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Pollex T, Marco-Ferreres R, Ciglar L, Ghavi-Helm Y, Rabinowitz A, Viales RR, Schaub C, Jankowski A, Girardot C, Furlong EEM. Chromatin gene-gene loops support the cross-regulation of genes with related function. Mol Cell 2024; 84:822-838.e8. [PMID: 38157845 DOI: 10.1016/j.molcel.2023.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Chromatin loops between gene pairs have been observed in diverse contexts in both flies and vertebrates. Combining high-resolution Capture-C, DNA fluorescence in situ hybridization, and genetic perturbations, we dissect the functional role of three loops between genes with related function during Drosophila embryogenesis. By mutating the loop anchor (but not the gene) or the gene (but not loop anchor), we disentangle loop formation and gene expression and show that the 3D proximity of paralogous gene loci supports their co-regulation. Breaking the loop leads to either an attenuation or enhancement of expression and perturbs their relative levels of expression and cross-regulation. Although many loops appear constitutive across embryogenesis, their function can change in different developmental contexts. Taken together, our results indicate that chromatin gene-gene loops act as architectural scaffolds that can be used in different ways in different contexts to fine-tune the coordinated expression of genes with related functions and sustain their cross-regulation.
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Affiliation(s)
- Tim Pollex
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Raquel Marco-Ferreres
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Lucia Ciglar
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Yad Ghavi-Helm
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Adam Rabinowitz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Aleksander Jankowski
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany.
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2
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Brown JL, Price JD, Erokhin M, Kassis JA. Context-dependent role of Pho binding sites in Polycomb complex recruitment in Drosophila. Genetics 2023; 224:iyad096. [PMID: 37216193 PMCID: PMC10411561 DOI: 10.1093/genetics/iyad096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/24/2023] Open
Abstract
Polycomb group (PcG) proteins maintain the silenced state of key developmental genes, but how these proteins are recruited to specific regions of the genome is still not completely understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) comprised of a flexible array of sites for sequence-specific DNA binding proteins, "PcG recruiters," including Pho, Spps, Cg, and GAF. Pho is thought to play a central role in PcG recruitment. Early data showed that mutation of Pho binding sites in PREs in transgenes abrogated the ability of those PREs to repress gene expression. In contrast, genome-wide experiments in pho mutants or by Pho knockdown showed that PcG proteins can bind to PREs in the absence of Pho. Here, we directly addressed the importance of Pho binding sites in 2 engrailed (en) PREs at the endogenous locus and in transgenes. Our results show that Pho binding sites are required for PRE activity in transgenes with a single PRE. In a transgene, 2 PREs together lead to stronger, more stable repression and confer some resistance to the loss of Pho binding sites. Making the same mutation in Pho binding sites has little effect on PcG-protein binding at the endogenous en gene. Overall, our data support the model that Pho is important for PcG binding but emphasize how multiple PREs and chromatin environment increase the ability of PREs to function in the absence of Pho. This supports the view that multiple mechanisms contribute to PcG recruitment in Drosophila.
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Affiliation(s)
- Janet Lesley Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua D Price
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Abstract
The Drosophila wing imaginal disc is a tissue of undifferentiated cells that are precursors of the wing and most of the notum of the adult fly. The wing disc first forms during embryogenesis from a cluster of ∼30 cells located in the second thoracic segment, which invaginate to form a sac-like structure. They undergo extensive proliferation during larval stages to form a mature larval wing disc of ∼35,000 cells. During this time, distinct cell fates are assigned to different regions, and the wing disc develops a complex morphology. Finally, during pupal stages the wing disc undergoes morphogenetic processes and then differentiates to form the adult wing and notum. While the bulk of the wing disc comprises epithelial cells, it also includes neurons and glia, and is associated with tracheal cells and muscle precursor cells. The relative simplicity and accessibility of the wing disc, combined with the wealth of genetic tools available in Drosophila, have combined to make it a premier system for identifying genes and deciphering systems that play crucial roles in animal development. Studies in wing imaginal discs have made key contributions to many areas of biology, including tissue patterning, signal transduction, growth control, regeneration, planar cell polarity, morphogenesis, and tissue mechanics.
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Affiliation(s)
- Bipin Kumar Tripathi
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Kenneth D Irvine
- Department of Molecular Biology and Biochemistry, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
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4
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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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5
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De S, Gehred ND, Fujioka M, Chan FW, Jaynes JB, Kassis JA. Defining the Boundaries of Polycomb Domains in Drosophila. Genetics 2020; 216:689-700. [PMID: 32948625 PMCID: PMC7648573 DOI: 10.1534/genetics.120.303642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/15/2020] [Indexed: 02/05/2023] Open
Abstract
Polycomb group (PcG) proteins are an important group of transcriptional repressors that act by modifying chromatin. PcG target genes are covered by the repressive chromatin mark H3K27me3. Polycomb repressive complex 2 (PRC2) is a multiprotein complex that is responsible for generating H3K27me3. In Drosophila, PRC2 is recruited by Polycomb Response Elements (PREs) and then trimethylates flanking nucleosomes, spreading the H3K27me3 mark over large regions of the genome, the "Polycomb domains." What defines the boundary of a Polycomb domain? There is experimental evidence that insulators, PolII, and active transcription can all form the boundaries of Polycomb domains. Here we divide the boundaries of larval Polycomb domains into six different categories. In one category, genes are transcribed toward the Polycomb domain, where active transcription is thought to stop the spreading of H3K27me3. In agreement with this, we show that introducing a transcriptional terminator into such a transcription unit causes an extension of the Polycomb domain. Additional data suggest that active transcription of a boundary gene may restrict the range of enhancer activity of a Polycomb-regulated gene.
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Affiliation(s)
- Sandip De
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Natalie D Gehred
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Fountane W Chan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - James B Jaynes
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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6
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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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7
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Ghotbi E, Lackey K, Wong V, Thompson KT, Caston EG, Haddadi M, Benes J, Jones RS. Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene. Genetics 2020; 214:623-634. [PMID: 31919108 PMCID: PMC7054010 DOI: 10.1534/genetics.119.302981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/06/2020] [Indexed: 11/18/2022] Open
Abstract
Polycomb-group (PcG) proteins are evolutionarily conserved epigenetic regulators whose primary function is to maintain the transcriptional repression of target genes. Recruitment of Drosophila melanogaster PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs). The functions or necessity for more than one PRE at a gene are not clear and individual PREs at some loci may have distinct regulatory roles. Various combinations of sequence-specific DNA-binding proteins are present at a given PRE, but only Pleiohomeotic (Pho) is present at all strong PREs. The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2. This observation indicated a possible dependence of PRE2 on PRE1 for PcG recruitment; however, we find here that PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites, Phol binding is less so and appears to play a minimal role in recruiting other PcG proteins to gt Another PRE-binding protein, Sp1/Kruppel-like factor, is dependent on the presence of Pho for PRE1 binding. Further, we show that, in addition to silencing gene expression, PcG proteins dampen transcription of an active gene.
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Affiliation(s)
- Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Kristina Lackey
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Vicki Wong
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Katie T Thompson
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Evan G Caston
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Minna Haddadi
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
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8
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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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9
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Gozalo A, Duke A, Lan Y, Pascual-Garcia P, Talamas JA, Nguyen SC, Shah PP, Jain R, Joyce EF, Capelson M. Core Components of the Nuclear Pore Bind Distinct States of Chromatin and Contribute to Polycomb Repression. Mol Cell 2019; 77:67-81.e7. [PMID: 31784359 DOI: 10.1016/j.molcel.2019.10.017] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/04/2019] [Accepted: 10/11/2019] [Indexed: 12/15/2022]
Abstract
Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, in Drosophila cells. Our investigation uncovered differential binding of these NPC subunits, where Nup107 preferentially targets active genes while Nup93 associates primarily with Polycomb-silenced regions. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites can be found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Importantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where different nuclear pores bind different types of chromatin via interactions with specific NPC sub-complexes, and a subset of Polycomb domains is stabilized by interactions with Nup93.
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Affiliation(s)
- Alejandro Gozalo
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ashley Duke
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica A Talamas
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Son C Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Parisha P Shah
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric F Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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De S, Cheng Y, Sun MA, Gehred ND, Kassis JA. Structure and function of an ectopic Polycomb chromatin domain. SCIENCE ADVANCES 2019; 5:eaau9739. [PMID: 30662949 PMCID: PMC6326746 DOI: 10.1126/sciadv.aau9739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/28/2018] [Indexed: 05/14/2023]
Abstract
Polycomb group proteins (PcGs) drive target gene repression and form large chromatin domains. In Drosophila, DNA elements known as Polycomb group response elements (PREs) recruit PcGs to the DNA. We have shown that, within the invected-engrailed (inv-en) Polycomb domain, strong, constitutive PREs are dispensable for Polycomb domain structure and function. We suggest that the endogenous chromosomal location imparts stability to this Polycomb domain. To test this possibility, a 79-kb en transgene was inserted into other chromosomal locations. This transgene is functional and forms a Polycomb domain. The spreading of the H3K27me3 repressive mark, characteristic of PcG domains, varies depending on the chromatin context of the transgene. Unlike at the endogenous locus, deletion of the strong, constitutive PREs from the transgene leads to both loss- and gain-of function phenotypes, demonstrating the important role of these regulatory elements. Our data show that chromatin context plays an important role in Polycomb domain structure and function.
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11
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Roumengous S, Rousset R, Noselli S. Polycomb and Hox Genes Control JNK-Induced Remodeling of the Segment Boundary during Drosophila Morphogenesis. Cell Rep 2017; 19:60-71. [PMID: 28380363 DOI: 10.1016/j.celrep.2017.03.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/03/2017] [Accepted: 03/09/2017] [Indexed: 12/24/2022] Open
Abstract
In segmented tissues, anterior and posterior compartments represent independent morphogenetic domains, which are made of distinct lineages separated by boundaries. During dorsal closure of the Drosophila embryo, specific "mixer cells" (MCs) are reprogrammed in a JNK-dependent manner to express the posterior determinant engrailed (en) and cross the segment boundary. Here, we show that JNK signaling induces de novo expression of en in the MCs through repression of Polycomb (Pc) and release of the en locus from the silencing PcG bodies. Whereas reprogramming occurs in MCs from all thoracic and abdominal segments, cell mixing is restricted to the central abdominal region. We demonstrate that this spatial control of MC remodeling depends on the antagonist activity of the Hox genes abdominal-A and Abdominal-B. Together, these results reveal an essential JNK/en/Pc/Hox gene regulatory network important in controlling both the plasticity of segment boundaries and developmental reprogramming.
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Affiliation(s)
| | - Raphaël Rousset
- Université Côte d'Azur, CNRS, INSERM, iBV, 06108 Nice, France.
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12
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Dye NA, Popović M, Spannl S, Etournay R, Kainmüller D, Ghosh S, Myers EW, Jülicher F, Eaton S. Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc. Development 2017; 144:4406-4421. [PMID: 29038308 DOI: 10.1242/dev.155069] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/05/2017] [Indexed: 12/30/2022]
Abstract
Quantitative analysis of the dynamic cellular mechanisms shaping the Drosophila wing during its larval growth phase has been limited, impeding our ability to understand how morphogen patterns regulate tissue shape. Such analysis requires explants to be imaged under conditions that maintain both growth and patterning, as well as methods to quantify how much cellular behaviors change tissue shape. Here, we demonstrate a key requirement for the steroid hormone 20-hydroxyecdysone (20E) in the maintenance of numerous patterning systems in vivo and in explant culture. We find that low concentrations of 20E support prolonged proliferation in explanted wing discs in the absence of insulin, incidentally providing novel insight into the hormonal regulation of imaginal growth. We use 20E-containing media to observe growth directly and to apply recently developed methods for quantitatively decomposing tissue shape changes into cellular contributions. We discover that whereas cell divisions drive tissue expansion along one axis, their contribution to expansion along the orthogonal axis is cancelled by cell rearrangements and cell shape changes. This finding raises the possibility that anisotropic mechanical constraints contribute to growth orientation in the wing disc.
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Affiliation(s)
- Natalie A Dye
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany
| | - Marko Popović
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| | - Stephanie Spannl
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany
| | - Raphaël Etournay
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany.,Unité de Génétique et Physiologie de l'Audition UMRS 1120, Département de Neurosciences, Institut Pasteur, 75015 Paris, France
| | - Dagmar Kainmüller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany.,Janelia Farm Research Campus, 19700 Helix Dr, Ashburn, VA 20147, USA
| | - Suhrid Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01309 Dresden, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany .,Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01309 Dresden, Germany
| | - Suzanne Eaton
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany .,Biotechnologisches Zentrum, Technische Universität Dresden, Tatzberg 47/49, 01309 Dresden, Germany
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13
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Dutta P, Li WX. The SERTAD protein Taranis plays a role in Polycomb-mediated gene repression. PLoS One 2017; 12:e0180026. [PMID: 28665982 PMCID: PMC5493352 DOI: 10.1371/journal.pone.0180026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 06/08/2017] [Indexed: 11/19/2022] Open
Abstract
The Polycomb group (PcG) proteins have been implicated in epigenetic transcriptional repression in development, stem cell maintenance and in cancer. The chromodomain protein Polycomb (Pc) is a key member of the PcG. Pc binds to the histone mark, trimethylated histone 3 lysine 27 (H3K27me3), to initiate transcriptional repression. How PcG proteins are recruited to target loci is not fully understood. Here we show that the Drosophila SERTA domain protein Taranis (Tara) is involved in transcriptional regulation of Pc target genes. Embryos lacking Tara exhibit a partial homeotic transformation of cuticular the segments, a phenotype associated with the loss of Pc function. Moreover, Drosophila embryos homozygous for a tara hypomorphic allele also misexpress engrailed, a Pc-regulated gene, and this phenotype is associated with the loss of Pc binding to the cis response element in the engrailed enhancer. In relation to that, Pc recruitment is reduced on the salivary gland polytene chromosomes and specifically at the engrailed locus. These results suggest that Tara might be required for positioning Pc to a subset of its target genes.
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Affiliation(s)
- Pranabananda Dutta
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
| | - Willis X. Li
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
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14
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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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15
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Chetverina DA, Elizar’ev PV, Lomaev DV, Georgiev PG, Erokhin MM. Control of the gene activity by polycomb and trithorax group proteins in Drosophila. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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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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17
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Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules. PLoS Genet 2015; 11:e1005376. [PMID: 26468882 PMCID: PMC4607503 DOI: 10.1371/journal.pgen.1005376] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/19/2015] [Indexed: 12/28/2022] Open
Abstract
The subdivision of cell populations in compartments is a key event during animal development. In Drosophila, the gene apterous (ap) divides the wing imaginal disc in dorsal vs ventral cell lineages and is required for wing formation. ap function as a dorsal selector gene has been extensively studied. However, the regulation of its expression during wing development is poorly understood. In this study, we analyzed ap transcriptional regulation at the endogenous locus and identified three cis-regulatory modules (CRMs) essential for wing development. Only when the three CRMs are combined, robust ap expression is obtained. In addition, we genetically and molecularly analyzed the trans-factors that regulate these CRMs. Our results propose a three-step mechanism for the cell lineage compartment expression of ap that includes initial activation, positive autoregulation and Trithorax-mediated maintenance through separable CRMs. The separation of cell populations into distinct functional units is essential for both vertebrate and invertebrate animal development. A classical paradigm for this phenomenon is the establishment of developmental compartments during Drosophila wing development. These compartments depend on the restricted expression of two selector genes, engrailed in the posterior compartment and apterous (ap) in the dorsal compartment. Yet, despite the central role these genes and their restricted expression patterns play in Drosophila development, we still do not understand how these patterns are established or maintained. Here, by dissecting the regulatory sequences required for ap expression, we solve this problem for this critical selector gene. We used a combination of experimental approaches to identify and functionally characterize the cis-regulatory modules (CRMs) that regulate ap expression during Drosophila wing development. For these analyses we implement a novel technique allowing us to study the function of these CRMs in vivo, at the native ap locus. We found three ap CRMs crucial for wing development: the Early (apE) and the D/V (apDV) enhancers and the ap PRE (apP). Only when all three regulatory elements are combined is a uniform and complete ap expression domain generated. In summary, our results indicate that ap is regulated in time and space by a three-step mechanism that generates a lineage compartment by integrating input from separate CRMs for the initiation, refinement and maintenance of its expression.
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18
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Cheng Y, Brunner AL, Kremer S, DeVido SK, Stefaniuk CM, Kassis JA. Co-regulation of invected and engrailed by a complex array of regulatory sequences in Drosophila. Dev Biol 2014; 395:131-43. [PMID: 25172431 DOI: 10.1016/j.ydbio.2014.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/23/2014] [Accepted: 08/19/2014] [Indexed: 11/16/2022]
Abstract
invected (inv) and engrailed (en) form a gene complex that extends about 115 kb. These two genes encode highly related homeodomain proteins that are co-regulated in a complex manner throughout development. Our dissection of inv/en regulatory DNA shows that most enhancers are spread throughout a 62 kb region. We used two types of constructs to analyze the function of this DNA: P-element based reporter constructs with small pieces of DNA fused to the en promoter driving lacZ expression and large constructs with HA-tagged en and inv inserted in the genome with the phiC31 system. In addition, we generated deletions of inv and en DNA in situ and assayed their effects on inv/en expression. Our results support and extend our knowledge of inv/en regulation. First, inv and en share regulatory DNA, most of which is flanking the en transcription unit. In support of this, a 79-kb HA-en transgene can rescue inv en double mutants to viable, fertile adults. In contrast, an 84-kb HA-inv transgene lacks most of the enhancers for inv/en expression. Second, there are multiple enhancers for inv/en stripes in embryos; some of these may be redundant but others play discrete roles at different stages of embryonic development. Finally, no small reporter construct gave expression in the posterior compartment of imaginal discs, a hallmark of inv/en expression. Robust expression of HA-en in the posterior compartment of imaginal discs is evident from the 79-kb HA-en transgene, while a 45-kb HA-en transgene gives weaker, variable imaginal disc expression. We suggest that the activity of the imaginal disc enhancer(s) is dependent on the chromatin structure of the inv/en domain.
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Affiliation(s)
- Yuzhong Cheng
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Alayne L Brunner
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Stefanie Kremer
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Sarah K DeVido
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Catherine M Stefaniuk
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Judith A Kassis
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States.
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19
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Herzog VA, Lempradl A, Trupke J, Okulski H, Altmutter C, Ruge F, Boidol B, Kubicek S, Schmauss G, Aumayr K, Ruf M, Pospisilik A, Dimond A, Senergin HB, Vargas ML, Simon JA, Ringrose L. A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element. Nat Genet 2014; 46:973-981. [PMID: 25108384 DOI: 10.1038/ng.3058] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/14/2014] [Indexed: 12/14/2022]
Abstract
Polycomb/Trithorax response elements (PRE/TREs) can switch their function reversibly between silencing and activation by mechanisms that are poorly understood. Here we show that a switch in forward and reverse noncoding transcription from the Drosophila melanogaster vestigial (vg) PRE/TRE switches the status of the element between silencing (induced by the forward strand) and activation (induced by the reverse strand). In vitro, both noncoding RNAs inhibit PRC2 histone methyltransferase activity, but, in vivo, only the reverse strand binds PRC2. Overexpression of the reverse strand evicts PRC2 from chromatin and inhibits its enzymatic activity. We propose that the interaction of RNAs with PRC2 is differentially regulated in vivo, allowing regulated inhibition of local PRC2 activity. Genome-wide analysis shows that strand switching of noncoding RNAs occurs at several hundred Polycomb-binding sites in fly and vertebrate genomes. This work identifies a previously unreported and potentially widespread class of PRE/TREs that switch function by switching the direction of noncoding RNA transcription.
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Affiliation(s)
- Veronika A Herzog
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Adelheid Lempradl
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Johanna Trupke
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Helena Okulski
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Christina Altmutter
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frank Ruge
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Bernd Boidol
- CeMM, Research Center for Molecular Medicine, Lazarettgasse 14, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine, Lazarettgasse 14, 1090 Vienna, Austria
| | - Gerald Schmauss
- IMP, Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Karin Aumayr
- IMP, Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Marius Ruf
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Andrew Dimond
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Hasene Basak Senergin
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Marcus L Vargas
- Department of Genetics, Cell Biology and Development, University of Minnesota. Minneapolis, Minnesota, USA
| | - Jeffrey A Simon
- Department of Genetics, Cell Biology and Development, University of Minnesota. Minneapolis, Minnesota, USA
| | - Leonie Ringrose
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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20
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Bowman SK, Deaton AM, Domingues H, Wang PI, Sadreyev RI, Kingston RE, Bender W. H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex. eLife 2014; 3:e02833. [PMID: 25082344 PMCID: PMC4139060 DOI: 10.7554/elife.02833] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The bithorax complex (BX-C) in Drosophila melanogaster is a cluster of homeotic genes that determine body segment identity. Expression of these genes is governed by cis-regulatory domains, one for each parasegment. Stable repression of these domains depends on Polycomb Group (PcG) functions, which include trimethylation of lysine 27 of histone H3 (H3K27me3). To search for parasegment-specific signatures that reflect PcG function, chromatin from single parasegments was isolated and profiled. The H3K27me3 profiles across the BX-C in successive parasegments showed a 'stairstep' pattern that revealed sharp boundaries of the BX-C regulatory domains. Acetylated H3K27 was broadly enriched across active domains, in a pattern complementary to H3K27me3. The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains lack H3K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely positioned H3K27 modifications as a central determinant of segment identity.
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Affiliation(s)
- Sarah K Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Aimee M Deaton
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Heber Domingues
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Peggy I Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Pathology, Harvard Medical School, Boston, United States
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States Department of Genetics, Harvard Medical School, Boston, United States
| | - Welcome Bender
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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21
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Steffen PA, Ringrose L. What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat Rev Mol Cell Biol 2014; 15:340-56. [PMID: 24755934 DOI: 10.1038/nrm3789] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In any biological system with memory, the state of the system depends on its history. Epigenetic memory maintains gene expression states through cell generations without a change in DNA sequence and in the absence of initiating signals. It is immensely powerful in biological systems - it adds long-term stability to gene expression states and increases the robustness of gene regulatory networks. The Polycomb group (PcG) and Trithorax group (TrxG) proteins can confer long-term, mitotically heritable memory by sustaining silent and active gene expression states, respectively. Several recent studies have advanced our understanding of the molecular mechanisms of this epigenetic memory during DNA replication and mitosis.
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Affiliation(s)
- Philipp A Steffen
- Institute of Molecular Biotechnology (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Leonie Ringrose
- Institute of Molecular Biotechnology (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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22
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Mapping polycomb response elements at the Drosophilla melanogaster giant locus. G3-GENES GENOMES GENETICS 2013; 3:2297-304. [PMID: 24170735 PMCID: PMC3852391 DOI: 10.1534/g3.113.008896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Polycomb-group (PcG) proteins are highly conserved epigenetic transcriptional regulators. They are capable of either maintaining the transcriptional silence of target genes through many cell cycles or enabling a dynamic regulation of gene expression in stem cells. In Drosophila melanogaster, recruitment of PcG proteins to targets requires the presence of at least one polycomb response element (PRE). Although the sequence requirements for PREs are not well-defined, the presence of Pho, a PRE-binding PcG protein, is a very good PRE indicator. In this study, we identify two PRE-containing regions at the PcG target gene, giant, one at the promoter, and another approximately 6 kb upstream. PRE-containing fragments, which coincide with localized presence of Pho in chromatin immunoprecipitations, were shown to maintain restricted expression of a lacZ reporter gene in embryos and to cause pairing-sensitive silencing of the mini-white gene in eyes. Our results also reinforce previous observations that although PRE maintenance and pairing-sensitive silencing activities are closely linked, the sequence requirements for these functions are not identical.
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23
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Fujioka M, Sun G, Jaynes JB. The Drosophila eve insulator Homie promotes eve expression and protects the adjacent gene from repression by polycomb spreading. PLoS Genet 2013; 9:e1003883. [PMID: 24204298 PMCID: PMC3814318 DOI: 10.1371/journal.pgen.1003883] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/29/2013] [Indexed: 12/18/2022] Open
Abstract
Insulators can block the action of enhancers on promoters and the spreading of repressive chromatin, as well as facilitating specific enhancer-promoter interactions. However, recent studies have called into question whether the activities ascribed to insulators in model transgene assays actually reflect their functions in the genome. The Drosophila even skipped (eve) gene is a Polycomb (Pc) domain with a Pc-group response element (PRE) at one end, flanked by an insulator, an arrangement also seen in other genes. Here, we show that this insulator has three major functions. It blocks the spreading of the eve Pc domain, preventing repression of the adjacent gene, TER94. It prevents activation of TER94 by eve regulatory DNA. It also facilitates normal eve expression. When Homie is deleted in the context of a large transgene that mimics both eve and TER94 regulation, TER94 is repressed. This repression depends on the eve PRE. Ubiquitous TER94 expression is “replaced” by expression in an eve pattern when Homie is deleted, and this effect is reversed when the PRE is also removed. Repression of TER94 is attributable to spreading of the eve Pc domain into the TER94 locus, accompanied by an increase in histone H3 trimethylation at lysine 27. Other PREs can functionally replace the eve PRE, and other insulators can block PRE-dependent repression in this context. The full activity of the eve promoter is also dependent on Homie, and other insulators can promote normal eve enhancer-promoter communication. Our data suggest that this is not due to preventing promoter competition, but is likely the result of the insulator organizing a chromosomal conformation favorable to normal enhancer-promoter interactions. Thus, insulator activities in a native context include enhancer blocking and enhancer-promoter facilitation, as well as preventing the spread of repressive chromatin. Insulators are specialized DNA elements that can separate the genome into functional units. Most of the current thinking about these elements comes from studies done with model transgenes. Studies of insulators within the specialized Hox gene complexes have suggested that model transgenes can reflect the normal functions of these elements in their native context. However, recent genome-wide studies have called this into question. This work analyzes the native function of an insulator that resides between the Drosophila genes eve and TER94, which are expressed in very different patterns. Also, the eve gene is a Polycomb (Pc) domain, a specialized type of chromatin that is found in many places throughout the genome. We show that this insulator has three major functions. It blocks the spreading of the eve Pc domain, preventing repression of TER94. It prevents activation of TER94 by eve regulatory DNA. It also facilitates normal eve expression. Each of these activities are consistent with those seen with model transgenes, and other known insulators can provide these functions in this context. This work provides a novel and convincing example of the normal role of insulators in regulating the eukaryotic genome, as well as providing insights into their mechanisms of action.
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Affiliation(s)
- Miki Fujioka
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Guizhi Sun
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - James B. Jaynes
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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24
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Abstract
Polycomb group response elements (PREs) play an essential role in gene regulation by the Polycomb group (PcG) repressor proteins in Drosophila. PREs are required for the recruitment and maintenance of repression by the PcG proteins. PREs are made up of binding sites for multiple DNA-binding proteins, but it is still unclear what combination(s) of binding sites is required for PRE activity. Here we compare the binding sites and activities of two closely linked yet separable PREs of the Drosophila engrailed (en) gene, PRE1 and PRE2. Both PRE1 and PRE2 contain binding sites for multiple PRE-DNA-binding proteins, but the number, arrangement, and spacing of the sites differs between the two PREs. These differences have functional consequences. Both PRE1 and PRE2 mediate pairing-sensitive silencing of mini-white, a functional assay for PcG repression; however, PRE1 requires two binding sites for Pleiohomeotic (Pho), whereas PRE2 requires only one Pho-binding site for this activity. Furthermore, for full pairing-sensitive silencing activity, PRE1 requires an AT-rich region not found in PRE2. These two PREs behave differently in a PRE embryonic and larval reporter construct inserted at an identical location in the genome. Our data illustrate the diversity of architecture and function of PREs.
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25
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Mayer LR, Diegelmann S, Abassi Y, Eichinger F, Pflugfelder GO. Enhancer trap infidelity in Drosophila optomotor-blind. Fly (Austin) 2013; 7:118-28. [PMID: 23519069 DOI: 10.4161/fly.23657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Reporter gene activity in enhancer trap lines is often implicitly assumed to mirror quite faithfully the endogenous expression of the "trapped" gene, even though there are numerous examples of enhancer trap infidelity. optomotor-blind (omb) is a 160 kb gene in which 16 independent P-element enhancer trap insertions of three different types have been mapped in a range of more than 60 kb. We have determined the expression pattern of these elements in wing, eye-antennal and leg imaginal discs as well as in the pupal tergites. We noted that one pGawB insertion (omb (P4) ) selectively failed to report parts of the omb pattern even though the missing pattern elements were apparent in all other 15 lines. We ruled out that omb (P4) was defective in the Gal4 promoter region or had inactivated genomic enhancers in the integration process. We propose that the Gal4 reporter gene in pGawB may be sensitive to orientation or promoter proximity effects.
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Affiliation(s)
- Lisa R Mayer
- Institute of Genetics, Johannes Gutenberg-Universität, Mainz, Germany
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26
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Kassis JA, Brown JL. Polycomb group response elements in Drosophila and vertebrates. ADVANCES IN GENETICS 2013; 81:83-118. [PMID: 23419717 DOI: 10.1016/b978-0-12-407677-8.00003-8] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Polycomb group genes (PcG) encode a group of about 16 proteins that were first identified in Drosophila as repressors of homeotic genes. PcG proteins are present in all metazoans and are best characterized as transcriptional repressors. In Drosophila, these proteins are known as epigenetic regulators because they remember, but do not establish, the patterned expression state of homeotic genes throughout development. PcG proteins, in general, are not DNA binding proteins, but act in protein complexes to repress transcription at specific target genes. How are PcG proteins recruited to the DNA? In Drosophila, there are specific regulatory DNA elements called Polycomb group response elements (PREs) that bring PcG protein complexes to the DNA. Drosophila PREs are made up of binding sites for a complex array of DNA binding proteins. Functional PRE assays in transgenes have shown that PREs act in the context of other regulatory DNA and PRE activity is highly dependent on genomic context. Drosophila PREs tend to regulate genes with a complex array of regulatory DNA in a cell or tissue-specific fashion and it is the interplay between regulatory DNA that dictates PRE function. In mammals, PcG proteins are more diverse and there are multiple ways to recruit PcG complexes, including RNA-mediated recruitment. In this review, we discuss evidence for PREs in vertebrates and explore similarities and differences between Drosophila and vertebrate PREs.
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Affiliation(s)
- Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA.
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Langlais KK, Brown JL, Kassis JA. Polycomb group proteins bind an engrailed PRE in both the "ON" and "OFF" transcriptional states of engrailed. PLoS One 2012; 7:e48765. [PMID: 23139817 PMCID: PMC3490902 DOI: 10.1371/journal.pone.0048765] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/05/2012] [Indexed: 11/25/2022] Open
Abstract
Polycomb group (PcG) and trithorax Group (trxG) proteins maintain the “OFF” and “ON” transcriptional states of HOX genes and other targets by modulation of chromatin structure. In Drosophila, PcG proteins are bound to DNA fragments called Polycomb group response elements (PREs). The prevalent model holds that PcG proteins bind PREs only in cells where the target gene is “OFF”. Another model posits that transcription through PREs disrupts associated PcG complexes, contributing to the establishment of the “ON” transcriptional state. We tested these two models at the PcG target gene engrailed. engrailed exists in a gene complex with invected, which together have 4 well-characterized PREs. Our data show that these PREs are not transcribed in embryos or larvae. We also examined whether PcG proteins are bound to an engrailed PRE in cells where engrailed is transcribed. By FLAG-tagging PcG proteins and expressing them specifically where engrailed is “ON” or “OFF”, we determined that components of three major PcG protein complexes are present at an engrailed PRE in both the “ON” and “OFF” transcriptional states in larval tissues. These results show that PcG binding per se does not determine the transcriptional state of engrailed.
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Affiliation(s)
| | | | - Judith A. Kassis
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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McEachern LA, Lloyd VK. The maize b1 paramutation control region causes epigenetic silencing in Drosophila melanogaster. Mol Genet Genomics 2012; 287:591-606. [DOI: 10.1007/s00438-012-0702-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
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Zeng J, Kirk BD, Gou Y, Wang Q, Ma J. Genome-wide polycomb target gene prediction in Drosophila melanogaster. Nucleic Acids Res 2012; 40:5848-63. [PMID: 22416065 PMCID: PMC3401425 DOI: 10.1093/nar/gks209] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
As key epigenetic regulators, polycomb group (PcG) proteins are responsible for the control of cell proliferation and differentiation as well as stem cell pluripotency and self-renewal. Aberrant epigenetic modification by PcG is strongly correlated with the severity and invasiveness of many types of cancers. Unfortunately, the molecular mechanism of PcG-mediated epigenetic regulation remained elusive, partly due to the extremely limited pool of experimentally confirmed PcG target genes. In order to facilitate experimental identification of PcG target genes, here we propose a novel computational method, EpiPredictor, that achieved significantly higher matching ratios with several recent chromatin immunoprecipitation studies than jPREdictor, an existing computational method. We further validated a subset of genes that were uniquely predicted by EpiPredictor by cross-referencing existing literature and by experimental means. Our data suggest that multiple transcription factor networking at the cis-regulatory elements is critical for PcG recruitment, while high GC content and high conservation level are also important features of PcG target genes. EpiPredictor should substantially expedite experimental discovery of PcG target genes by providing an effective initial screening tool. From a computational standpoint, our strategy of modelling transcription factor interaction with a non-linear kernel is original, effective and transferable to many other applications.
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Affiliation(s)
- Jia Zeng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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P-element homing is facilitated by engrailed polycomb-group response elements in Drosophila melanogaster. PLoS One 2012; 7:e30437. [PMID: 22276200 PMCID: PMC3261919 DOI: 10.1371/journal.pone.0030437] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 12/20/2011] [Indexed: 11/19/2022] Open
Abstract
P-element vectors are commonly used to make transgenic Drosophila and generally insert in the genome in a nonselective manner. However, when specific fragments of regulatory DNA from a few Drosophila genes are incorporated into P-transposons, they cause the vectors to be inserted near the gene from which the DNA fragment was derived. This is called P-element homing. We mapped the minimal DNA fragment that could mediate homing to the engrailed/invected region of the genome. A 1.6 kb fragment of engrailed regulatory DNA that contains two Polycomb-group response elements (PREs) was sufficient for homing. We made flies that contain a 1.5kb deletion of engrailed DNA (enΔ1.5) in situ, including the PREs and the majority of the fragment that mediates homing. Remarkably, homing still occurs onto the enΔ1. 5 chromosome. In addition to homing to en, P[en] inserts near Polycomb group target genes at an increased frequency compared to P[EPgy2], a vector used to generate 18,214 insertions for the Drosophila gene disruption project. We suggest that homing is mediated by interactions between multiple proteins bound to the homing fragment and proteins bound to multiple areas of the engrailed/invected chromatin domain. Chromatin structure may also play a role in homing.
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Modulation of the activity of a polycomb-group response element in Drosophila by a mutation in the transcriptional activator woc. G3-GENES GENOMES GENETICS 2011; 1:471-8. [PMID: 22384357 PMCID: PMC3276158 DOI: 10.1534/g3.111.001230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 09/19/2011] [Indexed: 01/10/2023]
Abstract
Polycomb group response elements (PRE) are cis-regulatory elements that bind Polycomb group proteins. We are studying a 181-bp PRE from the Drosophilaengrailed gene. This PRE causes pairing-sensitive silencing of mini-white in transgenes. Here we show that the 181-bp PRE also represses mini-white expression in flies with only one copy of the transgene. To isolate mutations that alter the activity of the 181-bp PRE, we screened for dominant suppressors of PRE-mediated mini-white repression. Dominant suppressors of mini-white repression were rare; we recovered only nine mutations out of 68,274 progeny screened. Two of the nine mutations isolated are due to the same single amino acid change in the transcriptional activator Woc (without children). Reversion experiments show that these are dominant gain-of-function mutations in woc. We suggest that Woc can interfere with the activity of the PRE. Our data have implications for how Polycomb group proteins act to either partially repress or completely silence their target genes.
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Okulski H, Druck B, Bhalerao S, Ringrose L. Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment. Epigenetics Chromatin 2011; 4:4. [PMID: 21410956 PMCID: PMC3070613 DOI: 10.1186/1756-8935-4-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/16/2011] [Indexed: 01/24/2023] Open
Abstract
Background Polycomb/Trithorax response elements (PREs) are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position. Results We adapted the ΦC31 site-specific integration tool to enable systematic quantitative comparison of PREs and sequence variants at identical genomic locations. In this adaptation, a miniwhite (mw) reporter in combination with eye-pigment analysis gives a quantitative readout of PRE function. We compared the Hox PRE Frontabdominal-7 (Fab-7) with a PRE from the vestigial (vg) gene at four landing sites. The analysis revealed that the Fab-7 and vg PREs have fundamentally different properties, both in terms of their interaction with the genomic environment at each site and their inherent silencing abilities. Furthermore, we used the ΦC31 tool to examine the effect of deletions and mutations in the vg PRE, identifying a 106 bp region containing a previously predicted motif (GTGT) that is essential for silencing. Conclusions This analysis showed that different PREs have quantifiably different properties, and that changes in as few as four base pairs have profound effects on PRE function, thus illustrating the power and sensitivity of ΦC31 site-specific integration as a tool for the rapid and quantitative dissection of elements of PRE design.
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Affiliation(s)
- Helena Okulski
- IMBA, Institute of Molecular Biotechnology GmBH, Dr, Bohr-Gasse 3, 1030 Vienna, Austria.
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Soshnikova N. Dynamics of Polycomb and Trithorax activities during development. ACTA ACUST UNITED AC 2011; 91:781-7. [DOI: 10.1002/bdra.20774] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Revised: 11/23/2010] [Accepted: 11/25/2010] [Indexed: 12/17/2022]
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Chromosomal organization at the level of gene complexes. Cell Mol Life Sci 2010; 68:977-90. [PMID: 21080026 PMCID: PMC3043239 DOI: 10.1007/s00018-010-0585-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 10/17/2010] [Accepted: 10/26/2010] [Indexed: 01/10/2023]
Abstract
Metazoan genomes primarily consist of non-coding DNA in comparison to coding regions. Non-coding fraction of the genome contains cis-regulatory elements, which ensure that the genetic code is read properly at the right time and space during development. Regulatory elements and their target genes define functional landscapes within the genome, and some developmentally important genes evolve by keeping the genes involved in specification of common organs/tissues in clusters and are termed gene complex. The clustering of genes involved in a common function may help in robust spatio-temporal gene expression. Gene complexes are often found to be evolutionarily conserved, and the classic example is the hox complex. The evolutionary constraints seen among gene complexes provide an ideal model system to understand cis and trans-regulation of gene function. This review will discuss the various characteristics of gene regulatory modules found within gene complexes and how they can be characterized.
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Schwartz YB, Kahn TG, Stenberg P, Ohno K, Bourgon R, Pirrotta V. Alternative epigenetic chromatin states of polycomb target genes. PLoS Genet 2010; 6:e1000805. [PMID: 20062800 PMCID: PMC2799325 DOI: 10.1371/journal.pgen.1000805] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 12/09/2009] [Indexed: 11/18/2022] Open
Abstract
Polycomb (PcG) regulation has been thought to produce stable long-term gene silencing. Genomic analyses in Drosophila and mammals, however, have shown that it targets many genes, which can switch state during development. Genetic evidence indicates that critical for the active state of PcG target genes are the histone methyltransferases Trithorax (TRX) and ASH1. Here we analyze the repertoire of alternative states in which PcG target genes are found in different Drosophila cell lines and the role of PcG proteins TRX and ASH1 in controlling these states. Using extensive genome-wide chromatin immunoprecipitation analysis, RNAi knockdowns, and quantitative RT-PCR, we show that, in addition to the known repressed state, PcG targets can reside in a transcriptionally active state characterized by formation of an extended domain enriched in ASH1, the N-terminal, but not C-terminal moiety of TRX and H3K27ac. ASH1/TRX N-ter domains and transcription are not incompatible with repressive marks, sometimes resulting in a "balanced" state modulated by both repressors and activators. Often however, loss of PcG repression results instead in a "void" state, lacking transcription, H3K27ac, or binding of TRX or ASH1. We conclude that PcG repression is dynamic, not static, and that the propensity of a target gene to switch states depends on relative levels of PcG, TRX, and activators. N-ter TRX plays a remarkable role that antagonizes PcG repression and preempts H3K27 methylation by acetylation. This role is distinct from that usually attributed to TRX/MLL proteins at the promoter. These results have important implications for Polycomb gene regulation, the "bivalent" chromatin state of embryonic stem cells, and gene expression in development.
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Affiliation(s)
- Yuri B. Schwartz
- Department of Molecular Biology and Biochemistry, Rutgers University, Nelson Laboratories, Piscataway, New Jersey, United States of America
| | - Tatyana G. Kahn
- Department of Molecular Biology and Biochemistry, Rutgers University, Nelson Laboratories, Piscataway, New Jersey, United States of America
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster, Umeå University, Umeå, Sweden
| | - Katsuhito Ohno
- Department of Molecular Biology and Biochemistry, Rutgers University, Nelson Laboratories, Piscataway, New Jersey, United States of America
| | - Richard Bourgon
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Nelson Laboratories, Piscataway, New Jersey, United States of America
- * E-mail:
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36
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Characterization of the polycomb group response elements of the Drosophila melanogaster invected Locus. Mol Cell Biol 2009; 30:820-8. [PMID: 19948883 DOI: 10.1128/mcb.01287-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Polycomb group proteins (PcGs) play a vital role throughout development by maintaining precise gene expression patterns. In Drosophila melanogaster, PcG-mediated gene silencing is achieved through DNA elements called Polycomb response elements (PREs); however, the mechanism for establishing silencing and the requirements and composition of a working PRE are not fully understood. We have used the computer program jPREdictor to uncover PREs located within the invected (inv) locus. The functionalities of these predicted PREs were tested in two different assays: one analyzing their abilities to maintain expression of a beta-galactosidase reporter gene and the other evaluating their abilities to establish pairing-sensitive silencing of the mini-white reporter in the vector pCaSpeR. We have identified two previously uncharacterized PREs at the inv gene and demonstrate that they produce similar results in the two assays. Our results indicate that clusters of protein binding sites do not accurately predict PREs and provide new insight into the DNA sequence requirements for the binding of the PcG protein Pho. Finally, our data show that PREs and regulatory DNA from different genes can function together to establish PcG-mediated silencing, highlighting the versatility of PREs despite discrepancies in the number and location of DNA binding sites.
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Fang M, Ren H, Liu J, Cadigan KM, Patel SR, Dressler GR. Drosophila ptip is essential for anterior/posterior patterning in development and interacts with the PcG and trxG pathways. Development 2009; 136:1929-38. [PMID: 19429789 DOI: 10.1242/dev.026559] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Development of the fruit fly Drosophila depends in part on epigenetic regulation carried out by the concerted actions of the Polycomb and Trithorax group of proteins, many of which are associated with histone methyltransferase activity. Mouse PTIP is part of a histone H3K4 methyltransferase complex and contains six BRCT domains and a glutamine-rich region. In this article, we describe an essential role for the Drosophila ortholog of the mammalian Ptip (Paxip1) gene in early development and imaginal disc patterning. Both maternal and zygotic ptip are required for segmentation and axis patterning during larval development. Loss of ptip results in a decrease in global levels of H3K4 methylation and an increase in the levels of H3K27 methylation. In cell culture, Drosophila ptip is required to activate homeotic gene expression in response to the derepression of Polycomb group genes. Activation of developmental genes is coincident with PTIP protein binding to promoter sequences and increased H3K4 trimethylation. These data suggest a highly conserved function for ptip in epigenetic control of development and differentiation.
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Affiliation(s)
- Ming Fang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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Fujioka M, Wu X, Jaynes JB. A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication. Development 2009; 136:3077-87. [PMID: 19675129 PMCID: PMC2730365 DOI: 10.1242/dev.036467] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2009] [Indexed: 12/11/2022]
Abstract
Insulator sequences help to organize the genome into discrete functional regions by preventing inappropriate cross-regulation. This is thought to be mediated in part through associations with other insulators located elsewhere in the genome. Enhancers that normally drive Drosophila even skipped (eve) expression are located closer to the TER94 transcription start site than to that of eve. We discovered that the region between these genes has enhancer-blocking activity, and that this insulator region also mediates homing of P-element transgenes to the eve-TER94 genomic neighborhood. Localization of these activities to within 0.6 kb failed to separate them. Importantly, homed transgenic promoters respond to endogenous eve enhancers from great distances, and this long-range communication depends on the homing/insulator region, which we call Homie. We also find that the eve promoter contributes to long-distance communication. However, even the basal hsp70 promoter can communicate with eve enhancers across distances of several megabases, when the communication is mediated by Homie. These studies show that, while Homie blocks enhancer-promoter communication at short range, it facilitates long-range communication between distant genomic regions, possibly by organizing a large chromosomal loop between endogenous and transgenic Homies.
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Affiliation(s)
- Miki Fujioka
- Department of Biochemistry and Molecular Biology and the Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Kwon D, Mucci D, Langlais KK, Americo JL, DeVido SK, Cheng Y, Kassis JA. Enhancer-promoter communication at the Drosophila engrailed locus. Development 2009; 136:3067-75. [PMID: 19675130 PMCID: PMC2730364 DOI: 10.1242/dev.036426] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2009] [Indexed: 12/11/2022]
Abstract
Enhancers are often located many tens of kilobases away from the promoter they regulate, sometimes residing closer to the promoter of a neighboring gene. How do they know which gene to activate? We have used homing P[en] constructs to study the enhancer-promoter communication at the engrailed locus. Here we show that engrailed enhancers can act over large distances, even skipping over other transcription units, choosing the engrailed promoter over those of neighboring genes. This specificity is achieved in at least three ways. First, early acting engrailed stripe enhancers exhibit promoter specificity. Second, a proximal promoter-tethering element is required for the action of the imaginal disc enhancer(s). Our data suggest that there are two partially redundant promoter-tethering elements. Third, the long-distance action of engrailed enhancers requires a combination of the engrailed promoter and sequences within or closely linked to the promoter proximal Polycomb-group response elements. These data show that multiple mechanisms ensure proper enhancer-promoter communication at the Drosophila engrailed locus.
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Affiliation(s)
- Deborah Kwon
- Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Schaaf CA, Misulovin Z, Sahota G, Siddiqui AM, Schwartz YB, Kahn TG, Pirrotta V, Gause M, Dorsett D. Regulation of the Drosophila Enhancer of split and invected-engrailed gene complexes by sister chromatid cohesion proteins. PLoS One 2009; 4:e6202. [PMID: 19587787 PMCID: PMC2703808 DOI: 10.1371/journal.pone.0006202] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 06/16/2009] [Indexed: 01/14/2023] Open
Abstract
The cohesin protein complex was first recognized for holding sister chromatids together and ensuring proper chromosome segregation. Cohesin also regulates gene expression, but the mechanisms are unknown. Cohesin associates preferentially with active genes, and is generally absent from regions in which histone H3 is methylated by the Enhancer of zeste [E(z)] Polycomb group silencing protein. Here we show that transcription is hypersensitive to cohesin levels in two exceptional cases where cohesin and the E(z)-mediated histone methylation simultaneously coat the entire Enhancer of split and invected-engrailed gene complexes in cells derived from Drosophila central nervous system. These gene complexes are modestly transcribed, and produce seven of the twelve transcripts that increase the most with cohesin knockdown genome-wide. Cohesin mutations alter eye development in the same manner as increased Enhancer of split activity, suggesting that similar regulation occurs in vivo. We propose that cohesin helps restrain transcription of these gene complexes, and that deregulation of similarly cohesin-hypersensitive genes may underlie developmental deficits in Cornelia de Lange syndrome.
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Affiliation(s)
- Cheri A. Schaaf
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Gurmukh Sahota
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Akbar M. Siddiqui
- Microarray Core Facility, Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Yuri B. Schwartz
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Tatyana G. Kahn
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
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Zhang H, Emmons SW. Regulation of the Caenorhabditis elegans posterior Hox gene egl-5 by microRNA and the polycomb-like gene sop-2. Dev Dyn 2009; 238:595-603. [PMID: 19235721 DOI: 10.1002/dvdy.21876] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In Caenorhabditis elegans, the domains of Hox gene expression are controlled by the novel global regulatory gene sop-2. We identified a region located 3' of the Hox gene egl-5 that promotes ectopic expression of an egl-5 reporter gene in a sop-2 mutant. SOP-2 could directly block positive regulatory factors acting in this region, or it could block their expression. We identified three possible miRNA binding sites within the egl-5 3' untranslated region (UTR). Cognate microRNAs are expressed in relevant tissues and can block egl-5 expression when expressed from a transgene. Mutation of the putative binding sites in the egl-5 3'UTR resulted in a modest degree of misexpression of a minimal egl-5 reporter gene, suggesting that microRNAs may contribute to the tight restriction of egl-5 expression to particular cell lineages.
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Affiliation(s)
- Hongjie Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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43
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Chen S, Rasmuson-Lestander Å. Regulation of the Drosophila engrailed gene by Polycomb repressor complex 2. Mech Dev 2009; 126:443-8. [DOI: 10.1016/j.mod.2009.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 01/02/2009] [Accepted: 01/17/2009] [Indexed: 12/01/2022]
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Fujioka M, Yusibova GL, Zhou J, Jaynes JB. The DNA-binding Polycomb-group protein Pleiohomeotic maintains both active and repressed transcriptional states through a single site. Development 2009; 135:4131-9. [PMID: 19029043 DOI: 10.1242/dev.024554] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Although epigenetic maintenance of either the active or repressed transcriptional state often involves overlapping regulatory elements, the underlying basis of this is not known. Epigenetic and pairing-sensitive silencing are related properties of Polycomb-group proteins, whereas their activities are generally opposed by the trithorax group. Both groups modify chromatin structure, but how their opposing activities are targeted to allow differential maintenance remains a mystery. Here, we identify a strong pairing-sensitive silencing (PSS) element at the 3' border of the Drosophila even skipped (eve) locus. This element can maintain repression during embryonic as well as adult eye development. Transgenic dissection revealed that silencing activity depends on a binding site for the Polycomb-group protein Pleiohomeotic (Pho) and on pho gene function. Binding sites for the trithorax-group protein GAGA factor also contribute, whereas sites for the known Polycomb response element binding factors Zeste and Dsp1 are dispensible. Normally, eve expression in the nervous system is maintained throughout larval stages. An enhancer that functions fully in embryos does not maintain expression, but the adjacent PSS element confers maintenance. This positive activity also depends on pho gene activity and on Pho binding. Thus, a DNA-binding complex requiring Pho is differentially regulated to facilitate epigenetic transcriptional memory of both the active and the repressed state.
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Affiliation(s)
- Miki Fujioka
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
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