101
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Analysis of Endogenous Protein Interactions of Polycomb Group of Proteins in Mouse Embryonic Stem Cells. Methods Mol Biol 2016. [PMID: 27659983 DOI: 10.1007/978-1-4939-6380-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
PRC1 complexes contain four core subunits: Pcgf, Phc, Ring1, and Cbx proteins. Interestingly, mammalian genomes have several paralogues for each subunit, which are differentially expressed depending on the cell type, differentiation program, and cellular stimuli. Therefore, identification and characterization of the specific architecture of different PRC1 complexes during cellular differentiation are essential to better understand the function and recruitment mechanism of PRC1 complexes. In this chapter we describe several methods to study Polycomb architecture, and identification of novel interactors in both pluripotent and differentiating mouse embryonic stem cells.
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102
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Abstract
The Keystone Symposium on Chromatin and Epigenetics, organized by Luciano Di Croce (Center for Genomic Regulation, Spain) and Yang Shi (Harvard Medical School, USA), took place 20 to 24 March 2016 at Whistler (British Columbia, Canada). The symposium brought together some of the most outstanding scientists studying how chromatin structure and epigenetic mechanisms regulate gene function in both development and disease. Junior scientists had the opportunity to interact with experienced researchers by presenting their work and discussing ideas and novel hypotheses. In order to foster interaction and networking, the scientific agenda was balanced with an extended social agenda. This meeting review describes several of the most provocative and exciting talks from the symposium, revealing how fast this research field is evolving and the profound impact it will have on human health.
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103
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Simandi Z, Horvath A, Wright LC, Cuaranta-Monroy I, De Luca I, Karolyi K, Sauer S, Deleuze JF, Gudas LJ, Cowley SM, Nagy L. OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation. Mol Cell 2016; 63:647-661. [PMID: 27499297 DOI: 10.1016/j.molcel.2016.06.039] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/07/2016] [Accepted: 06/30/2016] [Indexed: 01/30/2023]
Abstract
Cell type specification relies on the capacity of undifferentiated cells to properly respond to specific differentiation-inducing signals. Using genomic approaches along with loss- and gain-of-function genetic models, we identified OCT4-dependent mechanisms that provide embryonic stem cells with the means to customize their response to external cues. OCT4 binds a large set of low-accessible genomic regions. At these sites, OCT4 is required for proper enhancer and gene activation by recruiting co-regulators and RAR:RXR or β-catenin, suggesting an unexpected collaboration between the lineage-determining transcription factor and these differentiation-initiating, signal-dependent transcription factors. As a proof of concept, we demonstrate that overexpression of OCT4 in a kidney cell line is sufficient for signal-dependent activation of otherwise unresponsive genes in these cells. Our results uncover OCT4 as an integral and necessary component of signal-regulated transcriptional processes required for tissue-specific responses.
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Affiliation(s)
- Zoltan Simandi
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Lyndsey C Wright
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Isabella De Luca
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA
| | - Katalin Karolyi
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; CU Systems Medicine, University of Würzburg, 97070 Würzburg, Germany; Max Delbrück Center for Molecular Medicine (BISMB and BIH), 13125 Berlin, Germany
| | | | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Shaun M Cowley
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Laszlo Nagy
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; MTA-DE "Lendulet" Immunogenomics Research Group, University of Debrecen, 4032 Debrecen, Hungary.
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104
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Kloet SL, Makowski MM, Baymaz HI, van Voorthuijsen L, Karemaker ID, Santanach A, Jansen PWTC, Di Croce L, Vermeulen M. The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation. Nat Struct Mol Biol 2016; 23:682-690. [PMID: 27294783 PMCID: PMC4939079 DOI: 10.1038/nsmb.3248] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/17/2016] [Indexed: 12/16/2022]
Abstract
Although the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics and genome-wide profiling to study PcG proteins in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We found that the stoichiometry and genome-wide binding of PRC1 and PRC2 were highly dynamic during neural differentiation. Intriguingly, we observed a downregulation and loss of PRC2 from chromatin marked with trimethylated histone H3 K27 (H3K27me3) during differentiation, whereas PRC1 was retained at these sites. Additionally, we found PRC1 at enhancer and promoter regions independently of PRC2 binding and H3K27me3. Finally, overexpression of NPC-specific PRC1 interactors in ESCs led to increased Ring1b binding to, and decreased expression of, NPC-enriched Ring1b-target genes. In summary, our integrative analyses uncovered dynamic PcG subcomplexes and their widespread colocalization with active chromatin marks during differentiation.
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Affiliation(s)
- Susan L Kloet
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - H Irem Baymaz
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Lisa van Voorthuijsen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Ino D Karemaker
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Alexandra Santanach
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biomedical Genetics, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biomedical Genetics, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.,Cancer GenomiCs.nl (CGC.nl) Consortium, Center for Molecular Medicine, UMC Utrecht, The Netherlands
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105
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Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins. Trends Cell Biol 2016; 26:511-525. [PMID: 27198635 DOI: 10.1016/j.tcb.2016.04.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022]
Abstract
Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental regulatory genes. PcG proteins are recruited to specific regulatory elements to modify the chromatin surrounding them. In addition, they regulate the organization of their target genes in the 3D space of the nucleus, and this regulatory function of the 3D genome architecture is involved in cell differentiation and the maintenance of cellular memory. In this review we discuss recent advances in our understanding of how PcG proteins are recruited to chromatin to induce local and global changes in chromosome conformation and regulate their target genes.
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Affiliation(s)
- Marianne Entrevan
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
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106
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Emerging roles for Polycomb proteins in cancer. Curr Opin Genet Dev 2016; 36:50-8. [PMID: 27151431 DOI: 10.1016/j.gde.2016.03.013] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 03/31/2016] [Indexed: 12/22/2022]
Abstract
The activities of the heterogeneous Polycomb (PcG) group of proteins ensure that the developmental processes of proliferation and cellular identity establishment are carried out correctly. PcG proteins assemble stable multiprotein complexes that, together with additional factors, maintain their target genes in a transcriptionally repressive state. The biochemical and functional features of PcG proteins have been extensively investigated over the years. Here we analyse the biochemical and mechanistic proprieties of PcG proteins with respect to recent advances that link the genetic alterations of PcG activity to cancer development.
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107
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Si S, Nakajima-Takagi Y, Aoyama K, Oshima M, Saraya A, Sugishita H, Nakayama M, Ishikura T, Koseki H, Iwama A. Loss of Pcgf5 Affects Global H2A Monoubiquitination but Not the Function of Hematopoietic Stem and Progenitor Cells. PLoS One 2016; 11:e0154561. [PMID: 27136092 PMCID: PMC4852895 DOI: 10.1371/journal.pone.0154561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/17/2016] [Indexed: 12/11/2022] Open
Abstract
Polycomb-group RING finger proteins (Pcgf1-Pcgf6) are components of Polycomb repressive complex 1 (PRC1)-related complexes that catalyze monoubiquitination of histone H2A at lysine 119 (H2AK119ub1), an epigenetic mark associated with repression of genes. Pcgf5 has been characterized as a component of PRC1.5, one of the non-canonical PRC1, consisting of Ring1a/b, Rybp/Yaf2 and Auts2. However, the biological functions of Pcgf5 have not yet been identified. Here we analyzed the impact of the deletion of Pcgf5 specifically in hematopoietic stem and progenitor cells (HSPCs). Pcgf5 is expressed preferentially in hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) compared with committed myeloid progenitors and differentiated cells. We transplanted bone marrow (BM) cells from Rosa::Cre-ERT control and Cre-ERT;Pcgf5fl/fl mice into lethally irradiated recipient mice. At 4 weeks post-transplantation, we deleted Pcgf5 by injecting tamoxifen, however, no obvious changes in hematopoiesis were detected including the number of HSPCs during a long-term observation period following the deletion. Competitive BM repopulating assays revealed normal repopulating capacity of Pcgf5-deficient HSCs. Nevertheless, Pcgf5-deficient HSPCs showed a significant reduction in H2AK119ub1 levels compared with the control. ChIP-sequence analysis confirmed the reduction in H2AK119ub1 levels, but revealed no significant association of changes in H2AK119ub1 levels with gene expression levels. Our findings demonstrate that Pcgf5-containing PRC1 functions as a histone modifier in vivo, but its role in HSPCs is limited and can be compensated by other PRC1-related complexes in HSPCs.
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Affiliation(s)
- Sha Si
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yaeko Nakajima-Takagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazumasa Aoyama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motohiko Oshima
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsunori Saraya
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroki Sugishita
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 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 (IMS), Yokohama, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- * E-mail:
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108
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Zhou Y, Wang L, Vaseghi HR, Liu Z, Lu R, Alimohamadi S, Yin C, Fu JD, Wang GG, Liu J, Qian L. Bmi1 Is a Key Epigenetic Barrier to Direct Cardiac Reprogramming. Cell Stem Cell 2016; 18:382-95. [PMID: 26942853 PMCID: PMC4779178 DOI: 10.1016/j.stem.2016.02.003] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/01/2015] [Accepted: 02/12/2016] [Indexed: 02/08/2023]
Abstract
Direct reprogramming of induced cardiomyocytes (iCMs) suffers from low efficiency and requires extensive epigenetic repatterning, although the underlying mechanisms are largely unknown. To address these issues, we screened for epigenetic regulators of iCM reprogramming and found that reducing levels of the polycomb complex gene Bmi1 significantly enhanced induction of beating iCMs from neonatal and adult mouse fibroblasts. The inhibitory role of Bmi1 in iCM reprogramming is mediated through direct interactions with regulatory regions of cardiogenic genes, rather than regulation of cell proliferation. Reduced Bmi1 expression corresponded with increased levels of the active histone mark H3K4me3 and reduced levels of repressive H2AK119ub at cardiogenic loci, and de-repression of cardiogenic gene expression during iCM conversion. Furthermore, Bmi1 deletion could substitute for Gata4 during iCM reprogramming. Thus, Bmi1 acts as a critical epigenetic barrier to iCM production. Bypassing this barrier simplifies iCM generation and increases yield, potentially streamlining iCM production for therapeutic purposes.
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Affiliation(s)
- Yang Zhou
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haley Ruth Vaseghi
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ziqing Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sahar Alimohamadi
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Chaoying Yin
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ji-Dong Fu
- Department of Medicine, Heart and Vascular Research Center, MetroHealth Campus, Case Western Reserve University, Cleveland, OH 44109, USA
| | - Greg G Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA.
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109
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Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis. Cell Rep 2016; 14:332-46. [DOI: 10.1016/j.celrep.2015.12.034] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/26/2015] [Accepted: 12/04/2015] [Indexed: 12/18/2022] Open
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110
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Cohen I, Ezhkova E. Cbx4: A new guardian of p63's domain of epidermal control. J Cell Biol 2015; 212:9-11. [PMID: 26711501 PMCID: PMC4700485 DOI: 10.1083/jcb.201512032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023] Open
Abstract
Epigenetic regulators are essential for cell lineage choices during development. In this issue, Mardaryev et al. (2016. J. Cell Biol.http://dx.doi.org/10.1083/jcb.201506065) show that Polycomb subunit Cbx4 acts downstream of transcriptional regulator p63 to maintain epidermal progenitor identity and proliferation in the developing epidermis via Polycomb-dependent and -independent SUMO E3 ligase activities.
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Affiliation(s)
- Idan Cohen
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Elena Ezhkova
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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