1
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Zhao X, Yang X, Lv P, Xu Y, Wang X, Zhao Z, Du J. Polycomb regulates circadian rhythms in Drosophila in clock neurons. Life Sci Alliance 2024; 7:e202302140. [PMID: 37914396 PMCID: PMC10620068 DOI: 10.26508/lsa.202302140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Circadian rhythms are essential physiological feature for most living organisms. Previous studies have shown that epigenetic regulation plays a crucial role. There is a knowledge gap in the chromatin state of some key clock neuron clusters. In this study, we show that circadian rhythm is affected by the epigenetic regulator Polycomb (Pc) within the Drosophila clock neurons. To investigate the molecular mechanisms underlying the roles of Pc in these clock neuron clusters, we use targeted DamID (TaDa) to identify genes significantly bound by Pc in the neurons marked by C929-Gal4 (including l-LNvs cluster), R6-Gal4 (including s-LNvs cluster), R18H11-Gal4 (including DN1 cluster), and DVpdf-Gal4, pdf-Gal80 (including LNds cluster). It shows that Pc binds to the genes involved in the circadian rhythm pathways, arguing a direct role for Pc in regulating circadian rhythms through specific clock genes. This study shows the identification of Pc targets in the clock neuron clusters, providing potential resource for understanding the regulatory mechanisms of circadian rhythms by the PcG complex. Thus, this study provided an example for epigenetic regulation of adult behavior.
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Affiliation(s)
- Xianguo Zhao
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xingzhuo Yang
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Pengfei Lv
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuetong Xu
- https://ror.org/04v3ywz14 Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Xiangfeng Wang
- https://ror.org/04v3ywz14 Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Zhangwu Zhao
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Juan Du
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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2
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Askjaer P, Harr JC. Genetic approaches to revealing the principles of nuclear architecture. Curr Opin Genet Dev 2020; 67:52-60. [PMID: 33338753 DOI: 10.1016/j.gde.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosomes inside the eukaryotic nucleus is important for DNA replication, repair and gene expression. During development of multicellular organisms, different compendiums of genes are either repressed or activated to produce specific cell types. Genetic manipulation of tractable organisms is invaluable to elucidate chromosome configuration and the underlying mechanisms. Systematic inhibition of genes through RNA interference and, more recently, CRISPR/Cas9-based screens have identified new proteins with significant roles in nuclear organization. Coupling this with advances in imaging techniques, such as multiplexed DNA fluorescence in situ hybridization, and with tissue-specific genome profiling by DNA adenine methylation identification has increased our knowledge about the immense complexity and dynamics of the nucleus.
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Affiliation(s)
- Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville 41013, Spain.
| | - Jennifer C Harr
- Department of Biological Sciences, St. Mary's University, One Camino Santa Maria, San Antonio, TX, 78228, USA.
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3
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Van de Walle P, Muñoz-Jiménez C, Askjaer P, Schoofs L, Temmerman L. DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans. PLoS One 2020; 15:e0242939. [PMID: 33306687 PMCID: PMC7732058 DOI: 10.1371/journal.pone.0242939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/11/2020] [Indexed: 11/29/2022] Open
Abstract
Transcription factors govern many of the time- and tissue-specific gene expression events in living organisms. CEH-60, a homolog of the TALE transcription factor PBX in vertebrates, was recently characterized as a new regulator of intestinal lipid mobilization in Caenorhabditis elegans. Because CEH-60's orthologs and paralogs exhibit several other functions, notably in neuron and muscle development, and because ceh-60 expression is not limited to the C. elegans intestine, we sought to identify additional functions of CEH-60 through DNA adenine methyltransferase identification (DamID). DamID identifies protein-genome interaction sites through GATC-specific methylation. We here report 872 putative CEH-60 gene targets in young adult animals, and 587 in L2 larvae, many of which are associated with neuron development or muscle structure. In light of this, we investigate morphology and function of ceh-60 expressing AWC neurons, and contraction of pharyngeal muscles. We find no clear functional consequences of loss of ceh-60 in these assays, suggesting that in AWC neurons and pharyngeal muscle, CEH-60 function is likely more subtle or redundant with other factors.
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Affiliation(s)
- Pieter Van de Walle
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Celia Muñoz-Jiménez
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
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4
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Ilyin AA, Stolyarenko AD, Klenov MS, Shevelyov YY. Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells. Chromosoma 2020; 129:201-214. [PMID: 32500264 DOI: 10.1007/s00412-020-00738-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 05/05/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]
Abstract
Heterochromatin protein 1a (HP1a) is a well-known component of pericentromeric and telomeric heterochromatin in Drosophila. However, its role and the mechanisms of its binding in the chromosome arms (ChAs) remain largely unclear. Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamID-seq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. Although HP1a domains cover only 13% of ChAs, they non-randomly associate with 42% of TE insertions. Furthermore, HP1a on average propagates at 2-kb distances from the TE insertions. These data confirm the role of TEs in formation of HP1a islands in ChAs. However, only 18% of HP1a domains have adjacent TEs, indicating the existence of other mechanisms of HP1a domain formation besides spreading from TEs. In particular, many TE-independent HP1a domains correspond to the regions attached to the nuclear pore complexes (NPCs) or contain active gene promoters. However, HP1a occupancy on the promoters does not significantly influence expression of corresponding genes. At the same time, the steady-state transcript level of many genes located outside of HP1a domains was altered upon HP1a knockdown in the somatic cells of ovaries, thus pointing to the strong indirect effect of HP1a depletion. Collectively, our results support an existence of at least three different mechanisms of HP1a domain emergence in ChAs: spreading from TE insertions, transient interactions with the chromatin located near NPCs, and targeting to the promoters of moderately expressed genes.
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Affiliation(s)
- Artem A Ilyin
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182
| | - Anastasia D Stolyarenko
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182
| | - Mikhail S Klenov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182.
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182.
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5
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Redolfi J, Zhan Y, Valdes-Quezada C, Kryzhanovska M, Guerreiro I, Iesmantavicius V, Pollex T, Grand RS, Mulugeta E, Kind J, Tiana G, Smallwood SA, de Laat W, Giorgetti L. DamC reveals principles of chromatin folding in vivo without crosslinking and ligation. Nat Struct Mol Biol 2019; 26:471-480. [PMID: 31133702 PMCID: PMC6561777 DOI: 10.1038/s41594-019-0231-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/18/2019] [Indexed: 01/08/2023]
Abstract
Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after chromatin crosslinking. To measure chromosome structure in vivo, quantitatively and without crosslinking and ligation, we implemented a modified version of DamID named DamC, which combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and biophysical modelling of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of topologically associating domains (TADs), CTCF loops and confirms 3C-based measurements of the scaling of contact probabilities. Combining DamC with transposon-mediated genomic engineering shows that new loops can be formed between ectopic and endogenous CTCF sites, which redistributes physical interactions within TADs. DamC provides the first crosslinking- and ligation-free demonstration of the existence of key structural features of chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.
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Affiliation(s)
- Josef Redolfi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christian Valdes-Quezada
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Isabel Guerreiro
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | | | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW, Utrecht, the Netherlands.,University Medical Center Utrecht, Utrecht, the Netherlands
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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6
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Narbonne-Reveau K, Maurange C. Developmental regulation of regenerative potential in Drosophila by ecdysone through a bistable loop of ZBTB transcription factors. PLoS Biol 2019; 17:e3000149. [PMID: 30742616 PMCID: PMC6386533 DOI: 10.1371/journal.pbio.3000149] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 02/22/2019] [Accepted: 01/30/2019] [Indexed: 01/08/2023] Open
Abstract
In many organisms, the regenerative capacity of tissues progressively decreases as development progresses. However, the developmental mechanisms that restrict regenerative potential remain unclear. In Drosophila, wing imaginal discs become unable to regenerate upon damage during the third larval stage (L3). Here, we show that production of ecdysone after larvae reach their critical weight (CW) terminates the window of regenerative potential by acting on a bistable loop composed of two antagonistic Broad-complex/Tramtrack/Bric-à-brac Zinc-finger (ZBTB) genes: chinmo and broad (br). Around mid L3, ecdysone signaling silences chinmo and activates br to switch wing epithelial progenitors from a default self-renewing to a differentiation-prone state. Before mid L3, Chinmo promotes a strong regenerative response upon tissue damage. After mid L3, Br installs a nonpermissive state that represses regeneration. Transient down-regulation of ecdysone signaling or Br in late L3 larvae enhances chinmo expression in damaged cells that regain the capacity to regenerate. This work unveils a mechanism that ties the self-renewing and regenerative potential of epithelial progenitors to developmental progression. This study finds that the loss of regeneration potential in Drosophila wing imaginal discs is induced by the production of the steroid hormone ecdysone after the larva reaches its critical weight. Manipulating ecdysone signaling or the downstream transcription factors can uncouple regenerative properties from developmental progression. While some organisms exhibit remarkable regenerative abilities throughout their life, many animals, including mammals, present limited regenerative potential that progressively decreases during development. Understanding the mechanisms underlying this progressive loss is important to devise therapeutic approaches aiming at facilitating the regeneration of a damaged tissue throughout life. The fruitfly Drosophila is a powerful model organism to address such questions. Indeed, while tissues, such as imaginal discs, can fully regenerate if damaged during early development, they fail to do so upon damages during late development. We show here that restriction of regenerative potential occurring during midlarval stages is due to the production of a steroid hormone, named ecdysone. By genetically manipulating ecdysone signaling, we can uncouple regenerative abilities from developmental progression. In particular, we show that ecdysone signaling triggers a switch in the sequential expression of two transcription factors, Chinmo and Broad, that positively and negatively regulate the competence for imaginal disc regeneration, respectively. Our work therefore identifies a key developmental signal that restricts regenerative potential in insects and opens new perspectives on elucidating how regeneration-permissive transcriptional programs are locked as development progresses.
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Affiliation(s)
| | - Cédric Maurange
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
- * E-mail:
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7
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Pindyurin AV, Ilyin AA, Ivankin AV, Tselebrovsky MV, Nenasheva VV, Mikhaleva EA, Pagie L, van Steensel B, Shevelyov YY. The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a. Epigenetics Chromatin 2018; 11:65. [PMID: 30384843 PMCID: PMC6211408 DOI: 10.1186/s13072-018-0235-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background In most mammalian cell lines, chromatin located at the nuclear periphery is represented by condensed heterochromatin, as evidenced by microscopy observations and DamID mapping of lamina-associated domains (LADs) enriched in dimethylated Lys9 of histone H3 (H3K9me2). However, in Kc167 cell culture, the only Drosophilla cell type where LADs have previously been mapped, they are neither H3K9me2-enriched nor overlapped with the domains of heterochromatin protein 1a (HP1a). Results Here, using cell type-specific DamID we mapped genome-wide LADs, HP1a and Polycomb (Pc) domains from the central brain, Repo-positive glia, Elav-positive neurons and the fat body of Drosophila third instar larvae. Strikingly, contrary to Kc167 cells of embryonic origin, in neurons and, to a lesser extent, in glia and the fat body, HP1a domains appear to overlap strongly with LADs in both the chromosome arms and pericentromeric regions. Accordingly, centromeres reside closer to the nuclear lamina in neurons than in Kc167 cells. As expected, active gene promoters are mostly not present in LADs, HP1a and Pc domains. These domains are occupied by silent or weakly expressed genes with genes residing in the HP1a-bound LADs expressed at the lowest level. Conclusions In various differentiated Drosophila cell types, we discovered the existence of peripheral heterochromatin, similar to that observed in mammals. Our findings support the model that peripheral heterochromatin matures enhancing the repression of unwanted genes as cells terminally differentiate. Electronic supplementary material The online version of this article (10.1186/s13072-018-0235-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey V Pindyurin
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands. .,Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, 630090. .,Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, Novosibirsk, Russia, 630090.
| | - Artem A Ilyin
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182
| | - Anton V Ivankin
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia, 630090
| | - Mikhail V Tselebrovsky
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182.,QC Biochemistry Lab, Yaroslavl Pharmaceutical Complex for Production of Finished Dosage Forms, R-Pharm Group, Yaroslavl, Russia, 150061
| | - Valentina V Nenasheva
- Department of Viral and Cellular Molecular Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182
| | - Elena A Mikhaleva
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands.,Department of Cell Biology, Erasmus University Medical Center, 3015 GE, Rotterdam, The Netherlands
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia, 123182.
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8
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La Fortezza M, Grigolon G, Cosolo A, Pindyurin A, Breimann L, Blum H, van Steensel B, Classen AK. Correction to: DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis. Epigenetics Chromatin 2018; 11:38. [PMID: 29970137 PMCID: PMC6029416 DOI: 10.1186/s13072-018-0206-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marco La Fortezza
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Giovanna Grigolon
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Health Sciences and Technology, ETH Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Andrea Cosolo
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Alexey Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Laura Breimann
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany
| | - Bas van Steensel
- Division Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anne-Kathrin Classen
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany. .,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
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