151
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Polycomb complexes PRC1 and their function in hematopoiesis. Exp Hematol 2017; 48:12-31. [PMID: 28087428 DOI: 10.1016/j.exphem.2016.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 12/31/2022]
Abstract
Hematopoiesis, the process by which blood cells are continuously produced, is one of the best studied differentiation pathways. Hematological diseases are associated with reiterated mutations in genes encoding important gene expression regulators, including chromatin regulators. Among them, the Polycomb group (PcG) of proteins is an essential system of gene silencing involved in the maintenance of cell identities during differentiation. PcG proteins assemble into two major types of Polycomb repressive complexes (PRCs) endowed with distinct histone-tail-modifying activities. PRC1 complexes are histone H2A E3 ubiquitin ligases and PRC2 trimethylates histone H3. Established conceptions about their activities, mostly derived from work in embryonic stem cells, are being modified by new findings in differentiated cells. Here, we focus on PRC1 complexes, reviewing recent evidence on their intricate architecture, the diverse mechanisms of their recruitment to targets, and the different ways in which they engage in transcriptional control. We also discuss hematopoietic PRC1 gain- and loss-of-function mouse strains, including those that model leukemic and lymphoma diseases, in the belief that these genetic analyses provide the ultimate test for molecular mechanisms driving normal hematopoiesis and hematological malignancies.
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152
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H3K27 methylation: a promiscuous repressive chromatin mark. Curr Opin Genet Dev 2016; 43:31-37. [PMID: 27940208 DOI: 10.1016/j.gde.2016.11.001] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/21/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022]
Abstract
Polycomb Repressive Complex 2 (PRC2) is a multiprotein complex that catalyzes the methylation of lysine 27 on histone H3 (H3K27me). This histone modification is a feature of facultative heterochromatin in many eukaryotes and maintains transcriptional repression established during early development. Understanding how PRC2 targets regions of the genome to be methylated remains poorly understood. Different cell types can show disparate patterns of H3K27me, and chromatin perturbations, such as loss of marks of constitutive heterochromatin, can cause redistribution of H3K27me, implying that DNA sequence, per se, is not sufficient to define the distribution of this mark. Emerging information supports the idea that the chromatin context-including histone modifications, DNA methylation, transcription, chromatin structure and organization within the nucleus-informs PRC2 target selection.
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153
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Comet I, Riising EM, Leblanc B, Helin K. Maintaining cell identity: PRC2-mediated regulation of transcription and cancer. Nat Rev Cancer 2016; 16:803-810. [PMID: 27658528 DOI: 10.1038/nrc.2016.83] [Citation(s) in RCA: 316] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of Polycomb repressive complex 2 (PRC2), has attracted broad research attention in the past few years because of its involvement in the development and maintenance of many types of cancer and the use of specific EZH2 inhibitors in clinical trials. Several observations show that PRC2 can have both oncogenic and tumour-suppressive functions. We propose that these apparently opposing roles of PRC2 in cancer are a consequence of the molecular function of the complex in maintaining, rather than specifying, the transcriptional repression state of its several thousand target genes.
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Affiliation(s)
- Itys Comet
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Eva M Riising
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin Leblanc
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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154
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Cooper S, Grijzenhout A, Underwood E, Ancelin K, Zhang T, Nesterova TB, Anil-Kirmizitas B, Bassett A, Kooistra SM, Agger K, Helin K, Heard E, Brockdorff N. Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2. Nat Commun 2016; 7:13661. [PMID: 27892467 PMCID: PMC5133711 DOI: 10.1038/ncomms13661] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
The Polycomb repressive complexes PRC1 and PRC2 play a central role in developmental gene regulation in multicellular organisms. PRC1 and PRC2 modify chromatin by catalysing histone H2A lysine 119 ubiquitylation (H2AK119u1), and H3 lysine 27 methylation (H3K27me3), respectively. Reciprocal crosstalk between these modifications is critical for the formation of stable Polycomb domains at target gene loci. While the molecular mechanism for recognition of H3K27me3 by PRC1 is well defined, the interaction of PRC2 with H2AK119u1 is poorly understood. Here we demonstrate a critical role for the PRC2 cofactor Jarid2 in mediating the interaction of PRC2 with H2AK119u1. We identify a ubiquitin interaction motif at the amino-terminus of Jarid2, and demonstrate that this domain facilitates PRC2 localization to H2AK119u1 both in vivo and in vitro. Our findings ascribe a critical function to Jarid2 and define a key mechanism that links PRC1 and PRC2 in the establishment of Polycomb domains. The Polycomb repressive complexes PRC1 and PRC2 play a central role in developmental regulation of the genome in multicellular organisms. Here the authors describe how the PRC2 cofactor Jarid2 mediates the recruitment of the PRC2 complex to chromatin via interaction with H2AK119u1.
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Affiliation(s)
- Sarah Cooper
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anne Grijzenhout
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elizabeth Underwood
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Katia Ancelin
- Institut Curie, CNRS UMR3215, INSERM U934, 26 rue d'Ulm, Paris 75248, France
| | - Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tatyana B Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Burcu Anil-Kirmizitas
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Bassett
- Genome Engineering Oxford, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Susanne M Kooistra
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark.,Centre for Epigenetics, Ole Maaløes Vej 5, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Karl Agger
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark.,Centre for Epigenetics, Ole Maaløes Vej 5, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark.,Centre for Epigenetics, Ole Maaløes Vej 5, University of Copenhagen, 2200 Copenhagen, Denmark.,The Danish Stem Cell Center (Danstem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Edith Heard
- Institut Curie, CNRS UMR3215, INSERM U934, 26 rue d'Ulm, Paris 75248, France
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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155
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ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications. Methods Mol Biol 2016. [PMID: 27659973 DOI: 10.1007/978-1-4939-6380-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Chromatin Immunoprecipitation followed by massively parallel DNA sequencing (ChIP-sequencing) has emerged as an essential technique to study the genome-wide location of DNA- or chromatin-associated proteins, such as the Polycomb group (PcG) proteins. After being generated by the sequencer, raw ChIP-seq sequence reads need to be processed by a data analysis pipeline. Here we describe the computational steps required to process PcG ChIP-seq data, including alignment, peak calling, and downstream analysis.
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156
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Laugesen A, Højfeldt JW, Helin K. Role of the Polycomb Repressive Complex 2 (PRC2) in Transcriptional Regulation and Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026575. [PMID: 27449971 DOI: 10.1101/cshperspect.a026575] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The chromatin environment is modulated by a machinery of chromatin modifiers, required for the specification and maintenance of cell fate. Many mutations in the machinery have been linked to the development and progression of cancer. In this review, we give a brief introduction to Polycomb group (PcG) proteins, their assembly into Polycomb repressive complexes (PRCs) and the normal physiological roles of these complexes with a focus on the PRC2. We review the many findings of mutations in the PRC2 coding genes, both loss-of-function and gain-of-function, associated with human cancers and discuss potential molecular mechanisms involved in the contribution of PRC2 mutations to cancer development and progression. Finally, we discuss some of the recent advances in developing and testing drugs targeting the PRC2 as well as emerging results from clinical trials using these drugs in the treatment of human cancers.
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Affiliation(s)
- Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, DK-2200 Copenhagen N, Denmark The Danish Stem Cell Center (DanStem), University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jonas Westergaard Højfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, DK-2200 Copenhagen N, Denmark The Danish Stem Cell Center (DanStem), University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, DK-2200 Copenhagen N, Denmark The Danish Stem Cell Center (DanStem), University of Copenhagen, DK-2200 Copenhagen N, Denmark
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157
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Long HK, King HW, Patient RK, Odom DT, Klose RJ. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res 2016; 44:6693-706. [PMID: 27084945 PMCID: PMC5001583 DOI: 10.1093/nar/gkw258] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/09/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022] Open
Abstract
DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species.
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Affiliation(s)
- Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Roger K Patient
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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158
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Kinkley S, Helmuth J, Polansky JK, Dunkel I, Gasparoni G, Fröhler S, Chen W, Walter J, Hamann A, Chung HR. reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells. Nat Commun 2016; 7:12514. [PMID: 27530917 PMCID: PMC4992058 DOI: 10.1038/ncomms12514] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/11/2016] [Indexed: 01/06/2023] Open
Abstract
The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4(+) memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP-seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action.
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Affiliation(s)
- Sarah Kinkley
- Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Johannes Helmuth
- Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Julia K Polansky
- Experimental Rheumatology, German Rheumatism Research Center Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ilona Dunkel
- Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Gilles Gasparoni
- The Department of Genetics and Epigenetics, University of Saarland, Campus A2.4 66123 Saarbrücken, Germany
| | - Sebastian Fröhler
- The Laboratory of Functional Genomics and Systems Biology, Max Delbruck Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Wei Chen
- The Laboratory of Functional Genomics and Systems Biology, Max Delbruck Centrum for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Jörn Walter
- The Department of Genetics and Epigenetics, University of Saarland, Campus A2.4 66123 Saarbrücken, Germany
| | - Alf Hamann
- Experimental Rheumatology, German Rheumatism Research Center Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Ho-Ryun Chung
- Otto-Warburg-Laboratory: Epigenomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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159
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von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A. Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. Nat Neurosci 2016; 19:1321-30. [PMID: 27526204 PMCID: PMC5088783 DOI: 10.1038/nn.4360] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 12/13/2022]
Abstract
Normal brain function depends on the interaction between highly specialized neurons that operate within anatomically and functionally distinct brain regions. Neuronal specification is driven by transcriptional programs that are established during early neuronal development and remain in place in the adult brain. The fidelity of neuronal specification depends on the robustness of the transcriptional program that supports the neuron type-specific gene expression patterns. Here we show that polycomb repressive complex 2 (PRC2), which supports neuron specification during differentiation, contributes to the suppression of a transcriptional program that is detrimental to adult neuron function and survival. We show that PRC2 deficiency in striatal neurons leads to the de-repression of selected, predominantly bivalent PRC2 target genes that are dominated by self-regulating transcription factors normally suppressed in these neurons. The transcriptional changes in PRC2-deficient neurons lead to progressive and fatal neurodegeneration in mice. Our results point to a key role of PRC2 in protecting neurons against degeneration.
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Affiliation(s)
- Melanie von Schimmelmann
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip A Feinberg
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Josefa M Sullivan
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stacy M Ku
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Badimon
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary Kaye Duff
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zichen Wang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Scott Dewell
- Genomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ming-Hu Han
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York, USA
| | - Anne Schaefer
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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160
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Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet 2016; 12:e1006200. [PMID: 27466807 PMCID: PMC4965088 DOI: 10.1371/journal.pgen.1006200] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
Polycomb group response elements (PREs) in Drosophila are DNA-elements that recruit Polycomb proteins (PcG) to chromatin and regulate gene expression. PREs are easily recognizable in the Drosophila genome as strong peaks of PcG-protein binding over discrete DNA fragments; many small but statistically significant PcG peaks are also observed in PcG domains. Surprisingly, in vivo deletion of the four characterized strong PREs from the PcG regulated invected-engrailed (inv-en) gene complex did not disrupt the formation of the H3K27me3 domain and did not affect inv-en expression in embryos or larvae suggesting the presence of redundant PcG recruitment mechanism. Further, the 3D-structure of the inv-en domain was only minimally altered by the deletion of the strong PREs. A reporter construct containing a 7.5kb en fragment that contains three weak peaks but no large PcG peaks forms an H3K27me3 domain and is PcG-regulated. Our data suggests a model for the recruitment of PcG-complexes to Drosophila genes via interactions with multiple, weak PREs spread throughout an H3K27me3 domain.
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161
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Hosogane M, Funayama R, Shirota M, Nakayama K. Lack of Transcription Triggers H3K27me3 Accumulation in the Gene Body. Cell Rep 2016; 16:696-706. [PMID: 27396330 DOI: 10.1016/j.celrep.2016.06.034] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/07/2016] [Accepted: 06/05/2016] [Indexed: 10/21/2022] Open
Abstract
Trimethylated H3K27 (H3K27me3) is associated with transcriptional repression, and its abundance in chromatin is frequently altered in cancer. However, it has remained unclear how genomic regions modified by H3K27me3 are specified and formed. We previously showed that downregulation of transcription by oncogenic Ras signaling precedes upregulation of H3K27me3 level. Here, we show that lack of transcription as a result of deletion of the transcription start site of a gene is sufficient to increase H3K27me3 content in the gene body. We further found that histone deacetylation mediates Ras-induced gene silencing and subsequent H3K27me3 accumulation. The H3K27me3 level increased gradually after Ras activation, requiring at least 35 days to achieve saturation. Such maximal accumulation of H3K27me3 was reversed by forced induction of transcription with the dCas9-activator system. Thus, our results indicate that changes in H3K27me3 level, especially in the body of a subset of genes, are triggered by changes in transcriptional activity itself.
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Affiliation(s)
- Masaki Hosogane
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Sciences, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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162
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Piunti A, Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science 2016; 352:aad9780. [PMID: 27257261 DOI: 10.1126/science.aad9780] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression in metazoans is central for establishing cellular diversity, and its deregulation can result in pathological conditions. Although transcription factors are essential for implementing gene expression programs, they do not function in isolation and require the recruitment of various chromatin-modifying and -remodeling machineries. A classic example of developmental chromatin regulation is the balanced activities of the Polycomb group (PcG) proteins within the PRC1 and PRC2 complexes, and the Trithorax group (TrxG) proteins within the COMPASS family, which are highly mutated in a large number of human diseases. In this review, we will discuss the latest findings regarding the properties of the PcG and COMPASS families and the insight they provide into the epigenetic control of transcription under physiological and pathological settings.
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Affiliation(s)
- Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA.
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163
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Abstract
Ying Yang 1 (YY1) is a ubiquitously expressed transcription factor shown to be essential for pro-B-cell development. However, the role of YY1 in other B-cell populations has never been investigated. Recent bioinformatics analysis data have implicated YY1 in the germinal center (GC) B-cell transcriptional program. In accord with this prediction, we demonstrated that deletion of YY1 by Cγ1-Cre completely prevented differentiation of GC B cells and plasma cells. To determine if YY1 was also required for the differentiation of other B-cell populations, we deleted YY1 with CD19-Cre and found that all peripheral B-cell subsets, including B1 B cells, require YY1 for their differentiation. Transitional 1 (T1) B cells were the most dependent upon YY1, being sensitive to even a half-dosage of YY1 and also to short-term YY1 deletion by tamoxifen-induced Cre. We show that YY1 exerts its effects, in part, by promoting B-cell survival and proliferation. ChIP-sequencing shows that YY1 predominantly binds to promoters, and pathway analysis of the genes that bind YY1 show enrichment in ribosomal functions, mitochondrial functions such as bioenergetics, and functions related to transcription such as mRNA splicing. By RNA-sequencing analysis of differentially expressed genes, we demonstrated that YY1 normally activates genes involved in mitochondrial bioenergetics, whereas it normally down-regulates genes involved in transcription, mRNA splicing, NF-κB signaling pathways, the AP-1 transcription factor network, chromatin remodeling, cytokine signaling pathways, cell adhesion, and cell proliferation. Our results show the crucial role that YY1 plays in regulating broad general processes throughout all stages of B-cell differentiation.
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164
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Kong L, Tan L, Lv R, Shi Z, Xiong L, Wu F, Rabidou K, Smith M, He C, Zhang L, Qian Y, Ma D, Lan F, Shi Y, Shi YG. A primary role of TET proteins in establishment and maintenance of De Novo bivalency at CpG islands. Nucleic Acids Res 2016; 44:8682-8692. [PMID: 27288448 PMCID: PMC5062965 DOI: 10.1093/nar/gkw529] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
Ten Eleven Translocation (TET) protein-catalyzed 5mC oxidation not only creates novel DNA modifications, such as 5hmC, but also initiates active or passive DNA demethylation. TETs’ role in the crosstalk with specific histone modifications, however, is largely elusive. Here, we show that TET2-mediated DNA demethylation plays a primary role in the de novo establishment and maintenance of H3K4me3/H3K27me3 bivalent domains underlying methylated DNA CpG islands (CGIs). Overexpression of wild type (WT), but not catalytic inactive mutant (Mut), TET2 in low-TET-expressing cells results in an increase in the level of 5hmC with accompanying DNA demethylation at a subset of CGIs. Most importantly, this alteration is sufficient in making de novo bivalent domains at these loci. Genome-wide analysis reveals that these de novo synthesized bivalent domains are largely associated with a subset of essential developmental gene promoters, which are located within CGIs and are previously silenced due to DNA methylation. On the other hand, deletion of Tet1 and Tet2 in mouse embryonic stem (ES) cells results in an apparent loss of H3K27me3 at bivalent domains, which are associated with a particular set of key developmental gene promoters. Collectively, this study demonstrates the critical role of TET proteins in regulating the crosstalk between two key epigenetic mechanisms, DNA methylation and histone methylation (H3K4me3 and H3K27me3), particularly at CGIs associated with developmental genes.
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Affiliation(s)
- Lingchun Kong
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Li Tan
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Ruitu Lv
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zhennan Shi
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lijun Xiong
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Kimberlie Rabidou
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Smith
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Celestine He
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lei Zhang
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanyan Qian
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Duan Ma
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Fei Lan
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yang Shi
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China Division of Newborn Medicine, Children's Hospital Boston and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yujiang Geno Shi
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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165
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Pérez-Palacios R, Macías-Redondo S, Climent M, Contreras-Moreira B, Muniesa P, Schoorlemmer J. In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells. PLoS One 2016; 11:e0154268. [PMID: 27191592 PMCID: PMC4871433 DOI: 10.1371/journal.pone.0154268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 04/11/2016] [Indexed: 12/27/2022] Open
Abstract
Background Yin Yang 2 (YY2) is a zinc finger protein closely related to the well-characterized Yin Yang 1 (YY1). YY1 is a DNA-binding transcription factor, with defined functions in multiple developmental processes, such as implantation, cell differentiation, X inactivation, imprinting and organogenesis. Yy2 has been treated as a largely immaterial duplication of Yy1, as they share high homology in the Zinc Finger-region and similar if not identical in vitro binding sites. In contrast to these similarities, gene expression alterations in HeLa cells with attenuated levels of either Yy1 or Yy2 were to some extent gene-specific. Moreover, the chromatin binding sites for YY2, except for its association with transposable retroviral elements (RE) and Endogenous Retroviral Elements (ERVs), remain to be identified. As a first step towards defining potential Yy2 functions matching or complementary to Yy1, we considered in vivo DNA binding sites of YY2 in trophoblast stem (TS) cells. Results We report the presence of YY2 protein in mouse-derived embryonic stem (ES) and TS cell lines. Following up on our previous report on ERV binding by YY2 in TS cells, we investigated the tissue-specificity of REX1 and YY2 binding and confirm binding to RE/ERV targets in both ES cells and TS cells. Because of the higher levels of expression, we chose TS cells to understand the role of Yy2 in gene and chromatin regulation. We used in vivo YY2 association as a measure to identify potential target genes. Sequencing of chromatin obtained in chromatin-immunoprecipitation (ChIP) assays carried out with αYY2 serum allowed us to identify a limited number of chromatin targets for YY2. Some putative binding sites were validated in regular ChIP assays and gene expression of genes nearby was altered in the absence of Yy2. Conclusions YY2 binding to ERVs is not confined to TS cells. In vivo binding sites share the presence of a consensus binding motif. Selected sites were uniquely bound by YY2 as opposed to YY1, suggesting that YY2 exerts unique contributions to gene regulation. YY2 binding was not generally associated with gene promoters. However, several YY2 binding sites are linked to long noncoding RNA (lncRNA) genes and we show that the expression levels of a few of those are Yy2-dependent.
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Affiliation(s)
- Raquel Pérez-Palacios
- Instituto Aragonés de Ciencias de la Salud and Instituto de Investigación Sanitaria de Aragón (IIS-Aragón), Zaragoza, Spain
| | - Sofía Macías-Redondo
- Instituto Aragonés de Ciencias de la Salud and Instituto de Investigación Sanitaria de Aragón (IIS-Aragón), Zaragoza, Spain
| | - María Climent
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/ Miguel Servet 177, 50013 Zaragoza, Spain
| | - Bruno Contreras-Moreira
- ARAID Foundation, Zaragoza, Spain
- Estación Experimental de Aula Dei /CSIC, Av. Montañana 1.005, 50059 Zaragoza, Spain
| | - Pedro Muniesa
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/ Miguel Servet 177, 50013 Zaragoza, Spain
| | - Jon Schoorlemmer
- Instituto Aragonés de Ciencias de la Salud and Instituto de Investigación Sanitaria de Aragón (IIS-Aragón), Zaragoza, Spain
- ARAID Foundation, Zaragoza, Spain
- * E-mail:
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166
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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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167
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Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K, Fisher CL, Sibley CR, Foster BM, Bartke T, Ule J, Jenner RG. The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Res 2016; 26:896-907. [PMID: 27197219 PMCID: PMC4937559 DOI: 10.1101/gr.197632.115] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 05/05/2016] [Indexed: 12/17/2022]
Abstract
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon–intron boundaries and the 3′ UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, the release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.
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Affiliation(s)
- Manuel Beltran
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Christopher M Yates
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Lenka Skalska
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Marcus Dawson
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Filipa P Reis
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Keijo Viiri
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Cynthia L Fisher
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London WC1N 3BG, United Kingdom
| | - Benjamin M Foster
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Till Bartke
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London WC1N 3BG, United Kingdom
| | - Richard G Jenner
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
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168
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169
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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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170
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Pinter SF. A Tale of Two Cities: How Xist and its partners localize to and silence the bicompartmental X. Semin Cell Dev Biol 2016; 56:19-34. [PMID: 27072488 DOI: 10.1016/j.semcdb.2016.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
Sex chromosomal dosage compensation in mammals takes the form of X chromosome inactivation (XCI), driven by the non-coding RNA Xist. In contrast to dosage compensation systems of flies and worms, mammalian XCI has to restrict its function to the Xist-producing X chromosome, while leaving autosomes and active X untouched. The mechanisms behind the long-range yet cis-specific localization and silencing activities of Xist have long been enigmatic, but genomics, proteomics, super-resolution microscopy, and innovative genetic approaches have produced significant new insights in recent years. In this review, I summarize and integrate these findings with a particular focus on the redundant yet mutually reinforcing pathways that enable long-term transcriptional repression throughout the soma. This includes an exploration of concurrent epigenetic changes acting in parallel within two distinct compartments of the inactive X. I also examine how Polycomb repressive complexes 1 and 2 and macroH2A may bridge XCI establishment and maintenance. XCI is a remarkable phenomenon that operates across multiple scales, combining changes in nuclear architecture, chromosome topology, chromatin compaction, and nucleosome/nucleotide-level epigenetic cues. Learning how these pathways act in concert likely holds the answer to the riddle posed by Cattanach's and other autosomal translocations: What makes the X especially receptive to XCI?
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Affiliation(s)
- Stefan F Pinter
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-6403, USA.
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171
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Wang B, Yang Q, Harris CL, Nelson ML, Busboom JR, Zhu MJ, Du M. Nutrigenomic regulation of adipose tissue development - role of retinoic acid: A review. Meat Sci 2016; 120:100-106. [PMID: 27086067 DOI: 10.1016/j.meatsci.2016.04.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 12/17/2022]
Abstract
To improve the efficiency of animal production, livestock have been extensively selected or managed to reduce fat accumulation and increase lean growth, which reduces intramuscular or marbling fat content. To enhance marbling, a better understanding of the mechanisms regulating adipogenesis is needed. Vitamin A has recently been shown to have a profound impact on all stages of adipogenesis. Retinoic acid, an active metabolite of vitamin A, activates both retinoic acid receptors (RAR) and retinoid X receptors (RXR), inducing epigenetic changes in key regulatory genes governing adipogenesis. Additionally, Vitamin D and folates interact with the retinoic acid receptors to regulate adipogenesis. In this review, we discuss nutritional regulation of adipogenesis, focusing on retinoic acid and its impact on epigenetic modifications of key adipogenic genes.
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Affiliation(s)
- Bo Wang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, United States
| | - Qiyuan Yang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, United States
| | - Corrine L Harris
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, United States
| | - Mark L Nelson
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, United States
| | - Jan R Busboom
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, United States
| | - Mei-Jun Zhu
- School of Food Science, Washington State University, Pullman, WA 99164, United States
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, United States.
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172
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Panchin AY, Makeev VJ, Medvedeva YA. Preservation of methylated CpG dinucleotides in human CpG islands. Biol Direct 2016; 11:11. [PMID: 27005429 PMCID: PMC4804638 DOI: 10.1186/s13062-016-0113-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 03/14/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cytosine methylation in the CpG context. Meanwhile the CpG content in genomic regions called CpG islands (CGIs) is noticeably higher. This observation is usually explained by lower CpG > TpG substitution rates within CGIs due to reduced cytosine methylation levels. RESULTS By combining genome-wide data on substitutions and methylation levels in several human cell types we have shown that cytosine methylation in human sperm cells was strongly and consistently associated with increased CpG > TpG substitution rates. In contrast, this correlation was not observed for embryonic stem cells or fibroblasts. Surprisingly, the decreased sperm CpG methylation level was insufficient to explain the reduced CpG > TpG substitution rates in CGIs. CONCLUSIONS While cytosine methylation in human sperm cells is strongly associated with increased CpG > TpG substitution rates, substitution rates are significantly reduced within CGIs even after sperm CpG methylation levels and local GC content are controlled for. Our findings are consistent with strong negative selection preserving methylated CpGs within CGIs including intergenic ones.
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Affiliation(s)
- Alexander Y Panchin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, GSP-1, 119991, Russia.,Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia.,Moscow Institute of Physics and Technology, Moscow Regoin, 141700, Russia
| | - Yulia A Medvedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, GSP-1, 119991, Russia. .,Center for Bioengineering, Research Center of Biotechnology RAS, Russian Academy of Science, Moscow, 117312, Russia.
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173
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Campbell SA, Hoffman BG. Chromatin Regulators in Pancreas Development and Diabetes. Trends Endocrinol Metab 2016; 27:142-152. [PMID: 26783078 DOI: 10.1016/j.tem.2015.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 12/17/2022]
Abstract
The chromatin landscape of a cell is dynamic and can be altered by chromatin regulators that control nucleosome placement and DNA or histone modifications. Together with transcription factors, these complexes help dictate the transcriptional output of a cell and, thus, balance cell proliferation and differentiation while restricting tissue-specific gene expression. In this review, we describe current research on chromatin regulators and their roles in pancreas development and the maintenance of mature β cell function, which, once elucidated, will help us better understand how β cell differentiation occurs and is maintained. These studies have so far implicated proteins from several complexes that regulate DNA methylation, nucleosome remodeling, and histone acetylation and methylation that could become promising targets for diabetes therapy and stem cell differentiation.
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MESH Headings
- Animals
- Cell Differentiation
- Cell Proliferation
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/pathology
- Diabetes Mellitus, Type 1/physiopathology
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diabetes Mellitus, Type 2/physiopathology
- Epigenesis, Genetic
- Gene Expression Regulation, Developmental
- Histones/genetics
- Histones/metabolism
- Humans
- Insulin-Secreting Cells/cytology
- Insulin-Secreting Cells/metabolism
- Insulin-Secreting Cells/pathology
- Islets of Langerhans/cytology
- Islets of Langerhans/growth & development
- Islets of Langerhans/metabolism
- Islets of Langerhans/pathology
- Models, Biological
- Nucleosomes/metabolism
- Protein Processing, Post-Translational
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Affiliation(s)
- Stephanie A Campbell
- Child and Family Research Institute, British Columbia Children's Hospital and Sunny Hill Health Centre, 950 W28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Brad G Hoffman
- Child and Family Research Institute, British Columbia Children's Hospital and Sunny Hill Health Centre, 950 W28th Avenue, Vancouver, BC, V5Z 4H4, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 4E3, Canada.
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174
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Abstract
Differentiating somatic cells are progressively restricted to specialized functions during ontogeny, but they can be experimentally directed to form other cell types, including those with complete embryonic potential. Early nuclear reprogramming methods, such as somatic cell nuclear transfer (SCNT) and cell fusion, posed significant technical hurdles to precise dissection of the regulatory programmes governing cell identity. However, the discovery of reprogramming by ectopic expression of a defined set of transcription factors, known as direct reprogramming, provided a tractable platform to uncover molecular characteristics of cellular specification and differentiation, cell type stability and pluripotency. We discuss the control and maintenance of cellular identity during developmental transitions as they have been studied using direct reprogramming, with an emphasis on transcriptional and epigenetic regulation.
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175
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Walter M, Teissandier A, Pérez-Palacios R, Bourc'his D. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. eLife 2016; 5. [PMID: 26814573 PMCID: PMC4769179 DOI: 10.7554/elife.11418] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is extensively remodeled during mammalian gametogenesis and embryogenesis. Most transposons become hypomethylated, raising the question of their regulation in the absence of DNA methylation. To reproduce a rapid and extensive demethylation, we subjected mouse ES cells to chemically defined hypomethylating culture conditions. Surprisingly, we observed two phases of transposon regulation. After an initial burst of de-repression, various transposon families were efficiently re-silenced. This was accompanied by a reconfiguration of the repressive chromatin landscape: while H3K9me3 was stable, H3K9me2 globally disappeared and H3K27me3 accumulated at transposons. Interestingly, we observed that H3K9me3 and H3K27me3 occupy different transposon families or different territories within the same family, defining three functional categories of adaptive chromatin responses to DNA methylation loss. Our work highlights that H3K9me3 and, most importantly, polycomb-mediated H3K27me3 chromatin pathways can secure the control of a large spectrum of transposons in periods of intense DNA methylation change, ensuring longstanding genome stability.
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Affiliation(s)
- Marius Walter
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,Paris Science Lettres Research University, .,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France
| | - Aurélie Teissandier
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University, .,Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Paris, France.,Mines Paris Tech, Paris, France.,U900, Inserm, Paris, France
| | - Raquel Pérez-Palacios
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University,
| | - Déborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University,
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176
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EBNA3C Directs Recruitment of RBPJ (CBF1) to Chromatin during the Process of Gene Repression in EBV Infected B Cells. PLoS Pathog 2016; 12:e1005383. [PMID: 26751214 PMCID: PMC4708995 DOI: 10.1371/journal.ppat.1005383] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/14/2015] [Indexed: 12/05/2022] Open
Abstract
It is well established that Epstein-Barr virus nuclear antigen 3C (EBNA3C) can act as a potent repressor of gene expression, but little is known about the sequence of events occurring during the repression process. To explore further the role of EBNA3C in gene repression–particularly in relation to histone modifications and cell factors involved–the three host genes previously reported as most robustly repressed by EBNA3C were investigated. COBLL1, a gene of unknown function, is regulated by EBNA3C alone and the two co-regulated disintegrin/metalloproteases, ADAM28 and ADAMDEC1 have been described previously as targets of both EBNA3A and EBNA3C. For the first time, EBNA3C was here shown to be the main regulator of all three genes early after infection of primary B cells. Using various EBV-recombinants, repression over orders of magnitude was seen only when EBNA3C was expressed. Unexpectedly, full repression was not achieved until 30 days after infection. This was accurately reproduced in established LCLs carrying EBV-recombinants conditional for EBNA3C function, demonstrating the utility of the conditional system to replicate events early after infection. Using this system, detailed chromatin immunoprecipitation analysis revealed that the initial repression was associated with loss of activation-associated histone modifications (H3K9ac, H3K27ac and H3K4me3) and was independent of recruitment of polycomb proteins and deposition of the repressive H3K27me3 modification, which were only observed later in repression. Most remarkable, and in contrast to current models of RBPJ in repression, was the observation that this DNA-binding factor accumulated at the EBNA3C-binding sites only when EBNA3C was functional. Transient reporter assays indicated that repression of these genes was dependent on the interaction between EBNA3C and RBPJ. This was confirmed with a novel EBV-recombinant encoding a mutant of EBNA3C unable to bind RBPJ, by showing this virus was incapable of repressing COBLL1 or ADAM28/ADAMDEC1 in newly infected primary B cells. The Epstein-Barr nuclear protein EBNA3C is a well-characterised repressor of host gene expression in B cells growth-transformed by EBV. It is also well established that EBNA3C can interact with the cellular factor RBPJ, a DNA-binding factor in the Notch signalling pathway conserved from worms to humans. However, prior to this study, little was known about the role of the interaction between these two proteins during the repression of host genes. We therefore chose three genes–the expression of which is very robustly repressed by EBNA3C –to explore the molecular interactions involved. Hitherto these genes had not been shown to require RBPJ for EBNA3C-mediated repression. We have described the sequence of events during repression and challenge a widely held assumption that if a protein interacts with RBPJ it would be recruited to DNA because of the intrinsic capacity of RBPJ to bind specific sequences. We show that interaction with RBPJ is essential for the repression of all three genes during the infection of B cells by EBV, but that RBPJ itself is only recruited to the genes when EBNA3C is functional. These data suggest an unexpectedly complex interaction of multiple proteins when EBNA3C prevents the expression of cellular genes.
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177
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Putiri EL, Tiedemann RL, Liu C, Choi JH, Robertson KD. Impact of human MLL/COMPASS and polycomb complexes on the DNA methylome. Oncotarget 2015; 5:6338-52. [PMID: 25071008 PMCID: PMC4171634 DOI: 10.18632/oncotarget.2215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The correlation between DNA methylation and a subset of histone post-translational modifications (positive and negative) has hinted at an underlying regulatory crosstalk between histone marks and DNA methylation in patterning the human DNA methylome, an idea further supported by corresponding alterations to both histone marks and DNA methylation during malignant transformation. This study investigated the framework by which histone marks influence DNA methylation at a genome-wide level. Using RNAi in a pluripotent human embryonic carcinoma cell line we depleted essential components of the MLL/COMPASS, polycomb repressive complex 2 (PRC2), and PRC1 histone modifying complexes that establish, respectively, the post-translational modifications H3K4me3, H3K27me3, and H2AK119ub, and assayed the impact of the subsequent depletion of these marks on the DNA methylome. Absence of H2AK119ub resulted predominantly in hypomethylation across the genome. Depletion of H3K4me3 and, surprisingly, H3K27me3 caused CpG island hypermethylation at a subset of loci. Intriguingly, many promoters were co-regulated by all three histone marks, becoming hypermethylated with loss of H3K4me3 or H3K27me3 and hypomethylated with depletion of H2AK119ub, and many of these co-regulated loci were among those commonly targeted for aberrant hypermethylation in cancer. Taken together, our results elucidate novel roles for polycomb and MLL/COMPASS in regulating DNA methylation and define targets of this regulation.
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Affiliation(s)
- Emily L Putiri
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Rochelle L Tiedemann
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Cancer Center, Georgia Regents University, Augusta, GA
| | - Chunsheng Liu
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | - Jeong-Hyeon Choi
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN; Cancer Center, Georgia Regents University, Augusta, GA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN
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178
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Marino S, Di Foggia V. Invited Review: Polycomb group genes in the regeneration of the healthy and pathological skeletal muscle. Neuropathol Appl Neurobiol 2015; 42:407-22. [PMID: 26479276 DOI: 10.1111/nan.12290] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 10/14/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022]
Abstract
The polycomb group (PcG) proteins are epigenetic repressors required during key developmental processes, such as maintenance of cell identity and stem cell differentiation. To exert their repressive function, PcG proteins assemble on chromatin into multiprotein complexes, known as polycomb repressive complex 1 and 2. In this review, we will focus on the role and mode of function of PcG proteins in the development and regeneration of the skeletal muscle, both in normal and pathological conditions and we will discuss the emerging concept of modulation of their expression to enhance the muscle-specific regenerative process for patient benefit.
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Affiliation(s)
- S Marino
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - V Di Foggia
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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179
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Aranda S, Mas G, Di Croce L. Regulation of gene transcription by Polycomb proteins. SCIENCE ADVANCES 2015; 1:e1500737. [PMID: 26665172 PMCID: PMC4672759 DOI: 10.1126/sciadv.1500737] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/17/2015] [Indexed: 05/14/2023]
Abstract
The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Gloria Mas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. E-mail:
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180
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Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. Genome Biol 2015; 16:263. [PMID: 26607552 PMCID: PMC4659173 DOI: 10.1186/s13059-015-0827-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in each of these cell types. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating a mechanism involving altered TFBS occupancy. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0827-6) contains supplementary material, which is available to authorized users.
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181
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CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells. Sci Rep 2015; 5:16791. [PMID: 26582124 PMCID: PMC4652170 DOI: 10.1038/srep16791] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/14/2015] [Indexed: 12/24/2022] Open
Abstract
In embryonic stem (ES) cells, developmental regulators have a characteristic bivalent chromatin signature marked by simultaneous presence of both activation (H3K4me3) and repression (H3K27me3) signals and are thought to be in a 'poised' state for subsequent activation or silencing during differentiation. We collected eleven pairs (H3K4me3 and H3K27me3) of ChIP sequencing datasets in human ES cells and eight pairs in murine ES cells, and predicted high-confidence (HC) bivalent promoters. Over 85% of H3K27me3 marked promoters were bivalent in human and mouse ES cells. We found that (i) HC bivalent promoters were enriched for developmental factors and were highly likely to be differentially expressed upon transcription factor perturbation; (ii) murine HC bivalent promoters were occupied by both polycomb repressive component classes (PRC1 and PRC2) and grouped into four distinct clusters with different biological functions; (iii) HC bivalent and active promoters were CpG rich while H3K27me3-only promoters lacked CpG islands. Binding enrichment of distinct sets of regulators distinguished bivalent from active promoters. Moreover, a 'TCCCC' sequence motif was specifically enriched in bivalent promoters. Finally, this analysis will serve as a resource for future studies to further understand transcriptional regulation during embryonic development.
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182
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Moritz B, Becker PB, Göpfert U. CMV promoter mutants with a reduced propensity to productivity loss in CHO cells. Sci Rep 2015; 5:16952. [PMID: 26581326 PMCID: PMC4652263 DOI: 10.1038/srep16952] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/22/2015] [Indexed: 11/09/2022] Open
Abstract
The major immediate-early promoter and enhancer of the human cytomegalovirus (hCMV-MIE) is one of the most potent DNA elements driving recombinant gene expression in mammalian cells. Therefore, it is widely employed not only in research but also in large-scale industrial applications, e.g. for the production of therapeutic antibodies in Chinese hamster ovary cells (CHO). As we have reported previously, multi-site methylation of hCMV-MIE is linked to productivity loss in permanently transfected CHO cells lines. In particular, the cytosine located 179 bp upstream of the transcription start site (C-179) is frequently methylated. Therefore, our objective was to study whether mutation of C-179 and other cytosines within hCMV-MIE might lessen the instability of transgene expression. We discovered that the single mutation of C-179 to G can significantly stabilise the production of recombinant protein under control of hCMV-MIE in permanently transfected CHO cells.
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Affiliation(s)
- Benjamin Moritz
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Germany
| | - Peter B Becker
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig Maximilian University, Munich, Germany
| | - Ulrich Göpfert
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Germany
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183
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Brazel AJ, Vernimmen D. The complexity of epigenetic diseases. J Pathol 2015; 238:333-44. [PMID: 26419725 PMCID: PMC4982038 DOI: 10.1002/path.4647] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/10/2015] [Accepted: 09/21/2015] [Indexed: 12/29/2022]
Abstract
Over the past 30 years, a plethora of pathogenic mutations affecting enhancer regions and epigenetic regulators have been identified. Coupled with more recent genome‐wide association studies (GWAS) and epigenome‐wide association studies (EWAS) implicating major roles for regulatory mutations in disease, it is clear that epigenetic mechanisms represent important biomarkers for disease development and perhaps even therapeutic targets. Here, we discuss the diversity of disease‐causing mutations in enhancers and epigenetic regulators, with a particular focus on cancer. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ailbhe Jane Brazel
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian, UK
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184
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Chen PB, Chen HV, Acharya D, Rando OJ, Fazzio TG. R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol 2015; 22:999-1007. [PMID: 26551076 PMCID: PMC4677832 DOI: 10.1038/nsmb.3122] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
Numerous chromatin-remodeling factors are regulated by interactions with RNA, although the contexts and functions of RNA binding are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA, modulate the binding of two key chromatin regulatory complexes, Tip60–p400 and polycomb repressive complex 2 (PRC2) in mouse embryonic stem cells (ESCs). Like PRC2, the Tip60–p400 histone acetyltransferase complex binds to nascent transcripts, but unlike PRC2, transcription promotes chromatin binding by Tip60–p400. Interestingly, we observed higher Tip60–p400 and lower PRC2 levels at genes marked by promoter-proximal R-loops. Furthermore, disruption of R-loops broadly reduced Tip60–p400 and increased PRC2 occupancy genome-wide. Consistent with these alterations, ESCs with reduced R-loops exhibited impaired differentiation. These results show that R-loops act both positively and negatively to modulate the recruitment of key pluripotency regulators.
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Affiliation(s)
- Poshen B Chen
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Hsiuyi V Chen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diwash Acharya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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185
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Oravecz A, Apostolov A, Polak K, Jost B, Le Gras S, Chan S, Kastner P. Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2. Nat Commun 2015; 6:8823. [PMID: 26549758 PMCID: PMC4667618 DOI: 10.1038/ncomms9823] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/07/2015] [Indexed: 01/06/2023] Open
Abstract
T-cell development is accompanied by epigenetic changes that ensure the silencing of stem cell-related genes and the activation of lymphocyte-specific programmes. How transcription factors influence these changes remains unclear. We show that the Ikaros transcription factor forms a complex with Polycomb repressive complex 2 (PRC2) in CD4(-)CD8(-) thymocytes and allows its binding to more than 500 developmentally regulated loci, including those normally activated in haematopoietic stem cells and others induced by the Notch pathway. Loss of Ikaros in CD4(-)CD8(-) cells leads to reduced histone H3 lysine 27 trimethylation and ectopic gene expression. Furthermore, Ikaros binding triggers PRC2 recruitment and Ikaros interacts with PRC2 independently of the nucleosome remodelling and deacetylation complex. Our results identify Ikaros as a fundamental regulator of PRC2 function in developing T cells.
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Affiliation(s)
- Attila Oravecz
- Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 1 rue Laurent Fries, Illkirch 67404, France
| | - Apostol Apostolov
- Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 1 rue Laurent Fries, Illkirch 67404, France
| | - Katarzyna Polak
- Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 1 rue Laurent Fries, Illkirch 67404, France
| | - Bernard Jost
- IGBMC Microarray and Sequencing Platform, Illkirch 67404, France
| | | | - Susan Chan
- Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 1 rue Laurent Fries, Illkirch 67404, France
| | - Philippe Kastner
- Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 1 rue Laurent Fries, Illkirch 67404, France
- Faculté de Médecine, Université de Strasbourg, Strasbourg 67000, France
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186
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Blackledge NP, Rose NR, Klose RJ. Targeting Polycomb systems to regulate gene expression: modifications to a complex story. Nat Rev Mol Cell Biol 2015; 16:643-649. [PMID: 26420232 DOI: 10.1038/nrm4067.targeting] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Polycomb group proteins are transcriptional repressors that are essential for normal gene regulation during development. Recent studies suggest that Polycomb repressive complexes (PRCs) recognize and are recruited to their genomic target sites through a range of different mechanisms, which involve transcription factors, CpG island elements and non-coding RNAs. Together with the realization that the interplay between PRC1 and PRC2 is more intricate than was previously appreciated, this has increased our understanding of the vertebrate Polycomb system at the molecular level.
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Affiliation(s)
- Neil P Blackledge
- Department of Biochemistry, South Parks Road, University of Oxford, OX1 3QU
| | - Nathan R Rose
- Department of Biochemistry, South Parks Road, University of Oxford, OX1 3QU
| | - Robert J Klose
- Department of Biochemistry, South Parks Road, University of Oxford, OX1 3QU
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187
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Wu HC, Lin YC, Liu CH, Chung HC, Wang YT, Lin YW, Ma HI, Tu PH, Lawler SE, Chen RH. USP11 regulates PML stability to control Notch-induced malignancy in brain tumours. Nat Commun 2015; 5:3214. [PMID: 24487962 PMCID: PMC5645609 DOI: 10.1038/ncomms4214] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/07/2014] [Indexed: 01/31/2023] Open
Abstract
The promyelocytic leukaemia (PML) protein controls multiple tumour suppressive functions and is downregulated in diverse types of human cancers through incompletely characterized post-translational mechanisms. Here we identify USP11 as a PML regulator by RNAi screening. USP11 deubiquitinates and stabilizes PML, thereby counteracting the functions of PML ubiquitin ligases RNF4 and the KLHL20-Cul3 (Cullin 3)-Roc1 complex. We find that USP11 is transcriptionally repressed through a Notch/Hey1-dependent mechanism, leading to PML destabilization. In human glioma, Hey1 upregulation correlates with USP11 and PML downregulation and with high-grade malignancy. The Notch/Hey1-induced downregulation of USP11 and PML not only confers multiple malignant characteristics of aggressive glioma, including proliferation, invasiveness and tumour growth in an orthotopic mouse model, but also potentiates self-renewal, tumour-forming capacity and therapeutic resistance of patient-derived glioma-initiating cells. Our study uncovers a PML degradation mechanism through Notch/Hey1-induced repression of the PML deubiquitinase USP11 and suggests an important role for this pathway in brain tumour pathogenesis.
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Affiliation(s)
- Hsin-Chieh Wu
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lin
- 1] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan [2] Institute of Biochemical Sciences, National Taiwan University, Taipei 100, Taiwan
| | - Cheng-Hsin Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | | | - Ya-Ting Wang
- 1] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan [2] Institute of Biochemical Sciences, National Taiwan University, Taipei 100, Taiwan
| | - Ya-Wen Lin
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Department of Microbiology and Immunology, National Defense Medical Center, Taipei 114, Taiwan
| | - Hsin-I Ma
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Department of Neurological Surgery, Tri-service General Hospital, Taipei 114, Taiwan
| | - Pang-Hsien Tu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Sean E Lawler
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruey-Hwa Chen
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan [3] Institute of Biochemical Sciences, National Taiwan University, Taipei 100, Taiwan
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188
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The quest for mammalian Polycomb response elements: are we there yet? Chromosoma 2015; 125:471-96. [PMID: 26453572 PMCID: PMC4901126 DOI: 10.1007/s00412-015-0539-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
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189
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Sound of silence: the properties and functions of repressive Lys methyltransferases. Nat Rev Mol Cell Biol 2015. [PMID: 26204160 DOI: 10.1038/nrm4029] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The methylation of histone Lys residues by Lys methyltransferases (KMTs) regulates chromatin organization and either activates or represses gene expression, depending on the residue that is targeted. KMTs are emerging as key components in several cellular processes, and their deregulation is often associated with pathogenesis. Here, we review the current knowledge on the main KMTs that are associated with gene silencing: namely, those responsible for methylating histone H3 Lys 9 (H3K9), H3K27 and H4K20. We discuss their biochemical properties and the various mechanisms by which they are targeted to the chromatin and regulate gene expression, as well as new data on the interplay between them and other chromatin modifiers.
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190
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Targeting Polycomb systems to regulate gene expression: modifications to a complex story. Nat Rev Mol Cell Biol 2015; 16:643-649. [PMID: 26420232 DOI: 10.1038/nrm4067] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polycomb group proteins are transcriptional repressors that are essential for normal gene regulation during development. Recent studies suggest that Polycomb repressive complexes (PRCs) recognize and are recruited to their genomic target sites through a range of different mechanisms, which involve transcription factors, CpG island elements and non-coding RNAs. Together with the realization that the interplay between PRC1 and PRC2 is more intricate than was previously appreciated, this has increased our understanding of the vertebrate Polycomb system at the molecular level.
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191
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Maupetit-Méhouas S, Montibus B, Nury D, Tayama C, Wassef M, Kota SK, Fogli A, Cerqueira Campos F, Hata K, Feil R, Margueron R, Nakabayashi K, Court F, Arnaud P. Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive. Nucleic Acids Res 2015; 44:621-35. [PMID: 26400168 PMCID: PMC4737186 DOI: 10.1093/nar/gkv960] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/12/2015] [Indexed: 01/10/2023] Open
Abstract
Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly required for the process of imprinting and has to be faithfully maintained during the entire life-span. While the regulation of DNA methylation itself is well understood, the mechanisms whereby the opposite allele remains unmethylated are unclear. Here, we show that in the mouse, at maternally methylated ICRs, the paternal allele, which is constitutively associated with H3K4me2/3, is marked by default by H3K27me3 when these ICRs are transcriptionally inactive, leading to the formation of a bivalent chromatin signature. Our data suggest that at ICRs, chromatin bivalency has a protective role by ensuring that DNA on the paternal allele remains unmethylated and protected against spurious and unscheduled gene expression. Moreover, they provide the proof of concept that, beside pluripotent cells, chromatin bivalency is the default state of transcriptionally inactive CpG island promoters, regardless of the developmental stage, thereby contributing to protect cell identity.
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Affiliation(s)
- Stéphanie Maupetit-Méhouas
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Bertille Montibus
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - David Nury
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - 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
| | - Satya K Kota
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Anne Fogli
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Fabiana Cerqueira Campos
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Robert Feil
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Raphael 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
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Franck Court
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Philippe Arnaud
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
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192
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Khan AA, Lee AJ, Roh TY. Polycomb group protein-mediated histone modifications during cell differentiation. Epigenomics 2015; 7:75-84. [PMID: 25687468 DOI: 10.2217/epi.14.61] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins play an important role in the regulation of gene expression, especially genes encoding lineage-specific factors. Perturbations in PcG protein expression may trigger an unexpected developmental pathway, resulting in birth defects and developmental disabilities. Two Polycomb repressive complexes, PRC1 and PRC2, have been identified and are related with diverse cellular processes through histone modifications. Many developmental genes are trimethylated at histone H3 lysine 27 (H3K27me3) mediated by PRC2, which provides a binding site for PRC1. These processes contribute to chromatin compaction and transcriptional repression. In this review, we discuss about the complex formation of PcG proteins, the mechanism through which they are recruited to target sites and their functional roles in cell differentiation.
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Affiliation(s)
- Abdul Aziz Khan
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang, Gyeongbuk 790-784, Republic of Korea
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193
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Schwartz YB, Pirrotta V. Ruled by ubiquitylation: a new order for polycomb recruitment. Cell Rep 2015; 8:321-5. [PMID: 25061856 DOI: 10.1016/j.celrep.2014.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 11/20/2022] Open
Abstract
Polycomb complexes are found in most cells, but they must be targeted to specific genes in specific cell types in order to regulate pluripotency and differentiation. The recruitment of Polycomb complexes to specific targets has been widely thought to occur in two steps: first, one complex, PRC2, produces histone H3 lysine 27 (H3K27) trimethylation at a specific gene, and then the PRC1 complex is recruited by its ability to bind to H3K27me3. Now, three new articles turn this model upside-down by showing that binding of a variant PRC1 complex and subsequent H2A ubiquitylation of surrounding chromatin is sufficient to trigger the recruitment of PRC2 and H3K27 trimethylation. These studies also show that ubiquitylated H2A is directly sensed by PRC2 and that ablation of PRC1-mediated H2A ubiquitylation impairs genome-wide PRC2 binding and disrupts mouse development.
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Affiliation(s)
- Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Byggnad 6L, NUS, 901 87 Umeå, Sweden.
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA.
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194
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Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, Yi W, Zhou S, Chen T, Lu C, Atadja P, Liu XS, Li E, Zhang Y, Shou J. SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells. Genome Res 2015; 25:1325-35. [PMID: 26160163 PMCID: PMC4561491 DOI: 10.1101/gr.177576.114] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/08/2015] [Indexed: 11/25/2022]
Abstract
SETDB1, a histone methyltransferase responsible for methylation of histone H3 lysine 9 (H3K9), is involved in maintenance of embryonic stem (ES) cells and early embryonic development of the mouse. However, how SETDB1 regulates gene expression during development is largely unknown. Here, we characterized genome-wide SETDB1 binding and H3K9 trimethylation (H3K9me3) profiles in mouse ES cells and uncovered two distinct classes of SETDB1 binding sites, termed solo and ensemble peaks. The solo peaks were devoid of H3K9me3 and enriched near developmental regulators while the ensemble peaks were associated with H3K9me3. A subset of the SETDB1 solo peaks, particularly those near neural development–related genes, was found to be associated with Polycomb Repressive Complex 2 (PRC2) as well as PRC2-interacting proteins JARID2 and MTF2. Genetic deletion of Setdb1 reduced EZH2 binding as well as histone 3 lysine 27 (H3K27) trimethylation level at SETDB1 solo peaks and facilitated neural differentiation. Furthermore, we found that H3K27me3 inhibits SETDB1 methyltransferase activity. The currently identified reciprocal action between SETDB1 and PRC2 reveals a novel mechanism underlying ES cell pluripotency and differentiation regulation.
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Affiliation(s)
- Qi Fei
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Xiaoqin Yang
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hua Jiang
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Qian Wang
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yanyan Yu
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Yiling Yu
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Wei Yi
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Shaolian Zhou
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Taiping Chen
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA
| | - Chris Lu
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Peter Atadja
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Xiaole Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - En Li
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Yong Zhang
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jianyong Shou
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
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195
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Fukushige S, Horii A. Technological advances in epigenomics lead to a better understanding of inflammatory diseases, decitabine and H3K27me3. Epigenomics 2015; 7:133-6. [PMID: 25942529 DOI: 10.2217/epi.14.90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Shinichi Fukushige
- Department of Molecular Pathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
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196
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Bina M, Wyss P. Impact of the MLL1 morphemes on codon utilization and preservation in CpG Islands. Biopolymers 2015; 103:480-90. [PMID: 25991579 DOI: 10.1002/bip.22681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Phillip Wyss
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
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197
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Context-dependent actions of Polycomb repressors in cancer. Oncogene 2015; 35:1341-52. [DOI: 10.1038/onc.2015.195] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/15/2015] [Accepted: 05/05/2015] [Indexed: 12/21/2022]
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198
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Mozzetta C, Pontis J, Ait-Si-Ali S. Functional Crosstalk Between Lysine Methyltransferases on Histone Substrates: The Case of G9A/GLP and Polycomb Repressive Complex 2. Antioxid Redox Signal 2015; 22:1365-81. [PMID: 25365549 PMCID: PMC4432786 DOI: 10.1089/ars.2014.6116] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SIGNIFICANCE Methylation of histone H3 on lysine 9 and 27 (H3K9 and H3K27) are two epigenetic modifications that have been linked to several crucial biological processes, among which are transcriptional silencing and cell differentiation. RECENT ADVANCES Deposition of these marks is catalyzed by H3K9 lysine methyltransferases (KMTs) and polycomb repressive complex 2, respectively. Increasing evidence is emerging in favor of a functional crosstalk between these two major KMT families. CRITICAL ISSUES Here, we review the current knowledge on the mechanisms of action and function of these enzymes, with particular emphasis on their interplay in the regulation of chromatin states and biological processes. We outline their crucial roles played in tissue homeostasis, by controlling the fate of embryonic and tissue-specific stem cells, highlighting how their deregulation is often linked to the emergence of a number of malignancies and neurological disorders. FUTURE DIRECTIONS Histone methyltransferases are starting to be tested as drug targets. A new generation of highly selective chemical inhibitors is starting to emerge. These hold great promise for a rapid translation of targeting epigenetic drugs into clinical practice for a number of aggressive cancers and neurological disorders.
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Affiliation(s)
- Chiara Mozzetta
- Laboratoire Epigénétique et Destin Cellulaire, UMR7216, Centre National de la Recherche Scientifique CNRS, Université Paris Diderot , Sorbonne Paris Cité, Paris, France
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199
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Lee HG, Kahn TG, Simcox A, Schwartz YB, Pirrotta V. Genome-wide activities of Polycomb complexes control pervasive transcription. Genome Res 2015; 25:1170-81. [PMID: 25986499 PMCID: PMC4510001 DOI: 10.1101/gr.188920.114] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/15/2015] [Indexed: 11/24/2022]
Abstract
Polycomb group (PcG) complexes PRC1 and PRC2 are well known for silencing specific developmental genes. PRC2 is a methyltransferase targeting histone H3K27 and producing H3K27me3, essential for stable silencing. Less well known but quantitatively much more important is the genome-wide role of PRC2 that dimethylates ∼70% of total H3K27. We show that H3K27me2 occurs in inverse proportion to transcriptional activity in most non-PcG target genes and intergenic regions and is governed by opposing roaming activities of PRC2 and complexes containing the H3K27 demethylase UTX. Surprisingly, loss of H3K27me2 results in global transcriptional derepression proportionally greatest in silent or weakly transcribed intergenic and genic regions and accompanied by an increase of H3K27ac and H3K4me1. H3K27me2 therefore sets a threshold that prevents random, unscheduled transcription all over the genome and even limits the activity of highly transcribed genes. PRC1-type complexes also have global roles. Unexpectedly, we find a pervasive distribution of histone H2A ubiquitylated at lysine 118 (H2AK118ub) outside of canonical PcG target regions, dependent on the RING/Sce subunit of PRC1-type complexes. We show, however, that H2AK118ub does not mediate the global PRC2 activity or the global repression and is predominantly produced by a new complex involving L(3)73Ah, a homolog of mammalian PCGF3.
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Affiliation(s)
- Hun-Goo Lee
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Tatyana G Kahn
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA; Molecular Biology, Umeå University, NUS, 901 87 Umeå, Sweden
| | - Amanda Simcox
- Molecular Genetics, Ohio State University, Columbus, Ohio, USA
| | - Yuri B Schwartz
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA; Molecular Biology, Umeå University, NUS, 901 87 Umeå, Sweden
| | - Vincenzo Pirrotta
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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200
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Fowler T, Garruss AS, Ghosh A, De S, Becker KG, Wood WH, Weirauch MT, Smale ST, Aronow B, Sen R, Roy AL. Divergence of transcriptional landscape occurs early in B cell activation. Epigenetics Chromatin 2015; 8:20. [PMID: 25987903 PMCID: PMC4434543 DOI: 10.1186/s13072-015-0012-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/01/2015] [Indexed: 12/15/2022] Open
Abstract
Background Signaling via B cell receptor (BCR) and Toll-like receptors (TLRs) results in activation of B cells with distinct physiological outcomes, but transcriptional regulatory mechanisms that drive activation and distinguish these pathways remain unknown. Results Two hours after ligand exposure RNA-seq, ChIP-seq and computational methods reveal that BCR- or TLR-mediated activation of primary resting B cells proceeds via a large set of shared and a smaller subset of distinct signal-selective transcriptional responses. BCR stimulation resulted in increased global recruitment of RNA Pol II to promoters that appear to transit slowly to downstream regions. Conversely, lipopolysaccharide (LPS) stimulation involved an enhanced RNA Pol II transition from initiating to elongating mode accompanied by greater H3K4me3 activation markings compared to BCR stimulation. These rapidly diverging transcriptomic landscapes also show distinct repressing (H3K27me3) histone signatures, mutually exclusive transcription factor binding in promoters, and unique miRNA profiles. Conclusions Upon examination of genome-wide transcription and regulatory elements, we conclude that the B cell commitment to different activation states occurs much earlier than previously thought and involves a multi-faceted receptor-specific transcriptional landscape. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0012-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Trent Fowler
- Department of Developmental, Chemical and Molecular Biology, Sackler School of Biomedical Science, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111 USA
| | - Alexander S Garruss
- Wyss Institute for Biologically Inspired Engineering, Harvard University and Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Amalendu Ghosh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA
| | - Supriyo De
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA ; Gene Expression Unit, Laboratory of Genetics, National Institute on Aging, Baltimore, MD 21224 USA
| | - Kevin G Becker
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA ; Gene Expression Unit, Laboratory of Genetics, National Institute on Aging, Baltimore, MD 21224 USA
| | - William H Wood
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA ; Gene Expression Unit, Laboratory of Genetics, National Institute on Aging, Baltimore, MD 21224 USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095 USA
| | - Bruce Aronow
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA
| | - Ananda L Roy
- Department of Developmental, Chemical and Molecular Biology, Sackler School of Biomedical Science, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111 USA
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