1
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Vorobyeva NE, Krasnov AN, Erokhin M, Chetverina D, Mazina M. Su(Hw) interacts with Combgap to establish long-range chromatin contacts. Epigenetics Chromatin 2024; 17:17. [PMID: 38773468 PMCID: PMC11106861 DOI: 10.1186/s13072-024-00541-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear. RESULTS In this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators' binding. CONCLUSIONS This study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression.
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Affiliation(s)
- Nadezhda E Vorobyeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Marina Mazina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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2
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Gilbert G, Renaud Y, Teste C, Anglaret N, Bertrand R, Hoehn S, Jurkowski TP, Schuettengruber B, Cavalli G, Waltzer L, Vandel L. Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity. SCIENCE ADVANCES 2024; 10:eadn5861. [PMID: 38701218 PMCID: PMC11068012 DOI: 10.1126/sciadv.adn5861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS.
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Affiliation(s)
- Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Camille Teste
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Nadège Anglaret
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Sven Hoehn
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Tomasz P. Jurkowski
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
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3
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Brown JL, Zhang L, Rocha PP, Kassis JA, Sun MA. Polycomb protein binding and looping in the ON transcriptional state. SCIENCE ADVANCES 2024; 10:eadn1837. [PMID: 38657072 PMCID: PMC11042752 DOI: 10.1126/sciadv.adn1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
Polycomb group (PcG) proteins mediate epigenetic silencing of important developmental genes by modifying histones and compacting chromatin through two major protein complexes, PRC1 and PRC2. These complexes are recruited to DNA by CpG islands (CGIs) in mammals and Polycomb response elements (PREs) in Drosophila. When PcG target genes are turned OFF, PcG proteins bind to PREs or CGIs, and PREs serve as anchors that loop together and stabilize gene silencing. Here, we address which PcG proteins bind to PREs and whether PREs mediate looping when their targets are in the ON transcriptional state. While the binding of most PcG proteins decreases at PREs in the ON state, one PRC1 component, Ph, remains bound. Further, PREs can loop to each other and with presumptive enhancers in the ON state and, like CGIs, may act as tethering elements between promoters and enhancers. Overall, our data suggest that PREs are important looping elements for developmental loci in both the ON and OFF states.
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Affiliation(s)
- J. Lesley Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liangliang Zhang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pedro P. Rocha
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith A. Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
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4
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Bamgbose G, Tulin A. PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development. Life Sci Alliance 2024; 7:e202302369. [PMID: 38012002 PMCID: PMC10682175 DOI: 10.26508/lsa.202302369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
PARP-1 participates in various cellular processes, including gene regulation. In Drosophila, PARP-1 mutants undergo developmental arrest during larval-to-pupal transition. In this study, we investigated PARP-1 binding and its transcriptional regulatory role at this stage. Our findings revealed that PARP-1 binds and represses active metabolic genes, including glycolytic genes, whereas activating low-expression developmental genes, including a subset of "bivalent" genes in third-instar larvae. These bivalent promoters, characterized by dual enrichment of low H3K4me3 and high H3K27me3, a unimodal H3K4me1 enrichment at the transcription start site (conserved in C. elegans and zebrafish), H2Av depletion, and high accessibility, may persist throughout development. In PARP-1 mutant third-instar larvae, metabolic genes typically down-regulated during the larval-to-pupal transition in response to reduced energy needs were repressed by PARP-1. Simultaneously, developmental and bivalent genes typically active at this stage were activated by PARP-1. In addition, glucose and ATP levels were significantly reduced in PARP-1 mutants, suggesting an imbalance in metabolic regulation. We propose that PARP-1 is essential for maintaining the delicate balance between metabolic and developmental gene expression programs to ensure proper developmental progression.
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Affiliation(s)
- Gbolahan Bamgbose
- https://ror.org/04a5szx83 Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Alexei Tulin
- https://ror.org/04a5szx83 Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
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5
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Brown JL, Zhang L, Rocha PP, Kassis JA, Sun MA. Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565256. [PMID: 38076900 PMCID: PMC10705551 DOI: 10.1101/2023.11.02.565256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Polycomb group proteins (PcG) mediate epigenetic silencing of important developmental genes and other targets. In Drosophila, canonical PcG-target genes contain Polycomb Response Elements (PREs) that recruit PcG protein complexes including PRC2 that trimethylates H3K27 forming large H3K27me3 domains. In the OFF transcriptional state, PREs loop with each other and this looping strengthens silencing. Here we address the question of what PcG proteins bind to PREs when canonical PcG target genes are expressed, and whether PREs loop when these genes are ON. Our data show that the answer to this question is PRE-specific but general conclusions can be made. First, within a PcG-target gene, some regulatory DNA can remain covered with H3K27me3 and PcG proteins remain bound to PREs in these regions. Second, when PREs are within H3K27ac domains, PcG-binding decreases, however, this depends on the protein and PRE. The DNA binding protein GAF, and the PcG protein Ph remain at PREs even when other PcG proteins are greatly depleted. In the ON state, PREs can still loop with each other, but also form loops with presumptive enhancers. These data support the model that, in addition to their role in PcG silencing, PREs can act as "promoter-tethering elements" mediating interactions between promoter proximal PREs and distant enhancers.
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Affiliation(s)
- J. Lesley Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liangliang Zhang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pedro P Rocha
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Judith A. Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
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6
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Erokhin M, Mogila V, Lomaev D, Chetverina D. Polycomb Recruiters Inside and Outside of the Repressed Domains. Int J Mol Sci 2023; 24:11394. [PMID: 37511153 PMCID: PMC10379775 DOI: 10.3390/ijms241411394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/24/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The establishment and stable inheritance of individual patterns of gene expression in different cell types are required for the development of multicellular organisms. The important epigenetic regulators are the Polycomb group (PcG) and Trithorax group (TrxG) proteins, which control the silenced and active states of genes, respectively. In Drosophila, the PcG/TrxG group proteins are recruited to the DNA regulatory sequences termed the Polycomb response elements (PREs). The PREs are composed of the binding sites for different DNA-binding proteins, the so-called PcG recruiters. Currently, the role of the PcG recruiters in the targeting of the PcG proteins to PREs is well documented. However, there are examples where the PcG recruiters are also implicated in the active transcription and in the TrxG function. In addition, there is increasing evidence that the genome-wide PcG recruiters interact with the chromatin outside of the PREs and overlap with the proteins of differing regulatory classes. Recent studies of the interactomes of the PcG recruiters significantly expanded our understanding that they have numerous interactors besides the PcG proteins and that their functions extend beyond the regulation of the PRE repressive activity. Here, we summarize current data about the functions of the PcG recruiters.
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Affiliation(s)
- Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Vladic Mogila
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Dmitry Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
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7
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Erokhin M, Brown JL, Lomaev D, Vorobyeva NE, Zhang L, Fab L, Mazina M, Kulakovskiy I, Ziganshin R, Schedl P, Georgiev P, Sun MA, Kassis J, Chetverina D. Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila. Nucleic Acids Res 2023; 51:6087-6100. [PMID: 37140047 PMCID: PMC10325914 DOI: 10.1093/nar/gkad336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
The Polycomb group (PcG) proteins are fundamental epigenetic regulators that control the repressive state of target genes in multicellular organisms. One of the open questions is defining the mechanisms of PcG recruitment to chromatin. In Drosophila, the crucial role in PcG recruitment is thought to belong to DNA-binding proteins associated with Polycomb response elements (PREs). However, current data suggests that not all PRE-binding factors have been identified. Here, we report the identification of the transcription factor Crooked legs (Crol) as a novel PcG recruiter. Crol is a C2H2-type Zinc Finger protein that directly binds to poly(G)-rich DNA sequences. Mutation of Crol binding sites as well as crol CRISPR/Cas9 knockout diminish the repressive activity of PREs in transgenes. Like other PRE-DNA binding proteins, Crol co-localizes with PcG proteins inside and outside of H3K27me3 domains. Crol knockout impairs the recruitment of the PRC1 subunit Polyhomeotic and the PRE-binding protein Combgap at a subset of sites. The decreased binding of PcG proteins is accompanied by dysregulated transcription of target genes. Overall, our study identified Crol as a new important player in PcG recruitment and epigenetic regulation.
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Affiliation(s)
- Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - J Lesley Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitry Lomaev
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Nadezhda E Vorobyeva
- Group of transcriptional complexes dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liangliang Zhang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Lika V Fab
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Marina Yu Mazina
- Group of hormone-dependent transcription regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow119991, Russia
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Paul Schedl
- Department of Molecular Biology Princeton University, Princeton, NJ 08544, USA
| | - Pavel Georgiev
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
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8
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Solorzano J, Carrillo-de Santa Pau E, Laguna T, Busturia A. A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila. Dev Biol 2023; 495:63-75. [PMID: 36596335 DOI: 10.1016/j.ydbio.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 01/02/2023]
Abstract
Characterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore for the presence of gene regulatory circuits between two large groups of transcriptional regulators: the epigenetic group of the Polycomb/trithorax (PcG/trxG) proteins and the microRNAs (miRNAs). We have searched genome-wide for miRNA targets in PcG/trxG transcripts as well as for Polycomb Response Elements (PREs) in miRNA genes. Our results show that 10% of the analyzed miRNAs could be controlling PcG/trxG gene expression, while 40% of those miRNAs are putatively controlled by the selected set of PcG/trxG proteins. The integration of these analyses has resulted in the predicted existence of 3 classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits. In the first class, miRNA-PcG circuits are defined by miRNAs that reciprocally crosstalk with PcG. In the second, miRNA-trxG circuits are defined by miRNAs that reciprocally crosstalk with trxG. In the third class, miRNA-PcG/trxG shared circuits are defined by miRNAs that crosstalk with both PcG and trxG regulators. These putative regulatory circuits may uncover a novel mechanism in Drosophila for the control of PcG/trxG and miRNAs levels of expression. The computational framework developed here for Drosophila melanogaster can serve as a model case for similar analyses in other species. Moreover, our work provides, for the first time, a new and useful resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression.
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Affiliation(s)
- Jacobo Solorzano
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, 28049, Madrid, Spain; Centre de Recherches en Cancerologie de Toulouse, 2 Av. Hubert Curien, 31100, Toulouse, France
| | - Enrique Carrillo-de Santa Pau
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, CEI UAM+CSIC, 28049, Madrid, Spain
| | - Teresa Laguna
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, CEI UAM+CSIC, 28049, Madrid, Spain.
| | - Ana Busturia
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, 28049, Madrid, Spain.
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9
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Herman N, Kadener S, Shifman S. The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes. EMBO Rep 2022; 23:e54720. [PMID: 36245419 PMCID: PMC9724677 DOI: 10.15252/embr.202254720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Insulator proteins located at the boundaries of topological associated domains (TAD) are involved in higher-order chromatin organization and transcription regulation. However, it is still not clear how long-range contacts contribute to transcriptional regulation. Here, we show that relative-of-WOC (ROW) is essential for the long-range transcription regulation mediated by the boundary element-associated factor of 32kD (BEAF-32). We find that ROW physically interacts with heterochromatin proteins (HP1b and HP1c) and the insulator protein (BEAF-32). These proteins interact at TAD boundaries where ROW, through its AT-hook motifs, binds AT-rich sequences flanked by BEAF-32-binding sites and motifs. Knockdown of row downregulates genes that are long-range targets of BEAF-32 and bound indirectly by ROW (without binding motif). Analyses of high-throughput chromosome conformation capture (Hi-C) data reveal long-range interactions between promoters of housekeeping genes bound directly by ROW and promoters of developmental genes bound indirectly by ROW. Thus, our results show cooperation between BEAF-32 and the ROW complex, including HP1 proteins, to regulate the transcription of developmental and inducible genes through long-range interactions.
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Affiliation(s)
- Neta Herman
- Department of Genetics, The Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Sagiv Shifman
- Department of Genetics, The Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
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10
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Chetverina DA, Gorbenko FV, Lomaev DV, Georgiev PG, Erokhin MM. Recruitment to Chromatin of (GA)n-Associated Factors GAF and Psq in the Transgenic Model System Depends on the Presence of Architectural Protein Binding Sites. DOKL BIOCHEM BIOPHYS 2022; 506:210-214. [DOI: 10.1134/s1607672922050039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/05/2022]
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11
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Chetverina D, Vorobyeva NE, Mazina MY, Fab LV, Lomaev D, Golovnina A, Mogila V, Georgiev P, Ziganshin RH, Erokhin M. Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins. Cell Mol Life Sci 2022; 79:353. [PMID: 35676368 PMCID: PMC11072172 DOI: 10.1007/s00018-022-04383-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/14/2022] [Accepted: 05/08/2022] [Indexed: 01/08/2023]
Abstract
The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling the silenced and active states of genes in multicellular organisms, respectively. In Drosophila, PcG/TrxG proteins are recruited to the chromatin via binding to specific DNA sequences termed polycomb response elements (PREs). While precise mechanisms of the PcG/TrxG protein recruitment remain unknown, the important role is suggested to belong to sequence-specific DNA-binding factors. At the same time, it was demonstrated that the PRE DNA-binding proteins are not exclusively localized to PREs but can bind other DNA regulatory elements, including enhancers, promoters, and boundaries. To gain an insight into the PRE DNA-binding protein regulatory network, here, using ChIP-seq and immuno-affinity purification coupled to the high-throughput mass spectrometry, we searched for differences in abundance of the Combgap, Zeste, Psq, and Adf1 PRE DNA-binding proteins. While there were no conspicuous differences in co-localization of these proteins with other functional transcription factors, we show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste, and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia.
| | - Nadezhda E Vorobyeva
- Group of Dynamics of Transcriptional Complexes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina Yu Mazina
- Group of Hormone-Dependent Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Lika V Fab
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Dmitry Lomaev
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Alexandra Golovnina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Vladic Mogila
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Pavel Georgiev
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia.
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12
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Levo M, Raimundo J, Bing XY, Sisco Z, Batut PJ, Ryabichko S, Gregor T, Levine MS. Transcriptional coupling of distant regulatory genes in living embryos. Nature 2022; 605:754-760. [PMID: 35508662 PMCID: PMC9886134 DOI: 10.1038/s41586-022-04680-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 03/23/2022] [Indexed: 02/01/2023]
Abstract
The prevailing view of metazoan gene regulation is that individual genes are independently regulated by their own dedicated sets of transcriptional enhancers. Past studies have reported long-range gene-gene associations1-3, but their functional importance in regulating transcription remains unclear. Here we used quantitative single-cell live imaging methods to provide a demonstration of co-dependent transcriptional dynamics of genes separated by large genomic distances in living Drosophila embryos. We find extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases. Regulatory interconnectivity depends on promoter-proximal tethering elements, and perturbations in these elements uncouple transcription and alter the bursting dynamics of distant genes, suggesting a role of genome topology in the formation and stability of co-transcriptional hubs. Transcriptional coupling is detected throughout the fly genome and encompasses a broad spectrum of conserved developmental processes, suggesting a general strategy for long-range integration of gene activity.
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Affiliation(s)
- Michal Levo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - João Raimundo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xin Yang Bing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zachary Sisco
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Philippe J. Batut
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sergey Ryabichko
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA,Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, Paris, France,Corresponding authors
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Corresponding authors
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13
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Owen BM, Davidovich C. DNA binding by polycomb-group proteins: searching for the link to CpG islands. Nucleic Acids Res 2022; 50:4813-4839. [PMID: 35489059 PMCID: PMC9122586 DOI: 10.1093/nar/gkac290] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/25/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Polycomb group proteins predominantly exist in polycomb repressive complexes (PRCs) that cooperate to maintain the repressed state of thousands of cell-type-specific genes. Targeting PRCs to the correct sites in chromatin is essential for their function. However, the mechanisms by which PRCs are recruited to their target genes in mammals are multifactorial and complex. Here we review DNA binding by polycomb group proteins. There is strong evidence that the DNA-binding subunits of PRCs and their DNA-binding activities are required for chromatin binding and CpG targeting in cells. In vitro, CpG-specific binding was observed for truncated proteins externally to the context of their PRCs. Yet, the mere DNA sequence cannot fully explain the subset of CpG islands that are targeted by PRCs in any given cell type. At this time we find very little structural and biophysical evidence to support a model where sequence-specific DNA-binding activity is required or sufficient for the targeting of CpG-dinucleotide sequences by polycomb group proteins while they are within the context of their respective PRCs, either PRC1 or PRC2. We discuss the current knowledge and open questions on how the DNA-binding activities of polycomb group proteins facilitate the targeting of PRCs to chromatin.
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Affiliation(s)
- Brady M Owen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.,EMBL-Australia, Clayton, VIC, Australia
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14
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Vijayanathan M, Trejo-Arellano MG, Mozgová I. Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective. EPIGENOMES 2022; 6:3. [PMID: 35076495 PMCID: PMC8788455 DOI: 10.3390/epigenomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
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Affiliation(s)
- Mallika Vijayanathan
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - María Guadalupe Trejo-Arellano
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - Iva Mozgová
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
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15
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Erokhin MM, Shidlovskii YV, Lomaev DV, Georgiev PG, Chetverina DA. Sfmbt Co-purifies with Hangover and SWI/SNF-Remodelers in Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2021; 500:304-307. [PMID: 34697732 DOI: 10.1134/s1607672921050069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022]
Abstract
Polycomb group (PcG) proteins are chromatin-associated factors involved in the repression of gene transcription. In the present study, we characterized the interactome of the Sfmbt factor at the embryonic stage of development. For this, the Sfmbt protein complex was affinity purified from the nuclear extract, followed by highly specific peptide sequencing (IP/LC-MS). As a result, a number of previously uncharacterized Sfmbt interactions were discovered. In particular, Sfmbt top-interacting proteins include the DNA-binding protein Hangover and components of the SWI/SNF family of chromatin remodelers.
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Affiliation(s)
- M M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Y V Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - D V Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - P G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - D A Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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16
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Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation. Sci Rep 2021; 11:16963. [PMID: 34417521 PMCID: PMC8379230 DOI: 10.1038/s41598-021-96488-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/11/2021] [Indexed: 11/11/2022] Open
Abstract
Suppressor of Hairy wing [Su(Hw)] is an insulator protein that participates in regulating chromatin architecture and gene repression in Drosophila. In previous studies we have shown that Su(Hw) is also required for pre-replication complex (pre-RC) recruitment on Su(Hw)-bound sites (SBSs) in Drosophila S2 cells and pupa. Here, we describe the effect of Su(Hw) on developmentally regulated amplification of 66D and 7F Drosophila amplicons in follicle cells (DAFCs), widely used as models in replication studies. We show Su(Hw) binding co-localizes with all known DAFCs in Drosophila ovaries, whereas disruption of Su(Hw) binding to 66D and 7F DAFCs causes a two-fold decrease in the amplification of these loci. The complete loss of Su(Hw) binding to chromatin impairs pre-RC recruitment to all amplification regulatory regions of 66D and 7F loci at early oogenesis (prior to DAFCs amplification). These changes coincide with a considerable Su(Hw)-dependent condensation of chromatin at 66D and 7F loci. Although we observed the Brm, ISWI, Mi-2, and CHD1 chromatin remodelers at SBSs genome wide, their remodeler activity does not appear to be responsible for chromatin decondensation at the 66D and 7F amplification regulatory regions. We have discovered that, in addition to the CBP/Nejire and Chameau histone acetyltransferases, the Gcn5 acetyltransferase binds to 66D and 7F DAFCs at SBSs and this binding is dependent on Su(Hw). We propose that the main function of Su(Hw) in developmental amplification of 66D and 7F DAFCs is to establish a chromatin structure that is permissive to pre-RC recruitment.
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17
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Erokhin M, Gorbenko F, Lomaev D, Mazina MY, Mikhailova A, Garaev AK, Parshikov A, Vorobyeva NE, Georgiev P, Schedl P, Chetverina D. Boundaries potentiate polycomb response element-mediated silencing. BMC Biol 2021; 19:113. [PMID: 34078365 PMCID: PMC8170967 DOI: 10.1186/s12915-021-01047-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Background Epigenetic memory plays a critical role in the establishment and maintenance of cell identities in multicellular organisms. Polycomb and trithorax group (PcG and TrxG) proteins are responsible for epigenetic memory, and in flies, they are recruited to specialized DNA regulatory elements termed polycomb response elements (PREs). Previous transgene studies have shown that PREs can silence reporter genes outside of their normal context, often by pairing sensitive (PSS) mechanism; however, their silencing activity is non-autonomous and depends upon the surrounding chromatin context. It is not known why PRE activity depends on the local environment or what outside factors can induce silencing. Results Using an attP system in Drosophila, we find that the so-called neutral chromatin environments vary substantially in their ability to support the silencing activity of the well-characterized bxdPRE. In refractory chromosomal contexts, factors required for PcG-silencing are unable to gain access to the PRE. Silencing activity can be rescued by linking the bxdPRE to a boundary element (insulator). When placed next to the PRE, the boundaries induce an alteration in chromatin structure enabling factors critical for PcG silencing to gain access to the bxdPRE. When placed at a distance from the bxdPRE, boundaries induce PSS by bringing the bxdPREs on each homolog in close proximity. Conclusion This proof-of-concept study demonstrates that the repressing activity of PREs can be induced or enhanced by nearby boundary elements. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01047-8.
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Affiliation(s)
- Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Fedor Gorbenko
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.,Present address: Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dmitry Lomaev
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Marina Yu Mazina
- Group of Transcriptional Complexes Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mikhailova
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Azat K Garaev
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Aleksander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Nadezhda E Vorobyeva
- Group of Transcriptional Complexes Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Paul Schedl
- Department of Molecular Biology Princeton University, Princeton, NJ, 08544, USA.
| | - Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
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18
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Postika N, Schedl P, Georgiev P, Kyrchanova O. Mapping of functional elements of the Fab-6 boundary involved in the regulation of the Abd-B hox gene in Drosophila melanogaster. Sci Rep 2021; 11:4156. [PMID: 33603202 PMCID: PMC7892861 DOI: 10.1038/s41598-021-83734-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
The autonomy of segment-specific regulatory domains in the Bithorax complex is conferred by boundary elements and associated Polycomb response elements (PREs). The Fab-6 boundary is located at the junction of the iab-5 and iab-6 domains. Previous studies mapped it to a nuclease hypersensitive region 1 (HS1), while the iab-6 PRE was mapped to a second hypersensitive region HS2 nearly 3 kb away. To analyze the role of HS1 and HS2 in boundary we generated deletions of HS1 or HS1 + HS2 that have attP site for boundary replacement experiments. The 1389 bp HS1 deletion can be rescued by a 529 bp core Fab-6 sequence that includes two CTCF sites. However, Fab-6 HS1 cannot rescue the HS1 + HS2 deletion or substitute for another BX-C boundary - Fab-7. For this it must be combined with a PRE, either Fab-7 HS3, or Fab-6 HS2. These findings suggest that the boundary function of Fab-6 HS1 must be bolstered by a second element that has PRE activity.
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Affiliation(s)
- Nikolay Postika
- grid.419021.f0000 0004 0380 8267Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, Russia 119334
| | - Paul Schedl
- grid.419021.f0000 0004 0380 8267Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, Russia 119334 ,grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Pavel Georgiev
- grid.419021.f0000 0004 0380 8267Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, Russia 119334
| | - Olga Kyrchanova
- grid.419021.f0000 0004 0380 8267Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, Russia 119334 ,grid.419021.f0000 0004 0380 8267Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow, Russia 119334
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19
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Chetverina DA, Lomaev DV, Erokhin MM. Polycomb and Trithorax Group Proteins: The Long Road from Mutations in Drosophila to Use in Medicine. Acta Naturae 2020; 12:66-85. [PMID: 33456979 PMCID: PMC7800605 DOI: 10.32607/actanaturae.11090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved factors responsible for the repression and activation of the transcription of multiple genes in Drosophila and mammals. Disruption of the PcG/TrxG expression is associated with many pathological conditions, including cancer, which makes them suitable targets for diagnosis and therapy in medicine. In this review, we focus on the major PcG and TrxG complexes, the mechanisms of PcG/TrxG action, and their recruitment to chromatin. We discuss the alterations associated with the dysfunction of a number of factors of these groups in oncology and the current strategies used to develop drugs based on small-molecule inhibitors.
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Affiliation(s)
- D. A. Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D. V. Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - M. M. Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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20
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Soluri IV, Zumerling LM, Payan Parra OA, Clark EG, Blythe SA. Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. eLife 2020; 9:e53916. [PMID: 32347792 PMCID: PMC7190358 DOI: 10.7554/elife.53916] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/20/2022] Open
Abstract
Because chromatin determines whether information encoded in DNA is accessible to transcription factors, dynamic chromatin states in development may constrain how gene regulatory networks impart embryonic pattern. To determine the interplay between chromatin states and regulatory network function, we performed ATAC-seq on Drosophila embryos during the establishment of the segmentation network, comparing wild-type and mutant embryos in which all graded maternal patterning inputs are eliminated. While during the period between zygotic genome activation and gastrulation many regions maintain stable accessibility, cis-regulatory modules (CRMs) within the network undergo extensive patterning-dependent changes in accessibility. A component of the network, Odd-paired (opa), is necessary for pioneering accessibility of late segmentation network CRMs. opa-driven changes in accessibility are accompanied by equivalent changes in gene expression. Interfering with the timing of opa activity impacts the proper patterning of expression. These results indicate that dynamic systems for chromatin regulation directly impact the reading of embryonic patterning information.
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Affiliation(s)
- Isabella V Soluri
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Lauren M Zumerling
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Omar A Payan Parra
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
- Department of Neurobiology, Northwestern UniversityEvanstonUnited States
| | - Eleanor G Clark
- Program in Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
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21
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Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects. J Biosci 2020. [DOI: 10.1007/s12038-019-9975-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Srinivasan A, Mishra RK. Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects. J Biosci 2020; 45:12. [PMID: 31965990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The epigenetic memory is an essential aspect of multicellular organisms to maintain several cell types and their gene expression pattern. This complex process uses a number of protein factors and specific DNA elements within the developmental cues to achieve this. The protein factors involved in the process are the Polycomb group (PcG) members, and, accordingly, the DNA sequences that interact with these proteins are called Polycomb Response Elements (PREs). Since the PcG proteins are highly conserved among higher eukaryotes, including insects, and function at thousands of sites in the genomes, it is expected that PREs mayalso be present across the genome.However, the studies on PREs in insect species, other thanDrosophila, is currently lacking.We took a bioinformatics approach to develop an inclusive PRE prediction tool, 'PRE Mapper', to address this need. By applying this tool on the Drosophila melanogaster genome, we predicted greater than 20,000 PREs.When comparedwith the available PRE prediction methods, this tool shows far better performance by correctly identifying the in vivo binding sites of PcG proteins, identified by genome-scale ChIP experiments. Further analysis of the predicted PREs shows their cohabitation with chromatin domain boundary elements at several places in the Drosophila genome, possibly defining a composite epigenetic module.We analysed 10 insect genomes in this context and find several conserved features in PREs across the insect species with some variations in their occurrence frequency. These analyses leading to the identification of PREin insect genomes contribute to our understanding of epigenetic mechanisms in these organisms.
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Affiliation(s)
- Arumugam Srinivasan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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23
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Bredesen BA, Rehmsmeier M. DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements. Nucleic Acids Res 2019; 47:7781-7797. [PMID: 31340029 PMCID: PMC6735708 DOI: 10.1093/nar/gkz617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/01/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Polycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the seven motifs previously used, PREs are enriched in the GTGT motif, recently associated with the sequence-specific DNA binding protein Combgap. We investigated whether models trained on genome-wide Polycomb sites generalize to independent PREs when trained with control sequences generated by naive PRE models and including the GTGT motif. We also developed a new PRE predictor: SVM-MOCCA. Training PRE predictors with genome-wide experimental data improves generalization to independent data, and SVM-MOCCA predicts the majority of PREs in three independent experimental sets. We present 2908 candidate PREs enriched in sequence and chromatin signatures. 2412 of these are also enriched in H3K4me1, a mark of Trithorax activated chromatin, suggesting that PREs/TREs have a common sequence code.
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Affiliation(s)
- Bjørn André Bredesen
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway
| | - Marc Rehmsmeier
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway.,Integrated Research Institute (IRI) for the Life Sciences and Department of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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24
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Cheutin T, Cavalli G. The multiscale effects of polycomb mechanisms on 3D chromatin folding. Crit Rev Biochem Mol Biol 2019; 54:399-417. [PMID: 31698957 DOI: 10.1080/10409238.2019.1679082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins silence master regulatory genes required to properly confer cell identity during the development of both Drosophila and mammals. They may act through chromatin compaction and higher-order folding of chromatin inside the cell nucleus. During the last decade, analysis on interphase chromosome architecture discovered self-interacting regions named topologically associated domains (TADs). TADs result from the 3D chromatin folding of a succession of transcribed and repressed epigenomic domains and from loop extrusion mediated by cohesin/CTCF in mammals. Polycomb silenced chromatin constitutes one type of repressed epigenomic domains which form compacted nano-compartments inside cell nuclei. Recruitment of canonical PcG proteins on chromatin relies on initial binding to discrete elements and further spreading into large chromatin domains covered with H3K27me3. Some of these discrete elements have a bivalent nature both in mammals and Drosophila and are dynamically regulated during development. Loops can occur between them, suggesting that their interaction plays both functional and structural roles. Formation of large chromatin domains covered by H3K27me3 seems crucial for PcG silencing and PcG proteins might exert their function through compaction of these domains in both mammals and flies, rather than by directly controlling the nucleosomal accessibility of discrete regulatory elements. In addition, PcG chromatin domains interact over long genomic distances, shaping a higher-order chromatin network. Therefore, PcG silencing might rely on multiscale chromatin folding to maintain cell identity during differentiation.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
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25
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Vidal M. Polycomb Assemblies Multitask to Regulate Transcription. EPIGENOMES 2019; 3:12. [PMID: 34968234 PMCID: PMC8594731 DOI: 10.3390/epigenomes3020012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 02/06/2023] Open
Abstract
The Polycomb system is made of an evolutionary ancient group of proteins, present throughout plants and animals. Known initially from developmental studies with the fly Drosophila melanogaster, they were associated with stable sustainment of gene repression and maintenance of cell identity. Acting as multiprotein assemblies with an ability to modify chromatin, through chemical additions to histones and organization of topological domains, they have been involved subsequently in control of developmental transitions and in cell homeostasis. Recent work has unveiled an association of Polycomb components with transcriptionally active loci and the promotion of gene expression, in clear contrast with conventional recognition as repressors. Focusing on mammalian models, I review here advances concerning roles in transcriptional control. Among new findings highlighted is the regulation of their catalytic properties, recruiting to targets, and activities in chromatin organization and compartmentalization. The need for a more integrated approach to the study of the Polycomb system, given its fundamental complexity and its adaptation to cell context, is discussed.
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Affiliation(s)
- Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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26
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Burlin AI, Tillib SV. Differentially Expressed Long Noncoding RNAs in the Promoter Region of the fork head Gene in Drosophila melanogaster Detected by Northern Blot Hybridization. Mol Biol 2019. [DOI: 10.1134/s0026893319030038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tian K, Henderson RE, Parker R, Brown A, Johnson JE, Bateman JR. Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans. PLoS Genet 2019; 15:e1008152. [PMID: 31075100 PMCID: PMC6530868 DOI: 10.1371/journal.pgen.1008152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 04/23/2019] [Indexed: 01/10/2023] Open
Abstract
For many genes, proper gene expression requires coordinated and dynamic interactions between multiple regulatory elements, each of which can either promote or silence transcription. In Drosophila, the complexity of the regulatory landscape is further complicated by the tight physical pairing of homologous chromosomes, which can permit regulatory elements to interact in trans, a phenomenon known as transvection. To better understand how gene expression can be programmed through cis- and trans-regulatory interactions, we analyzed transvection effects for a collection of alleles of the eyes absent (eya) gene. We find that trans-activation of a promoter by the eya eye-specific enhancers is broadly supported in many allelic backgrounds, and that the availability of an enhancer to act in trans can be predicted based on the molecular lesion of an eya allele. Furthermore, by manipulating promoter availability in cis and in trans, we demonstrate that the eye-specific enhancers of eya show plasticity in their promoter preference between two different transcriptional start sites, which depends on promoter competition between the two potential targets. Finally, we show that certain alleles of eya demonstrate pairing-sensitive silencing resulting from trans-interactions between Polycomb Response Elements (PREs), and genetic and genomic data support a general role for PcG proteins in mediating transcriptional silencing at eya. Overall, our data highlight how eya gene regulation relies upon a complex but plastic interplay between multiple enhancers, promoters, and PREs. Gene regulation requires interactions between regions of DNA known as regulatory elements, which, in combination, determine where and when a gene will be active or silenced. Some genes use just a few regulatory elements, whereas others rely on highly complex interactions between many different elements that are poorly understood. While we typically imagine regulatory elements interacting with one another along the length of a single chromosome, in a curious phenomenon called transvection, elements can communicate between two different chromosomes that are held in close proximity. Here, we use the study of transvection to better understand how different regulatory elements contribute to the expression of eyes absent (eya), a gene required for proper eye development in Drosophila. Our data show that a class of elements that initiate eya gene expression, called promoters, will compete with one another for activation by eya’s enhancers, a second class of regulatory element, with the promoter that is closest to the enhancers being the favored target for activation. Furthermore, our study of transvection uncovers an important role for a silencing element, called a PRE, in opposing eya gene expression. Overall, our study sheds new light on how different elements combine to produce patterned expression of eya.
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Affiliation(s)
- Katherine Tian
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Rachel E. Henderson
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Reyna Parker
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Alexia Brown
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Justine E. Johnson
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
| | - Jack R. Bateman
- Biology Department, Bowdoin College, Brunswick, Maine, United States of America
- * E-mail:
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Sadasivam DA, Huang DH. Feedback regulation by antagonistic epigenetic factors potentially maintains developmental homeostasis in Drosophila. J Cell Sci 2018; 131:jcs.210179. [PMID: 29661849 DOI: 10.1242/jcs.210179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 04/04/2018] [Indexed: 01/09/2023] Open
Abstract
Drosophila Polycomb group (PcG) repressors confer epigenetically heritable silencing on key regulatory genes through histone H3 trimethylation on lysine 27 (H3K27me3). How the silencing state withstands antagonistic activities from co-expressed trithorax group (trxG) activators is unclear. Upon overexpression of Trx H3K4 methylase, to perturb the silenced state, we find a dynamic process triggered in a stepwise fashion to neutralize the inductive impacts from excess Trx. Shortly after Trx overexpression, there are global increases in H3K4 trimethylation and RNA polymerase II phosphorylation, marking active transcription. Subsequently, these patterns diminish at the same time as the levels of Set1, an abundant H3K4 methylase involved in productive transcription, reduce. Concomitantly, the global H3K27me3 level is markedly reduced, corresponding to an increase in the amount of Utx demethylase. Finally, excess Pc repressive complex 1 (PRC1) is induced and located to numerous ectopic chromosomal sites independently of H3K27me3 and several key recruitment factors. The observation that PRC1 becomes almost completely colocalized with Trx suggests new aspects of recruitment and antagonistic interaction. We propose that these events represent a feedback circuitry ensuring the stability of the silenced state.
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Affiliation(s)
| | - Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529
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Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho. Proc Natl Acad Sci U S A 2018; 115:E1839-E1848. [PMID: 29432187 DOI: 10.1073/pnas.1716299115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA binding "PcG recruiters," including Pho, Cg, and Spps. To understand their roles in PcG recruitment, we compared Pho-, Cg-, and Spps-binding sites against H3K27me3 and key PcG proteins by ChIP-seq in wild-type and mutant third instar larvae. H3K27me3 in canonical Polycomb domains is decreased after the reduction of any recruiter. Reduction of Spps and Pho, but not Cg, causes the redistribution of H3K27me3 to heterochromatin. Regions with dramatically depleted H3K27me3 after Spps knockout are usually accompanied by decreased Pho binding, suggesting their cooperative binding. PcG recruiters, the PRC2 component E(z), and the PRC1 components Psc and Ph cobind thousands of active genes outside of H3K27me3 domains. This study demonstrates the importance of distinct PcG recruiters for the establishment of unique Polycomb domains. Different PcG recruiters can act both cooperatively and independently at specific PcG target genes, highlighting the complexity and diversity of PcG recruitment mechanisms.
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Khan S, Iqbal M, Tariq M, Baig SM, Abbas W. Epigenetic regulation of HIV-1 latency: focus on polycomb group (PcG) proteins. Clin Epigenetics 2018; 10:14. [PMID: 29441145 PMCID: PMC5800276 DOI: 10.1186/s13148-018-0441-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/05/2018] [Indexed: 01/10/2023] Open
Abstract
HIV-1 latency allows the virus to persist until reactivation, in a transcriptionally silent form in its cellular reservoirs despite the presence of effective cART. Such viral persistence represents a major barrier to HIV eradication since treatment interruption leads to rebound plasma viremia. Polycomb group (PcG) proteins have recently got a considerable attention in regulating HIV-1 post-integration latency as they are involved in the repression of proviral gene expression through the methylation of histones. This epigenetic regulation plays an important role in the establishment and maintenance of HIV-1 latency. In fact, PcG proteins act in complexes and modulate the epigenetic signatures of integrated HIV-1 promoter. Key role played by PcG proteins in the molecular control of HIV-1 latency has led to hypothesize that PcG proteins may represent a valuable target for future HIV-1 therapy in purging HIV-1 reservoirs. In this regard, various small molecules have been synthesized or explored to specifically block the epigenetic activity of PcG. In this review, we will highlight the possible therapeutic approaches to achieve either a functional or sterilizing cure of HIV-1 infection with special focus on histone methylation by PcG proteins together with current and novel pharmacological approaches to reactivate HIV-1 from latency that could ultimately lead towards a better clearance of viral latent reservoirs.
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Affiliation(s)
- Sheraz Khan
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Tariq
- Department of Biology (Epigenetics group), SBA School of Science and Engineering, LUMS, Lahore, 54792 Pakistan
| | - Shahid M. Baig
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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Davis TL, Rebay I. Pleiotropy in Drosophila organogenesis: Mechanistic insights from Combgap and the retinal determination gene network. Fly (Austin) 2018; 12:62-70. [PMID: 29125381 DOI: 10.1080/19336934.2017.1402994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Master regulatory transcription factors cooperate in networks to shepherd cells through organogenesis. In the Drosophila eye, a collection of master control proteins known as the retinal determination gene network (RDGN) switches the direction and targets of its output to choreograph developmental transitions, but the molecular partners that enable such regulatory flexibility are not known. We recently showed that two RDGN members, Eyes absent (Eya) and Sine oculis (So), promote exit from the terminal cell cycle known as the second mitotic wave (SMW) to permit differentiation. A search for co-factors identified the ubiquitously expressed Combgap (Cg) as a novel transcriptional partner that impedes cell cycle exit and interferes with Eya-So activity specifically in this context. Here, we argue that Cg acts as a flexible transcriptional platform that contributes to numerous gene expression outcomes by a variety of mechanisms. For example, Cg provides repressive activities that dampen Eya-So output, but not by recruiting Polycomb chromatin-remodeling complexes as it does in other contexts. We propose that master regulators depend on both specifically expressed co-factors that assemble the combinatorial code and broadly expressed partners like Cg that recruit the diverse molecular activities needed to appropriately regulate their target enhancers.
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Affiliation(s)
- Trevor L Davis
- a Committee on Development, Regeneration, and Stem Cell Biology , University of Chicago , Chicago , IL , USA
| | - Ilaria Rebay
- a Committee on Development, Regeneration, and Stem Cell Biology , University of Chicago , Chicago , IL , USA.,b Ben May Department for Cancer Research , University of Chicago , Chicago , IL , USA
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33
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Abstract
The question of how noncoding RNAs are involved in Polycomb group (PcG) and Trithorax group (TrxG) regulation has been on an extraordinary journey over the last three decades. Favored models have risen and fallen, and healthy debates have swept back and forth. The field has recently reached a critical mass of compelling data that throws light on several previously unresolved issues. The time is ripe for a fruitful combination of these findings with two other long-running avenues of research, namely the biochemical properties of the PcG/TrxG system and the application of theoretical mathematical models toward an understanding of the system's regulatory properties. I propose that integrating our current knowledge of noncoding RNA into a quantitative biochemical and theoretical framework for PcG and TrxG regulation has the potential to reconcile several apparently conflicting models and identifies fascinating questions for future research.
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Affiliation(s)
- Leonie Ringrose
- Integrated Research Institute for Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
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Kassis JA, Kennison JA, Tamkun JW. Polycomb and Trithorax Group Genes in Drosophila. Genetics 2017; 206:1699-1725. [PMID: 28778878 PMCID: PMC5560782 DOI: 10.1534/genetics.115.185116] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/15/2017] [Indexed: 01/08/2023] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) genes encode important regulators of development and differentiation in metazoans. These two groups of genes were discovered in Drosophila by their opposing effects on homeotic gene (Hox) expression. PcG genes collectively behave as genetic repressors of Hox genes, while the TrxG genes are necessary for HOX gene expression or function. Biochemical studies showed that many PcG proteins are present in two protein complexes, Polycomb repressive complexes 1 and 2, which repress transcription via chromatin modifications. TrxG proteins activate transcription via a variety of mechanisms. Here we summarize the large body of genetic and biochemical experiments in Drosophila on these two important groups of genes.
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Affiliation(s)
- Judith A Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - James A Kennison
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - John W Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
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35
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Davis TL, Rebay I. Antagonistic regulation of the second mitotic wave by Eyes absent-Sine oculis and Combgap coordinates proliferation and specification in the Drosophila retina. Development 2017; 144:2640-2651. [PMID: 28619818 DOI: 10.1242/dev.147231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/08/2017] [Indexed: 12/12/2022]
Abstract
The transition from proliferation to specification is fundamental to the development of appropriately patterned tissues. In the developing Drosophila eye, Eyes absent (Eya) and Sine oculis (So) orchestrate the progression of progenitor cells from asynchronous cell division to G1 arrest and neuronal specification at the morphogenetic furrow. Here, we uncover a novel role for Eya and So in promoting cell cycle exit in the second mitotic wave (SMW), a synchronized, terminal cell division that occurs several hours after passage of the furrow. We show that Combgap (Cg), a zinc-finger transcription factor, antagonizes Eya-So function in the SMW. Based on the ability of Cg to attenuate Eya-So transcriptional output in vivo and in cultured cells and on meta analysis of their chromatin occupancy profiles, we speculate that Cg limits Eya-So activation of select target genes posterior to the furrow to ensure properly timed mitotic exit. Our work supports a model in which context-specific modulation of transcriptional activity enables Eya and So to promote both entry into and exit from the cell cycle in a distinct spatiotemporal sequence.
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Affiliation(s)
- Trevor L Davis
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ilaria Rebay
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA .,Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
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36
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Dissecting chromatin-mediated gene regulation and epigenetic memory through mathematical modelling. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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37
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Erceg J, Pakozdi T, Marco-Ferreres R, Ghavi-Helm Y, Girardot C, Bracken AP, Furlong EEM. Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements. Genes Dev 2017; 31:590-602. [PMID: 28381411 PMCID: PMC5393054 DOI: 10.1101/gad.292870.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/03/2017] [Indexed: 11/24/2022]
Abstract
Here, Erceg et al. studied the occupancy of the Drosophila PhoRC during embryogenesis and revealed extensive co-occupancy at developmental enhancers. By using an established in vivo assay for Polycomb response element (PRE) activity, they show that a subset of characterized developmental enhancers can function as PREs and silence transcription in a Polycomb-dependent manner, thereby suggesting that reuse of the same elements by the PcG system may help fine-tune gene expression and ensure the timely maintenance of cell identities. Developmental gene expression is tightly regulated through enhancer elements, which initiate dynamic spatio–temporal expression, and Polycomb response elements (PREs), which maintain stable gene silencing. These two cis-regulatory functions are thought to operate through distinct dedicated elements. By examining the occupancy of the Drosophila pleiohomeotic repressive complex (PhoRC) during embryogenesis, we revealed extensive co-occupancy at developmental enhancers. Using an established in vivo assay for PRE activity, we demonstrated that a subset of characterized developmental enhancers can function as PREs, silencing transcription in a Polycomb-dependent manner. Conversely, some classic Drosophila PREs can function as developmental enhancers in vivo, activating spatio–temporal expression. This study therefore uncovers elements with dual function: activating transcription in some cells (enhancers) while stably maintaining transcriptional silencing in others (PREs). Given that enhancers initiate spatio–temporal gene expression, reuse of the same elements by the Polycomb group (PcG) system may help fine-tune gene expression and ensure the timely maintenance of cell identities.
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Affiliation(s)
- Jelena Erceg
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Tibor Pakozdi
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Raquel Marco-Ferreres
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Yad Ghavi-Helm
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Charles Girardot
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg D69117, Germany
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Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov AV, Moresco JJ, Blokhina T, Wolle D, Aoki T, Ryabykh V, Yates JR, Shidlovskii YV, Georgiev P, Schedl P, Chetverina D. The GAGA factor regulatory network: Identification of GAGA factor associated proteins. PLoS One 2017; 12:e0173602. [PMID: 28296955 PMCID: PMC5351981 DOI: 10.1371/journal.pone.0173602] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Drosophila GAGA factor (GAF) has an extraordinarily diverse set of functions that include the activation and silencing of gene expression, nucleosome organization and remodeling, higher order chromosome architecture and mitosis. One hypothesis that could account for these diverse activities is that GAF is able to interact with partners that have specific and dedicated functions. To test this possibility we used affinity purification coupled with high throughput mass spectrometry to identify GAF associated partners. Consistent with this hypothesis the GAF interacting network includes a large collection of factors and complexes that have been implicated in many different aspects of gene activity, chromosome structure and function. Moreover, we show that GAF interactions with a small subset of partners is direct; however for many others the interactions could be indirect, and depend upon intermediates that serve to diversify the functional capabilities of the GAF protein.
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Affiliation(s)
- Dmitry Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mikhailova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - James J. Moresco
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tatiana Blokhina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Vladimir Ryabykh
- Institute of Animal Physiology, Biochemistry and Nutrition, Borovsk, Russia
| | - John R. Yates
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | | | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
- * E-mail: (DC); (PS); (PG)
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
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Hitrik A, Popliker M, Gancz D, Mukamel Z, Lifshitz A, Schwartzman O, Tanay A, Gilboa L. Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C. PLoS Genet 2016; 12:e1006330. [PMID: 27846223 PMCID: PMC5147775 DOI: 10.1371/journal.pgen.1006330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/29/2016] [Indexed: 01/26/2023] Open
Abstract
The development of niches for tissue-specific stem cells is an important aspect of stem cell biology. Determination of niche size and niche numbers during organogenesis involves precise control of gene expression. How this is achieved in the context of a complex chromatin landscape is largely unknown. Here we show that the nuclear protein Combgap (Cg) supports correct ovarian niche formation in Drosophila by controlling ecdysone-Receptor (EcR)- mediated transcription and long-range chromatin contacts in the broad locus (BR-C). Both cg and BR-C promote ovarian growth and the development of niches for germ line stem cells. BR-C levels were lower when Combgap was either reduced or over-expressed, indicating an intricate regulation of the BR-C locus by Combgap. Polytene chromosome stains showed that Cg co-localizes with EcR, the major regulator of BR-C, at the BR-C locus and that EcR binding to chromatin was sensitive to changes in Cg levels. Proximity ligation assay indicated that the two proteins could reside in the same complex. Finally, chromatin conformation analysis revealed that EcR-bound regions within BR-C, which span ~30 KBs, contacted each other. Significantly, these contacts were stabilized in an ecdysone- and Combgap-dependent manner. Together, these results highlight Combgap as a novel regulator of chromatin structure that promotes transcription of ecdysone target genes and ovarian niche formation. Germ line stem cells (GSCs) supply either eggs or sperm throughout the life- time of many organisms, including mammals. For their function, GSCs require input from somatic niche cells. Understanding how niches form during development is an important initial step in understanding how stem cell units form, and by extension, how they may regenerate. In this work we describe a new function for the chromatin binding protein Combgap in ovarian niche formation of the model organism Drosophila melanogaster. Combgap is required for the correct expression of another factor, BR-C, in somatic ovarian cells. BR-C is one of the central target genes of the steroid hormone ecdysone, and its expression is controlled by the ecdysone receptor (EcR). Interestingly, EcR-enriched regions within the BR-C locus are engaged in long-range contacts that are stabilized by ecdysone in a Combgap-depended manner. We also found that EcR binding to chromatin depends on WT levels of Combgap. BR-C regulates GSC unit establishment, intestinal stem cells, immune responses, and many other processes. Understanding Combgaps’ function in shaping the BR-C chromatin landscape is a first step towards better appreciation of how this important locus is controlled, and the general machinery coupling gene expression to 3D chromatin structure.
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Affiliation(s)
- Anna Hitrik
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Malka Popliker
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Dana Gancz
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Mukamel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Schwartzman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Mol. Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Childhood Leukemia Research Institute, Sheba Medical Center, Ramat Gan, Israel
| | - Amos Tanay
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Gilboa
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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40
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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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41
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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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