucidate the in vivo role of mouse Pcl2, we generated Pcl2 mutant mice. Phenotypic analyses indicate the normal development of left-right asymmetry in the Pcl2 mutant mice. However, Pcl2 mutant mice exhibit posterior transformation of axial skeletons and other phenotypic defects, with a relatively low penetrance. These results demonstrate that Pcl2 is dispensable for the normal left-right axis development in mice.
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Affiliation(s)
- Shusheng Wang
- Division of Developmental Biology, Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, USA
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45
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Gyurján I, Molnár A, Borsy A, Stéger V, Hackler L, Zomborszky Z, Papp P, Duda E, Deák F, Lakatos P, Puskás LG, Orosz L. Gene expression dynamics in deer antler: mesenchymal differentiation toward chondrogenesis. Mol Genet Genomics 2006; 277:221-35. [PMID: 17146666 DOI: 10.1007/s00438-006-0190-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 10/26/2006] [Indexed: 12/16/2022]
Abstract
Annual re-growth of deer antler represents a unique example of complete organ regeneration. Because antler mesenchymal cells retain their embryonic capacity to develop into cartilage or bone, studying antler development provides a natural system to follow gene expression changes during mesenchymal differentiation toward chondrogenic/osteogenic lineage. To identify novel genes involved either in early events of mesenchymal cell specialization or in robust bone development, we have introduced a 3 K heterologous microarray set-up (deer cDNA versus mouse template). Fifteen genes were differentially expressed; genes for housekeeping, regulatory functions (components of different signaling pathways, including FGF, TGFbeta, Wnt), and genes encoding members of the Polycomb group were represented. Expression dynamics for genes are visualized by an expression logo. The expression profile of the gene C21orf70 of unknown function is described along with the effects when over-expressed; furthermore the nuclear localization of the cognate protein is shown. In this report, we demonstrate the particular advantage of the velvet antler model in bone research for: (1) identification of mesenchymal and precartilaginous genes and (2) targeting genes upregulated in robust cartilage development.
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Affiliation(s)
- István Gyurján
- Institute of Genetics, Agricultural Biotechnology Center, Szent-Györgyi Albert u 4, 2101, Gödöllo, Hungary
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Gearhart MD, Corcoran CM, Wamstad JA, Bardwell VJ. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. Mol Cell Biol 2006; 26:6880-9. [PMID: 16943429 PMCID: PMC1592854 DOI: 10.1128/mcb.00630-06] [Citation(s) in RCA: 265] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The corepressor BCOR potentiates transcriptional repression by the proto-oncoprotein BCL6 and suppresses the transcriptional activity of a common mixed-lineage leukemia fusion partner, AF9. Mutations in human BCOR cause male lethal, X-linked oculofaciocardiodental syndrome. We identified a BCOR complex containing Polycomb group (PcG) and Skp-Cullin-F-box subcomplexes. The PcG proteins include RING1, RYBP, NSPC1, a Posterior Sex Combs homolog, and RNF2, an E3 ligase for the mono-ubiquitylation of H2A. BCOR complex components and mono-ubiquitylated H2A localize to BCL6 targets, indicating that the BCOR complex employs PcG proteins to expand the repertoire of enzymatic activities that can be recruited by BCL6. This also suggests that BCL6 can target PcG proteins to DNA. In addition, the BCOR complex contains components of a second ubiquitin E3 ligase, namely, SKP1 and FBXL10 (JHDM1B). We show that BCOR coimmunoprecipitates isoforms of FBXL10 which contain a JmjC domain that recently has been determined to have histone H3K36 demethylase activity. The recruitment of two distinct classes of E3 ubiquitin ligases and a histone demethylase by BCOR suggests that BCOR uses a unique combination of epigenetic modifications to direct gene silencing.
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Affiliation(s)
- Micah D Gearhart
- Department of Genetics, Cell Biology and Development, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
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Nolte C, Rastegar M, Amores A, Bouchard M, Grote D, Maas R, Kovacs EN, Postlethwait J, Rambaldi I, Rowan S, Yan YL, Zhang F, Featherstone M. Stereospecificity and PAX6 function direct Hoxd4 neural enhancer activity along the antero-posterior axis. Dev Biol 2006; 299:582-93. [PMID: 17010333 DOI: 10.1016/j.ydbio.2006.08.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Revised: 08/16/2006] [Accepted: 08/25/2006] [Indexed: 12/14/2022]
Abstract
The antero-posterior (AP) and dorso-ventral (DV) patterning of the neural tube is controlled in part by HOX and PAX transcription factors, respectively. We have reported on a neural enhancer of Hoxd4 that directs expression in the CNS with the correct anterior border in the hindbrain. Comparison to the orthologous enhancer of zebrafish revealed seven conserved footprints including an obligatory retinoic acid response element (RARE), and adjacent sites D, E and F. Whereas enhancer function in the embryonic CNS is destroyed by separation of the RARE from sites D-E-F by a half turn of DNA, it is rescued by one full turn, suggesting stereospecific constraints between DNA-bound retinoid receptors and the factor(s) recognizing sites D-E-F. Alterations in the DV trajectory of the Hoxd4 anterior expression border following mutation of site D or E implicated transcriptional regulators active across the DV axis. We show that PAX6 specifically binds sites D and E in vitro, and use chromatin immunoprecipitation to demonstrate recruitment of PAX6 to the Hoxd4 neural enhancer in mouse embryos. Hoxd4 expression throughout the CNS is reduced in Pax6 mutant Sey(Neu) animals on embryonic day 8. Additionally, stage-matched zebrafish embryos having decreased pax6a and/or pax6b activity display malformed rhombomere boundaries and an anteriorized hoxd4a expression border. These results reveal an evolutionarily conserved role for Pax6 in AP-restricted expression of vertebrate Hoxd4 orthologs.
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Affiliation(s)
- Christof Nolte
- McGill Cancer Centre, McGill University, 3655 Promenade Sir-William-Osler, Montreal, QC, Canada H3G 1Y6
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48
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Okada A, Fujiwara M. Molecular approaches to developmental malformations using analogous forms of valproic acid. Congenit Anom (Kyoto) 2006; 46:68-75. [PMID: 16732764 DOI: 10.1111/j.1741-4520.2006.00105.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The teratogenic potential of valproic acid has been well established both in experimental models and in human clinical studies. Evidence from many previous studies has shown that VPA is an appropriate drug model for studying chemical structure-teratogenicity relationships. Using molecular techniques of DNA microarray (GeneChip system) or quantitative real-time polymerase chain reaction with low teratogenic VPA analogs as comparative control drugs, we attempted to identify the genes involved with the molecular mechanisms of VPA teratogenicity in the neural tube and the axial skeleton of the mouse embryo. The recent development of DNA microarray enables a genome-wide approach to the identification of genes correlated with the teratogenicity of chemicals (teratogenomics). The VPA-induced changes in gene expression seen during mouse embryogenesis provides information for understanding how VPA disrupts normal embryonic development, and also provides leads for the development of safer medicines.
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Affiliation(s)
- Akinobu Okada
- Drug Safety Research Laboratories, Astellas Pharma, Yodogawa-ku, Osaka, Japan.
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49
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Sato T, Endoh M, Yoshida H, Yasuo S, Katsuno T, Saito Y, Isono KI, Koseki H. Mammalian Polycomb complexes are required for Peyer's patch development by regulating lymphoid cell proliferation. Gene 2006; 379:166-74. [PMID: 16815646 DOI: 10.1016/j.gene.2006.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Revised: 05/10/2006] [Accepted: 05/11/2006] [Indexed: 10/24/2022]
Abstract
The vertebrate Polycomb Group (PcG) genes encode proteins that form large multimeric and chromatin-associated complexes implicated in the stable repression of developmentally essential genes. Rnf110 and Phc2 are shown to be components of mammalian PcG multimeric complexes in HeLa cells. Here we report defects in Peyer's patch (PP) development in Rnf110 mutant mice, which is synergically exaggerated by Phc2 mutation. PP development involves a series of inductive interactions and subsequent differentiation and proliferation between lymphoid and mesenchymal cells in late gestational stage. Rnf110 and Phc2 mutations impair development of PP anlagen by affecting proliferation of lymphoid lineage cells populated in PP anlagen in gene-dosage dependent manner. We suggest that PcG complexes may act to mediate certain inductive signals maybe through IL-7Ralpha to allow sufficient proliferation of lymphoid inducer cells during PP organogenesis.
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Affiliation(s)
- Toru Sato
- Department of Clinical Cell Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba, Japan
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Sánchez-Beato M, Sánchez E, González-Carreró J, Morente M, Díez A, Sánchez-Verde L, Martín MC, Cigudosa JC, Vidal M, Piris MA. Variability in the expression of polycomb proteins in different normal and tumoral tissues. A pilot study using tissue microarrays. Mod Pathol 2006; 19:684-94. [PMID: 16528373 DOI: 10.1038/modpathol.3800577] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In spite of the known function of polycomb group (PcG) genes in stem cell self-renewal, control of cellular proliferation and differentiation, its role in cancer pathogenesis is still poorly understood. We studied the expression by immunohistochemistry of several PcG-maintenance complex proteins (RING1, RNF2, BMI1, MEL18, HPH1 and RYBP) in nontumoral (154 samples) and tumoral (550 samples) human tissues using Tissue Microarrays. For selected genes (BMI1 and RING1) FISH analysis has been also carried out. PcG proteins had a tissue- and cell-type-specific expression pattern. Some of them were highly selectively expressed, such as HPH1, which was detected in germ cells in testis, pituitary and parathyroid glands and Langerhans islets, and RYBP, which was found in placenta, umbilical cord and thyroid gland. By contrast, RING1 was ubiquitously expressed in every normal tissue analyzed. Changes in expression associated with tumoral transformation have been found for BMI1 and RNF2, which exhibited increased expression in a large series of tumors, including gastrointestinal tumors, pituitary and parathyroid adenomas, and lymphomas, compared with their expression in normal-cell counterparts. The high level of expression of BMI1 protein observed in mantle-cell lymphomas and pituitary adenomas is associated in some cases with amplification of BMI1 locus. These findings imply that upregulation of BMI1 may constitute a malignancy marker in different types of cancer, mainly in lymphoid and endocrine tumors. RING1 was lost in a group of renal-cell carcinomas and testicular germ-cell tumors. Lastly, RYBP is anomalously expressed in Hodgkin's lymphomas and oligodendrogliomas, among others tumors. A significant finding of the study is the identification of unique PcG profiles for some tumors, such as testicular germ-cell tumors, which have high levels of HPH1 expression and loss of RING1 and/or BMI1; pituitary adenomas, which expressed every PcG protein analyzed; and clear-cell renal-cell carcinoma, which was the only tumor other than testicular germ-cell tumors that did not express RING1.
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Affiliation(s)
- Margarita Sánchez-Beato
- Lymphoma Group, Molecular Pathology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain.
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