501
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Pethe P, Pursani V, Bhartiya D. Lineage specific expression of Polycomb Group Proteins in human embryonic stem cells in vitro. Cell Biol Int 2015; 39:600-10. [PMID: 25572667 DOI: 10.1002/cbin.10431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/26/2014] [Indexed: 02/05/2023]
Abstract
Human embryonic (hES) stem cells are an excellent model to study lineage specification and differentiation into various cell types. Differentiation necessitates repression of specific genes not required for a particular lineage. Polycomb Group (PcG) proteins are key histone modifiers, whose primary function is gene repression. PcG proteins form complexes called Polycomb Repressive Complexes (PRCs), which catalyze histone modifications such as H2AK119ub1, H3K27me3, and H3K9me3. PcG proteins play a crucial role during differentiation of stem cells. The expression of PcG transcripts during differentiation of hES cells into endoderm, mesoderm, and ectoderm lineage is yet to be shown. In-house derived hES cell line KIND1 was differentiated into endoderm, mesoderm, and ectoderm lineages; followed by characterization using RT-PCR for HNF4A, CDX2, MEF2C, TBX5, SOX1, and MAP2. qRT-PCR and western blotting was performed to compare expression of PcG transcripts and proteins across all the three lineages. We observed that cells differentiated into endoderm showed upregulation of RING1B, BMI1, EZH2, and EED transcripts. Mesoderm differentiation was characterized by significant downregulation of all PcG transcripts during later stages. BMI1 and RING1B were upregulated while EZH2, SUZ12, and EED remained low during ectoderm differentiation. Western blotting also showed distinct expression of BMI1 and EZH2 during differentiation into three germ layers. Our study shows that hES cells differentiating into endoderm, mesoderm, and ectoderm lineages show distinct PcG expression profile at transcript and protein level.
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Affiliation(s)
- Prasad Pethe
- Stem Cell Biology Department, National Institute for Research in Reproductive Health (NIRRH), Jehangir Merwanji Street, Parel, Mumbai, 400012, India
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502
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503
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504
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Brancaccio A, Palacios D. Chromatin signaling in muscle stem cells: interpreting the regenerative microenvironment. Front Aging Neurosci 2015; 7:36. [PMID: 25904863 PMCID: PMC4387924 DOI: 10.3389/fnagi.2015.00036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/04/2015] [Indexed: 12/12/2022] Open
Abstract
Muscle regeneration in the adult occurs in response to damage at expenses of a population of adult stem cells, the satellite cells. Upon injury, either physical or genetic, signals released within the satellite cell niche lead to the commitment, expansion and differentiation of the pool of muscle progenitors to repair damaged muscle. To achieve this goal satellite cells undergo a dramatic transcriptional reprogramming to coordinately activate and repress specific subset of genes. Although the epigenetics of muscle regeneration has been extensively discussed, less emphasis has been put on how extra-cellular cues are translated into the specific chromatin reorganization necessary for progression through the myogenic program. In this review we will focus on how satellite cells sense the regenerative microenvironment in physiological and pathological circumstances, paying particular attention to the mechanism through which the external stimuli are transduced to the nucleus to modulate chromatin structure and gene expression. We will discuss the pathways involved and how alterations in this chromatin signaling may contribute to satellite cells dysfunction during aging and disease.
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Affiliation(s)
- Arianna Brancaccio
- Laboratory of Epigenetics and Signaling, IRCCS Fondazione Santa Lucia Rome, Italy
| | - Daniela Palacios
- Laboratory of Epigenetics and Signaling, IRCCS Fondazione Santa Lucia Rome, Italy
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505
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Boulard M, Edwards JR, Bestor TH. FBXL10 protects Polycomb-bound genes from hypermethylation. Nat Genet 2015; 47:479-85. [DOI: 10.1038/ng.3272] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/13/2015] [Indexed: 12/15/2022]
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506
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PcG and trxG in plants - friends or foes. Trends Genet 2015; 31:252-62. [PMID: 25858128 DOI: 10.1016/j.tig.2015.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.
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507
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Systematic discovery of Xist RNA binding proteins. Cell 2015; 161:404-16. [PMID: 25843628 DOI: 10.1016/j.cell.2015.03.025] [Citation(s) in RCA: 732] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/29/2015] [Accepted: 03/11/2015] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA-protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3' RNA processing machinery. Xist, an essential lncRNA for X chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK, which participates in Xist-mediated gene silencing and histone modifications but not Xist localization, and Drosophila Split ends homolog Spen, which interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.
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508
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Tardat M, Albert M, Kunzmann R, Liu Z, Kaustov L, Thierry R, Duan S, Brykczynska U, Arrowsmith CH, Peters AHFM. Cbx2 targets PRC1 to constitutive heterochromatin in mouse zygotes in a parent-of-origin-dependent manner. Mol Cell 2015; 58:157-71. [PMID: 25801166 DOI: 10.1016/j.molcel.2015.02.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/22/2014] [Accepted: 02/05/2015] [Indexed: 11/17/2022]
Abstract
Polycomb repressive complexes PRC1 and PRC2 regulate expression of genes involved in proliferation and development. In mouse early embryos, however, canonical PRC1 localizes to paternal pericentric heterochromatin (pat-PCH), where it represses transcription of major satellite repeats. In contrast, maternal PCH (mat-PCH) is enriched for H3 lysine 9 tri-methylation (H3K9me3) and Hp1β. How PRC1 is targeted to pat-PCH, yet excluded from mat-PCH, has remained elusive. Here, we identify a PRC1 targeting mechanism that relies on Cbx2 and Hp1β. Cbx2 directs catalytically active PRC1 to PCH via its chromodomain (CD(Cbx2)) and neighboring AT-hook (AT(Cbx2)) binding to H3K27me3 and AT-rich major satellites, respectively. CD(Cbx2) prevents AT(Cbx2) from interacting with DNA at PCH marked by H3K9me3 and Hp1β. Loss-of-function studies show that Hp1β and not H3K9me3 prevents PRC1 targeting to mat-PCH. Our findings indicate that CD(Cbx2) and AT(Cbx2) separated by a short linker function together to integrate H3K9me3/HP1 and H3K27me3 states.
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Affiliation(s)
- Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Mareike Albert
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Rico Kunzmann
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Zichuan Liu
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Lilia Kaustov
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Raphael Thierry
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Urszula Brykczynska
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland.
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509
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Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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510
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Xiao J, Wagner D. Polycomb repression in the regulation of growth and development in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:15-24. [PMID: 25449722 DOI: 10.1016/j.pbi.2014.10.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 05/18/2023]
Abstract
Chromatin state is critical for cell identity and development in multicellular eukaryotes. Among the regulators of chromatin state, Polycomb group (PcG) proteins stand out because of their role in both establishment and maintenance of cell identity. PcG proteins act in two major complexes in metazoans and plants. These complexes function to epigenetically-in a mitotically heritable manner-prevent expression of important developmental regulators at the wrong stage of development or in the wrong tissue. In Arabidopsis, PcG function is required throughout the life cycle from seed germination to embryo formation. Recent studies have expanded our knowledge regarding the biological roles and the regulation of the activity of PcG complexes. In this review, we discuss novel functions of Polycomb repression in plant development as well as advances in understanding PcG complex recruitment, activity regulation and removal in Arabidopsis and other plant species.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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511
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Abstract
In this Opinion article, we summarize how changes in DNA methylation occur during aging in mammals and discuss examples of how such events may contribute to the aging process. We explore mechanisms that could facilitate DNA methylation changes in a site-specific manner and highlight a model in which region-specific DNA hypermethylation during aging is facilitated in a competitive manner by destabilization of the Polycomb repressive complex.
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512
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Sanulli S, Justin N, Teissandier A, Ancelin K, Portoso M, Caron M, Michaud A, Lombard B, da Rocha ST, Offer J, Loew D, Servant N, Wassef M, Burlina F, Gamblin SJ, Heard E, Margueron R. Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation. Mol Cell 2015; 57:769-783. [PMID: 25620564 PMCID: PMC4352895 DOI: 10.1016/j.molcel.2014.12.020] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 08/01/2014] [Accepted: 12/12/2014] [Indexed: 02/06/2023]
Abstract
Polycomb Group (PcG) proteins maintain transcriptional repression throughout development, mostly by regulating chromatin structure. Polycomb Repressive Complex 2 (PRC2), a component of the Polycomb machinery, is responsible for the methylation of histone H3 lysine 27 (H3K27me2/3). Jarid2 was previously identified as a cofactor of PRC2, regulating PRC2 targeting to chromatin and its enzymatic activity. Deletion of Jarid2 leads to impaired orchestration of gene expression during cell lineage commitment. Here, we reveal an unexpected crosstalk between Jarid2 and PRC2, with Jarid2 being methylated by PRC2. This modification is recognized by the Eed core component of PRC2 and triggers an allosteric activation of PRC2’s enzymatic activity. We show that Jarid2 methylation is important to promote PRC2 activity at a locus devoid of H3K27me3 and for the correct deposition of this mark during cell differentiation. Our results uncover a regulation loop where Jarid2 methylation fine-tunes PRC2 activity depending on the chromatin context. PRC2 methylates Jarid2 on K116 Jarid2 methylation promotes PRC2 activity H3K27me3 and Jarid2-K116me3 bind to the aromatic cage of Eed Jarid2 methylation regulates H3K27me3 deposition during ESC differentiation
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Affiliation(s)
- Serena Sanulli
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Neil Justin
- MRC National Institute for Medical Research, The Ridgeway, London, Mill Hill NW7 1AA, UK
| | - Aurélie Teissandier
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U900, 26 Rue d'Ulm, 75005 Paris, France; Mines ParisTech, 35 Rue Saint Honoré, 77305 Fontainebleau, France
| | - Katia Ancelin
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Manuela Portoso
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Matthieu Caron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Audrey Michaud
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Berangère Lombard
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; Laboratory of Proteomics and Mass Spectrometry, 26 Rue d'Ulm, 75005 Paris, France
| | - Simao T da Rocha
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - John Offer
- MRC National Institute for Medical Research, The Ridgeway, London, Mill Hill NW7 1AA, UK
| | - Damarys Loew
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; Laboratory of Proteomics and Mass Spectrometry, 26 Rue d'Ulm, 75005 Paris, France
| | - Nicolas Servant
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U900, 26 Rue d'Ulm, 75005 Paris, France; Mines ParisTech, 35 Rue Saint Honoré, 77305 Fontainebleau, France
| | - Michel Wassef
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Fabienne Burlina
- Sorbonnes Universités, UPMC Univ Paris 06, CNRS, ENS, UMR7203 LBM, 4 Place Jussieu, 75005 Paris, France
| | - Steve J Gamblin
- MRC National Institute for Medical Research, The Ridgeway, London, Mill Hill NW7 1AA, UK
| | - Edith Heard
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Raphaël Margueron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France.
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513
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Abstract
Posttranslational modifications of histone proteins represent a fundamental means to define distinctive epigenetic states and regulate gene expression during development and differentiation. Aberrations in various chromatin-modulation pathways are commonly used by tumors to initiate and maintain oncogenesis, including lymphomagenesis. Recently, increasing evidence has demonstrated that polycomb group (PcG) proteins, a subset of histone-modifying enzymes known to be crucial for B-cell maturation and differentiation, play a central role in malignant transformation of B cells. PcG hyperactivity in B-cell lymphomas is caused by overexpression or recurrent mutations of PcG genes and deregulation of microRNAs (miRNAs) or transcription factors such as c-MYC, which regulate PcG expression. Interplays of PcG and miRNA deregulations often establish a vicious signal-amplification loop in lymphoma associated with adverse clinical outcomes. Importantly, aberrant enzymatic activities associated with polycomb deregulation, notably those caused by EZH2 gain-of-function mutations, have provided a rationale for developing small-molecule inhibitors as novel therapies. In this review, we summarize our current understanding of PcG-mediated gene silencing, interplays of PcG with other epigenetic regulators such as miRNAs during B-cell differentiation and lymphomagenesis, and recent advancements in targeted strategies against PcG as promising therapeutics for B-cell malignancies.
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514
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Spruijt CG, Vermeulen M. DNA methylation: old dog, new tricks? Nat Struct Mol Biol 2015; 21:949-54. [PMID: 25372310 DOI: 10.1038/nsmb.2910] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/30/2014] [Indexed: 12/17/2022]
Abstract
DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation can also have different outcomes, including activation of transcription. This is evidenced by the fact that transcription factors can interact with methylated DNA sequences. Furthermore, in certain cellular contexts, genes containing methylated promoters are highly transcribed. Interestingly, this uncoupling between methylated DNA and repression of transcription seems to be particularly evident in germ cells and pluripotent cells. Thus, contrary to previous assumptions, DNA methylation is not exclusively associated with repression of transcription initiation.
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Affiliation(s)
- Cornelia G Spruijt
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands. [3] Cancer Genomics Netherlands, the Netherlands
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515
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Subramanian* V, Fields* PA, Boyer LA. H2A.Z: a molecular rheostat for transcriptional control. F1000PRIME REPORTS 2015; 7:01. [PMID: 25705384 PMCID: PMC4311278 DOI: 10.12703/p7-01] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The replacement of nucleosomal H2A with the histone variant H2A.Z is critical for regulating DNA-mediated processes across eukaryotes and for early development of multicellular organisms. How this variant performs these seemingly diverse roles has remained largely enigmatic. Here, we discuss recent mechanistic insights that have begun to reveal how H2A.Z functions as a molecular rheostat for gene control. We focus on specific examples in metazoans as a model for understanding how H2A.Z integrates information from histone post-translational modifications, other histone variants, and transcription factors (TFs) to regulate proper induction of gene expression programs in response to cellular cues. Finally, we propose a general model of how H2A.Z incorporation regulates chromatin states in diverse processes.
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516
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Yakushiji-Kaminatsui N, Kondo T, Endo TA, Koseki Y, Kondo K, Ohara O, Vidal M, Koseki H. RING1 contributes to early proximal-distal specification of the forelimb bud by restricting Meis2 expression. Development 2015; 143:276-85. [DOI: 10.1242/dev.127506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/08/2015] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins play a pivotal role in silencing development-related genes and help to maintain various stem and precursor cells and regulate their differentiation. PcG factors also regulate dynamic and complex regional specification, particularly in mammals, but this activity is mechanistically not well understood. In this study, we focused on proximal-distal (PD) patterning of the forelimb bud to elucidate how PcG factors contribute to a regional specification process that depends on developmental signals. Depletion of RING1 proteins, which are essential components of the Polycomb repressive complex-1 (PRC1), led to severe defects in forelimb formation along the PD axis. We show that preferential defects in early distal specification in Ring1-deficient forelimb buds accompany failures in repression of proximal signal circuitry bound by RING1B, including Meis2/1, and activation of distal signal circuitry in the prospective distal region. Additional deletion of Meis2 induced partial restoration of distal gene expression and limb formation seen in the Ring1-deficient mice, suggesting a critical role for RING1-dependent repression of Meis2 and likely Meis1 for distal specification. We suggest that the RING1/MEIS2/1 axis is regulated by early PD signals and contributes to initiation or maintenance of the distal signal circuitry.
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Affiliation(s)
- Nayuta Yakushiji-Kaminatsui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Takaho A. Endo
- Laboratory for Integrative Genomics, RIKEN IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kaori Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas, Department of Cellular and Molecular Biology, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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517
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Bianchi A, Lanzuolo C. Into the chromatin world: Role of nuclear architecture in epigenome regulation. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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518
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Lomniczi A, Wright H, Ojeda SR. Epigenetic regulation of female puberty. Front Neuroendocrinol 2015; 36:90-107. [PMID: 25171849 PMCID: PMC6824271 DOI: 10.1016/j.yfrne.2014.08.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/15/2014] [Accepted: 08/20/2014] [Indexed: 12/18/2022]
Abstract
Substantial progress has been made in recent years toward deciphering the molecular and genetic underpinnings of the pubertal process. The availability of powerful new methods to interrogate the human genome has led to the identification of genes that are essential for puberty to occur. Evidence has also emerged suggesting that the initiation of puberty requires the coordinated activity of gene sets organized into functional networks. At a cellular level, it is currently thought that loss of transsynaptic inhibition, accompanied by an increase in excitatory inputs, results in the pubertal activation of GnRH release. This concept notwithstanding, a mechanism of epigenetic repression targeting genes required for the pubertal activation of GnRH neurons was recently identified as a core component of the molecular machinery underlying the central restraint of puberty. In this chapter we will discuss the potential contribution of various mechanisms of epigenetic regulation to the hypothalamic control of female puberty.
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Affiliation(s)
- Alejandro Lomniczi
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave, Beaverton, OR 97006, USA.
| | - Hollis Wright
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave, Beaverton, OR 97006, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave, Beaverton, OR 97006, USA.
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519
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Inagaki T, Iwasaki S, Matsumura Y, Kawamura T, Tanaka T, Abe Y, Yamasaki A, Tsurutani Y, Yoshida A, Chikaoka Y, Nakamura K, Magoori K, Nakaki R, Osborne TF, Fukami K, Aburatani H, Kodama T, Sakai J. The FBXL10/KDM2B scaffolding protein associates with novel polycomb repressive complex-1 to regulate adipogenesis. J Biol Chem 2014; 290:4163-77. [PMID: 25533466 DOI: 10.1074/jbc.m114.626929] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Polycomb repressive complex 1 (PRC1) plays an essential role in the epigenetic repression of gene expression during development and cellular differentiation via multiple effector mechanisms, including ubiquitination of H2A and chromatin compaction. However, whether it regulates the stepwise progression of adipogenesis is unknown. Here, we show that FBXL10/KDM2B is an anti-adipogenic factor that is up-regulated during the early phase of 3T3-L1 preadipocyte differentiation and in adipose tissue in a diet-induced model of obesity. Interestingly, inhibition of adipogenesis does not require the JmjC demethylase domain of FBXL10, but it does require the F-box and leucine-rich repeat domains, which we show recruit a noncanonical polycomb repressive complex 1 (PRC1) containing RING1B, SKP1, PCGF1, and BCOR. Knockdown of either RING1B or SKP1 prevented FBXL10-mediated repression of 3T3-L1 preadipocyte differentiation indicating that PRC1 formation mediates the inhibitory effect of FBXL10 on adipogenesis. Using ChIP-seq, we show that FBXL10 recruits RING1B to key specific genomic loci surrounding the key cell cycle and the adipogenic genes Cdk1, Uhrf1, Pparg1, and Pparg2 to repress adipogenesis. These results suggest that FBXL10 represses adipogenesis by targeting a noncanonical PRC1 complex to repress key genes (e.g. Pparg) that control conversion of pluripotent cells into the adipogenic lineage.
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Affiliation(s)
- Takeshi Inagaki
- From the Division of Metabolic Medicine, the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan,
| | | | | | - Takeshi Kawamura
- the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan, Laboratory for Systems Biology and Medicine
| | - Toshiya Tanaka
- From the Division of Metabolic Medicine, the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan, Laboratory for Systems Biology and Medicine
| | - Yohei Abe
- From the Division of Metabolic Medicine
| | | | | | - Ayano Yoshida
- From the Division of Metabolic Medicine, the Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Yoko Chikaoka
- the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan, Laboratory for Systems Biology and Medicine
| | - Kanako Nakamura
- From the Division of Metabolic Medicine, the Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Kenta Magoori
- From the Division of Metabolic Medicine, the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan
| | - Ryo Nakaki
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
| | - Timothy F Osborne
- the Metabolic Disease Program, Sanford-Burnham Medical Research Institute, Orlando, Florida 32827, and
| | - Kiyoko Fukami
- the Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Hiroyuki Aburatani
- the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan, Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
| | | | - Juro Sakai
- From the Division of Metabolic Medicine, the Translational Systems Biology and Medicine Initiative Center for Disease Biology and Integrative Medicine, University of Tokyo, Tokyo 153-8904, Japan,
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520
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Product binding enforces the genomic specificity of a yeast polycomb repressive complex. Cell 2014; 160:204-18. [PMID: 25533783 DOI: 10.1016/j.cell.2014.11.039] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/30/2014] [Accepted: 11/12/2014] [Indexed: 11/22/2022]
Abstract
We characterize the Polycomb system that assembles repressive subtelomeric domains of H3K27 methylation (H3K27me) in the yeast Cryptococcus neoformans. Purification of this PRC2-like protein complex reveals orthologs of animal PRC2 components as well as a chromodomain-containing subunit, Ccc1, which recognizes H3K27me. Whereas removal of either the EZH or EED ortholog eliminates H3K27me, disruption of mark recognition by Ccc1 causes H3K27me to redistribute. Strikingly, the resulting pattern of H3K27me coincides with domains of heterochromatin marked by H3K9me. Indeed, additional removal of the C. neoformans H3K9 methyltransferase Clr4 results in loss of both H3K9me and the redistributed H3K27me marks. These findings indicate that the anchoring of a chromatin-modifying complex to its product suppresses its attraction to a different chromatin type, explaining how enzymes that act on histones, which often harbor product recognition modules, may deposit distinct chromatin domains despite sharing a highly abundant and largely identical substrate-the nucleosome.
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521
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Affiliation(s)
- Jürg Müller
- Max Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Martinsried 82152, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg 69117, Germany
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522
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Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 2014; 514:591-6. [PMID: 25355358 PMCID: PMC4215650 DOI: 10.1038/nature13890] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/26/2014] [Indexed: 12/24/2022]
Abstract
The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in higher eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c. However, the molecular mechanism of nucleosome substrate recognition by PRC1 or other chromatin enzymes is unclear. Here we present the crystal structure of the Ring1B/Bmi1/UbcH5c E3-E2 complex (the PRC1 ubiquitylation module) bound to its nucleosome core particle substrate. The structure shows how a chromatin enzyme achieves substrate specificity by interacting with multiple nucleosome surfaces spatially distinct from the site of catalysis. Our structure further reveals an unexpected role for the ubiquitin E2 enzyme in substrate recognition, and provides insight into how the related histone H2A E3 ligase, BRCA1, interacts with and ubiquitylates the nucleosome.
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523
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Fereres S, Simón R, Mohd-Sarip A, Verrijzer CP, Busturia A. dRYBP counteracts chromatin-dependent activation and repression of transcription. PLoS One 2014; 9:e113255. [PMID: 25415640 PMCID: PMC4240632 DOI: 10.1371/journal.pone.0113255] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/21/2014] [Indexed: 12/31/2022] Open
Abstract
Chromatin dependent activation and repression of transcription is regulated by the histone modifying enzymatic activities of the trithorax (trxG) and Polycomb (PcG) proteins. To investigate the mechanisms underlying their mutual antagonistic activities we analyzed the function of Drosophila dRYBP, a conserved PcG- and trxG-associated protein. We show that dRYBP is itself ubiquitylated and binds ubiquitylated proteins. Additionally we show that dRYBP maintains H2A monoubiquitylation, H3K4 monomethylation and H3K36 dimethylation levels and does not affect H3K27 trimethylation levels. Further we show that dRYBP interacts with the repressive SCE and dKDM2 proteins as well as the activating dBRE1 protein. Analysis of homeotic phenotypes and post-translationally modified histones levels show that dRYBP antagonizes dKDM2 and dBRE1 functions by respectively preventing H3K36me2 demethylation and H2B monoubiquitylation. Interestingly, our results show that inactivation of dBRE1 produces trithorax-like related homeotic transformations, suggesting that dBRE1 functions in the regulation of homeotic genes expression. Our findings indicate that dRYBP regulates morphogenesis by counteracting transcriptional repression and activation. Thus, they suggest that dRYBP may participate in the epigenetic plasticity important during normal and pathological development.
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Affiliation(s)
- Sol Fereres
- Centro de Biología Molecular “Severo Ochoa” CSIC-UAM, c) Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Rocío Simón
- Centro de Biología Molecular “Severo Ochoa” CSIC-UAM, c) Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Adone Mohd-Sarip
- Department of Biochemistry and Center for Biomedical Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - C. Peter Verrijzer
- Department of Biochemistry and Center for Biomedical Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Ana Busturia
- Centro de Biología Molecular “Severo Ochoa” CSIC-UAM, c) Nicolás Cabrera 1, 28049 Madrid, Spain
- * E-mail:
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524
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Saksouk N, Barth TK, Ziegler-Birling C, Olova N, Nowak A, Rey E, Mateos-Langerak J, Urbach S, Reik W, Torres-Padilla ME, Imhof A, Déjardin J, Simboeck E. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Mol Cell 2014; 56:580-94. [PMID: 25457167 DOI: 10.1016/j.molcel.2014.10.001] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/22/2014] [Accepted: 09/30/2014] [Indexed: 11/25/2022]
Abstract
Constitutive heterochromatin is typically defined by high levels of DNA methylation and H3 lysine 9 trimethylation (H3K9Me3), whereas facultative heterochromatin displays DNA hypomethylation and high H3 lysine 27 trimethylation (H3K27Me3). The two chromatin types generally do not coexist at the same loci, suggesting mutual exclusivity. During development or in cancer, pericentromeric regions can adopt either epigenetic state, but the switching mechanism is unknown. We used a quantitative locus purification method to characterize changes in pericentromeric chromatin-associated proteins in mouse embryonic stem cells deficient for either the methyltransferases required for DNA methylation or H3K9Me3. DNA methylation controls heterochromatin architecture and inhibits Polycomb recruitment. BEND3, a protein enriched on pericentromeric chromatin in the absence of DNA methylation or H3K9Me3, allows Polycomb recruitment and H3K27Me3, resulting in a redundant pathway to generate repressive chromatin. This suggests that BEND3 is a key factor in mediating a switch from constitutive to facultative heterochromatin.
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Affiliation(s)
- Nehmé Saksouk
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Teresa K Barth
- Munich Centre of Integrated Protein Science and Adolf Butenandt Institute, Group, Ludwig-Maximillians University of Munich, Schillerstrasse 44, 80336 Munich, Germany
| | - Celine Ziegler-Birling
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France
| | - Nelly Olova
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Agnieszka Nowak
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Elodie Rey
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Julio Mateos-Langerak
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Serge Urbach
- Functional Proteomics Facility, Institute of Functional Genomics, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Wolf Reik
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Maria-Elena Torres-Padilla
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France
| | - Axel Imhof
- Munich Centre of Integrated Protein Science and Adolf Butenandt Institute, Group, Ludwig-Maximillians University of Munich, Schillerstrasse 44, 80336 Munich, Germany
| | - Jérome Déjardin
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France.
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525
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Scelfo A, Piunti A, Pasini D. The controversial role of the Polycomb group proteins in transcription and cancer: how much do we not understand Polycomb proteins? FEBS J 2014; 282:1703-22. [PMID: 25315766 DOI: 10.1111/febs.13112] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022]
Abstract
Polycomb group proteins (PcGs) are a large protein family that includes diverse biochemical features assembled together in two large multiprotein complexes. These complexes maintain gene transcriptional repression in a cell type specific manner by modifying the surrounding chromatin to control development, differentiation and cell proliferation. PcGs are also involved in several diseases. PcGs are often directly or indirectly implicated in cancer development for which they have been proposed as potential targets for cancer therapeutic strategies. However, in the last few years a series of discoveries about the basic properties of PcGs and the identification of specific genetic alterations affecting specific Polycomb proteins in different tumours have converged to challenge old dogmas about PcG biological and molecular functions. In this review, we analyse these new data in the context of the old knowledge, highlighting the controversies and providing new models of interpretation and ideas that will perhaps bring some order among apparently contradicting observations.
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Affiliation(s)
- Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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526
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Corley M, Kroll KL. The roles and regulation of Polycomb complexes in neural development. Cell Tissue Res 2014; 359:65-85. [PMID: 25367430 DOI: 10.1007/s00441-014-2011-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/17/2014] [Indexed: 12/20/2022]
Abstract
In the developing mammalian nervous system, common progenitors integrate both cell extrinsic and intrinsic regulatory programs to produce distinct neuronal and glial cell types as development proceeds. This spatiotemporal restriction of neural progenitor differentiation is enforced, in part, by the dynamic reorganization of chromatin into repressive domains by Polycomb repressive complexes, effectively limiting the expression of fate-determining genes. Here, we review the distinct roles that Polycomb repressive complexes play during neurogenesis and gliogenesis, while also highlighting recent work describing the molecular mechanisms that govern their dynamic activity in neural development. Further investigation of the way in which Polycomb complexes are regulated in neural development will enable more precise manipulation of neural progenitor differentiation facilitating the efficient generation of specific neuronal and glial cell types for many biological applications.
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Affiliation(s)
- Matthew Corley
- Department of Developmental Biology, Washington University School of Medicine, 320 McDonnell Sciences Building, Campus Box 8103, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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527
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Kawakami E, Tokunaga A, Ozawa M, Sakamoto R, Yoshida N. The histone demethylase Fbxl11/Kdm2a plays an essential role in embryonic development by repressing cell-cycle regulators. Mech Dev 2014; 135:31-42. [PMID: 25463925 DOI: 10.1016/j.mod.2014.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/02/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
Methylation and de-methylation of histone lysine residues play pivotal roles in mammalian early development; these modifications influence chromatin architecture and regulate gene transcription. Fbxl11 (F-box and leucine-rich repeat 11)/Kdm2a is a histone demethylase that selectively removes mono- and di-methylation from histone H3K36. Previously, two other histone H3K36 demethylases (Jmjd5 or Fbxl10) were analyzed based on the phenotypes of the corresponding knockout (KO) mice; the results of those studies implicated H3K36 demethylases in cell proliferation, apoptosis, and senescence (Fukuda et al., 2011; Ishimura et al., 2012). To elucidate the physiological role of Fbxl11, we generated and examined Fbxl11 KO mice. Fbxl11 was expressed throughout the body during embryogenesis, and the Fbxl11 KO mice exhibited embryonic lethality at E10.5-12.5, accompanied with severe growth defects leading to reduced body size. Furthermore, knockout of Fbxl11 decreased cell proliferation and increased apoptosis. The lack of Fbxl11 resulted in downregulation of the Polycomb group protein (PcG) Ezh2, PcG mediated H2A ubiquitination and upregulation of the cyclin-dependent kinase inhibitor p21Cip1. Taken together, our findings suggest that Fbxl11 plays an essential role in embryonic development and homeostasis by regulating cell proliferation and survival.
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Affiliation(s)
- Eri Kawakami
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; The Tokunaga Laboratory, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu-shi, Oita 879-5593, Japan
| | - Akinori Tokunaga
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; The Tokunaga Laboratory, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasamamachi, Yufu-shi, Oita 879-5593, Japan.
| | - Manabu Ozawa
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Reiko Sakamoto
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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528
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Schuettengruber B, Oded Elkayam N, Sexton T, Entrevan M, Stern S, Thomas A, Yaffe E, Parrinello H, Tanay A, Cavalli G. Cooperativity, specificity, and evolutionary stability of Polycomb targeting in Drosophila. Cell Rep 2014; 9:219-233. [PMID: 25284790 DOI: 10.1016/j.celrep.2014.08.072] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/08/2014] [Accepted: 08/27/2014] [Indexed: 12/21/2022] Open
Abstract
Metazoan genomes are partitioned into modular chromosomal domains containing active or repressive chromatin. In flies, Polycomb group (PcG) response elements (PREs) recruit PHO and other DNA-binding factors and act as nucleation sites for the formation of Polycomb repressive domains. The sequence specificity of PREs is not well understood. Here, we use comparative epigenomics and transgenic assays to show that Drosophila domain organization and PRE specification are evolutionarily conserved despite significant cis-element divergence within Polycomb domains, whereas cis-element evolution is strongly correlated with transcription factor binding divergence outside of Polycomb domains. Cooperative interactions of PcG complexes and their recruiting factor PHO stabilize PHO recruitment to low-specificity sequences. Consistently, PHO recruitment to sites within Polycomb domains is stabilized by PRC1. These data suggest that cooperative rather than hierarchical interactions among low-affinity sequences, DNA-binding factors, and the Polycomb machinery are giving rise to specific and strongly conserved 3D structures in Drosophila.
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Affiliation(s)
- Bernd Schuettengruber
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Noa Oded Elkayam
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Sexton
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Marianne Entrevan
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Shani Stern
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aubin Thomas
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Eitan Yaffe
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hugues Parrinello
- Montpellier GenomiX IBiSA, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Giacomo Cavalli
- Institute of Human Genetics, UPR 1142, CNRS, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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529
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Affiliation(s)
- Itys Comet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark, and the Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- 1] Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark, and the Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark. [2] Danish Stem Cell Center (DanStem), Copenhagen, Denmark
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530
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Wachter E, Quante T, Merusi C, Arczewska A, Stewart F, Webb S, Bird A. Synthetic CpG islands reveal DNA sequence determinants of chromatin structure. eLife 2014; 3:e03397. [PMID: 25259796 PMCID: PMC4204011 DOI: 10.7554/elife.03397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022] Open
Abstract
The mammalian genome is punctuated by CpG islands (CGIs), which differ sharply from the bulk genome by being rich in G + C and the dinucleotide CpG. CGIs often include transcription initiation sites and display ‘active’ histone marks, notably histone H3 lysine 4 methylation. In embryonic stem cells (ESCs) some CGIs adopt a ‘bivalent’ chromatin state bearing simultaneous ‘active’ and ‘inactive’ chromatin marks. To determine whether CGI chromatin is developmentally programmed at specific genes or is imposed by shared features of CGI DNA, we integrated artificial CGI-like DNA sequences into the ESC genome. We found that bivalency is the default chromatin structure for CpG-rich, G + C-rich DNA. A high CpG density alone is not sufficient for this effect, as A + T-rich sequence settings invariably provoke de novo DNA methylation leading to loss of CGI signature chromatin. We conclude that both CpG-richness and G + C-richness are required for induction of signature chromatin structures at CGIs. DOI:http://dx.doi.org/10.7554/eLife.03397.001 The building blocks of DNA are four molecules commonly named ‘A’, ‘T’, ‘C’ and ‘G’. The order of these DNA letters in a gene contains the instructions to make specific proteins or other molecules. Other stretches of DNA contain codes that direct the cell's machinery to genes that need to be switched on or switched off. The start of a gene, for example, has a stretch of DNA called a promoter, which is where the molecular machinery that switches on the gene is assembled. A human cell can contain over two and half metres of DNA. To get this length to fit inside the cell, the DNA is wrapped tightly around proteins to form a structure called chromatin. However, this packing can make it difficult to access the right gene at the right time. As such, chromatin is often marked with small chemical tags that earmark which genes should be either activated or inactivated, and/or that cause the DNA to unpack. Most gene promoters contain a sequence of DNA with many Cs and Gs found one after the other, called a CpG island. Researchers have previously shown that the chromatin of CpG islands has two types of chemical markings—one that normally marks active genes, and another that often marks inactive genes. It was suggested that having both kinds of markings allows CpG islands to prime nearby genes, so that they are ready to be quickly switched on or off as the cell develops. However, the features of the DNA sequence in these CpG islands that are important for this process had not been directly tested. Wachter et al. have now inserted an artificial DNA sequence that included a CpG island into mouse stem cells. The chromatin around these CpG islands was readily marked with both activating and inactivating chemical marks. Furthermore, by changing the sequence of the artificial DNA, Wachter et al. revealed that these chemical marks were only added when the DNA sequences contained a lot of Cs followed by Gs. Other artificial sequences with lots of Cs and Gs, but where Gs were rarely found immediately after the Cs, had neither of the two chemical marks on the chromatin. This suggests that nearby genes would be harder to locate and activate as the cell grows and develops. On the other hand, when the DNA contained a lot of As and Ts, the chemical marks were added directly to the DNA (rather than to the chromatin)—and this prevented both the activating and the inactivating chemical marks being added to the chromatin. Now that the common features of CpG islands that influence chromatin are known, the next step is to find out how this is achieved. Further work will be needed to uncover which proteins in a cell interpret these DNA sequence such that nearby genes can be switched on or off. DOI:http://dx.doi.org/10.7554/eLife.03397.002
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Affiliation(s)
- Elisabeth Wachter
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Timo Quante
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Cara Merusi
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Aleksandra Arczewska
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Francis Stewart
- Genomics and Biotechnology Centre, Technische Universitaet Dresden, Dresden, Germany
| | - Shaun Webb
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Bird
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
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531
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Campos EI, Stafford JM, Reinberg D. Epigenetic inheritance: histone bookmarks across generations. Trends Cell Biol 2014; 24:664-74. [PMID: 25242115 DOI: 10.1016/j.tcb.2014.08.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/22/2022]
Abstract
Multiple circuitries ensure that cells respond correctly to the environmental cues within defined cellular programs. There is increasing evidence suggesting that cellular memory for these adaptive processes can be passed on through cell divisions and generations. However, the mechanisms by which this epigenetic information is transferred remain elusive, largely because it requires that such memory survive through gross chromatin remodeling events during DNA replication, mitosis, meiosis, and developmental reprogramming. Elucidating the processes by which epigenetic information survives and is transmitted is a central challenge in biology. In this review, we consider recent advances in understanding mechanisms of epigenetic inheritance with a focus on histone segregation at the replication fork, and how an epigenetic memory may get passed through the paternal lineage.
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Affiliation(s)
- Eric I Campos
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - James M Stafford
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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532
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Beck S, Lee BK, Kim J. Multi-layered global gene regulation in mouse embryonic stem cells. Cell Mol Life Sci 2014; 72:199-216. [PMID: 25227241 PMCID: PMC4284393 DOI: 10.1007/s00018-014-1734-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 02/05/2023]
Abstract
Embryonic stem (ES) cells derived from the inner cell mass of developing embryos have tremendous potential in regenerative medicine due to their unique properties: ES cells can be maintained for a prolonged time without changes in their cellular characteristics in vitro (self-renewal), while sustaining the capacity to give rise to all cell types of adult organisms (pluripotency). In addition to the development of protocols to manipulate ES cells for therapeutic applications, understanding how such unique properties are maintained has been one of the key questions in stem cell research. During the past decade, advances in high-throughput technologies have enabled us to systematically monitor multiple layers of gene regulatory mechanisms in ES cells. In this review, we briefly summarize recent findings on global gene regulatory modes in ES cells, mainly focusing on the regulatory factors responsible for transcriptional and epigenetic regulations as well as their modular regulatory patterns throughout the genome.
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Affiliation(s)
- Samuel Beck
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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533
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Rinaldi L, Benitah SA. Epigenetic regulation of adult stem cell function. FEBS J 2014; 282:1589-604. [PMID: 25060320 DOI: 10.1111/febs.12946] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 01/09/2023]
Abstract
Understanding the cellular and molecular mechanisms that specify cell lineages throughout development, and that maintain tissue homeostasis during adulthood, is paramount towards our understanding of why we age or develop pathologies such as cancer. Epigenetic mechanisms ensure that genetically identical cells acquire different fates during embryonic development and are therefore essential for the proper progression of development. How they do so is still a matter of intense investigation, but there is sufficient evidence indicating that they act in a concerted manner with inductive signals and tissue-specific transcription factors to promote and stabilize fate changes along the three germ layers during development. In consequence, it is generally hypothesized that epigenetic mechanisms are also required for the continuous maintenance of cell fate during adulthood. However, in vivo models in which different epigenetic factors have been depleted in different tissues do not show overt changes in cell lineage, thus not strongly supporting this view. Instead, the function of some of these factors appears to be primarily associated with tissue functionality, and a strong causal relationship has been established between their misregulation and a diseased state. In this review, we summarize our current knowledge of the role of epigenetic factors in adult stem cell function and tissue homeostasis.
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Affiliation(s)
- Lorenzo Rinaldi
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
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534
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Bowman SK, Deaton AM, Domingues H, Wang PI, Sadreyev RI, Kingston RE, Bender W. H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex. eLife 2014; 3:e02833. [PMID: 25082344 PMCID: PMC4139060 DOI: 10.7554/elife.02833] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The bithorax complex (BX-C) in Drosophila melanogaster is a cluster of homeotic genes that determine body segment identity. Expression of these genes is governed by cis-regulatory domains, one for each parasegment. Stable repression of these domains depends on Polycomb Group (PcG) functions, which include trimethylation of lysine 27 of histone H3 (H3K27me3). To search for parasegment-specific signatures that reflect PcG function, chromatin from single parasegments was isolated and profiled. The H3K27me3 profiles across the BX-C in successive parasegments showed a 'stairstep' pattern that revealed sharp boundaries of the BX-C regulatory domains. Acetylated H3K27 was broadly enriched across active domains, in a pattern complementary to H3K27me3. The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains lack H3K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely positioned H3K27 modifications as a central determinant of segment identity.
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Affiliation(s)
- Sarah K Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Aimee M Deaton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Heber Domingues
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Peggy I Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Pathology, Harvard Medical School, Boston, United States
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Welcome Bender
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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535
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Somatic embryogenesis - Stress-induced remodeling of plant cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:385-402. [PMID: 25038583 DOI: 10.1016/j.bbagrm.2014.07.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
Plants as sessile organisms have remarkable developmental plasticity ensuring heir continuous adaptation to the environment. An extreme example is somatic embryogenesis, the initiation of autonomous embryo development in somatic cells in response to exogenous and/or endogenous signals. In this review I briefly overview the various pathways that can lead to embryo development in plants in addition to the fertilization of the egg cell and highlight the importance of the interaction of stress- and hormone-regulated pathways during the induction of somatic embryogenesis. Somatic embryogenesis can be initiated in planta or in vitro, directly or indirectly, and the requirement for dedifferentiation as well as the way to achieve developmental totipotency in the various systems is discussed in light of our present knowledge. The initiation of all forms of the stress/hormone-induced in vitro as well as the genetically provoked in planta somatic embryogenesis requires extensive and coordinated genetic reprogramming that has to take place at the chromatin level, as the embryogenic program is under strong epigenetic repression in vegetative plant cells. Our present knowledge on chromatin-based mechanisms potentially involved in the somatic-to-embryogenic developmental transition is summarized emphasizing the potential role of the chromatin to integrate stress, hormonal, and developmental pathways leading to the activation of the embryogenic program. The role of stress-related chromatin reorganization in the genetic instability of in vitro cultures is also discussed. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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536
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Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep 2014; 7:1456-1470. [PMID: 24857660 PMCID: PMC4062935 DOI: 10.1016/j.celrep.2014.04.012] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/12/2014] [Accepted: 04/11/2014] [Indexed: 11/24/2022] Open
Abstract
The mechanisms by which the major Polycomb group (PcG) complexes PRC1 and PRC2 are recruited to target sites in vertebrate cells are not well understood. Building on recent studies that determined a reciprocal relationship between DNA methylation and Polycomb activity, we demonstrate that, in methylation-deficient embryonic stem cells (ESCs), CpG density combined with antagonistic effects of H3K9me3 and H3K36me3 redirects PcG complexes to pericentric heterochromatin and gene-rich domains. Surprisingly, we find that PRC1-linked H2A monoubiquitylation is sufficient to recruit PRC2 to chromatin in vivo, suggesting a mechanism through which recognition of unmethylated CpG determines the localization of both PRC1 and PRC2 at canonical and atypical target sites. We discuss our data in light of emerging evidence suggesting that PcG recruitment is a default state at licensed chromatin sites, mediated by interplay between CpG hypomethylation and counteracting H3 tail modifications. Absence of DNA methylation recruits Polycomb complexes to pericentric heterochromatin H3K9me3 antagonizes activity of PRC2, but not PRC1, at pericentric heterochromatin CpG density and antagonism by H3 modifications define genome-wide Polycomb occupancy PRC1-mediated H2AK119u1 recruits PRC2 and H3K27me3
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