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Asif-Laidin A, Casier K, Ziriat Z, Boivin A, Viodé E, Delmarre V, Ronsseray S, Carré C, Teysset L. Modeling early germline immunization after horizontal transfer of transposable elements reveals internal piRNA cluster heterogeneity. BMC Biol 2023; 21:117. [PMID: 37226160 PMCID: PMC10210503 DOI: 10.1186/s12915-023-01616-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND A fraction of all genomes is composed of transposable elements (TEs) whose mobility needs to be carefully controlled. In gonads, TE activity is repressed by PIWI-interacting RNAs (piRNAs), a class of small RNAs synthesized by heterochromatic loci enriched in TE fragments, called piRNA clusters. Maintenance of active piRNA clusters across generations is secured by maternal piRNA inheritance providing the memory for TE repression. On rare occasions, genomes encounter horizontal transfer (HT) of new TEs with no piRNA targeting them, threatening the host genome integrity. Naïve genomes can eventually start to produce new piRNAs against these genomic invaders, but the timing of their emergence remains elusive. RESULTS Using a set of TE-derived transgenes inserted in different germline piRNA clusters and functional assays, we have modeled a TE HT in Drosophila melanogaster. We have found that the complete co-option of these transgenes by a germline piRNA cluster can occur within four generations associated with the production of new piRNAs all along the transgenes and the germline silencing of piRNA sensors. Synthesis of new transgenic TE piRNAs is linked to piRNA cluster transcription dependent on Moonshiner and heterochromatin mark deposition that propagates more efficiently on short sequences. Moreover, we found that sequences located within piRNA clusters can have different piRNA profiles and can influence transcript accumulation of nearby sequences. CONCLUSIONS Our study reveals that genetic and epigenetic properties, such as transcription, piRNA profiles, heterochromatin, and conversion efficiency along piRNA clusters, could be heterogeneous depending on the sequences that compose them. These findings suggest that the capacity of transcriptional signal erasure induced by the chromatin complex specific of the piRNA cluster can be incomplete through the piRNA cluster loci. Finally, these results have revealed an unexpected level of complexity that highlights a new magnitude of piRNA cluster plasticity fundamental for the maintenance of genome integrity.
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Affiliation(s)
- Amna Asif-Laidin
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Karine Casier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
- Present Address: CNRS, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Telomere Biology, Paris, F-75005, France
| | - Zoheir Ziriat
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Antoine Boivin
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Elise Viodé
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Valérie Delmarre
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Stéphane Ronsseray
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Clément Carré
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France
| | - Laure Teysset
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & Small RNA Biology", Paris, F-75005, France.
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Yoth M, Jensen S, Brasset E. The Intricate Evolutionary Balance between Transposable Elements and Their Host: Who Will Kick at Goal and Convert the Next Try? BIOLOGY 2022; 11:710. [PMID: 35625438 PMCID: PMC9138309 DOI: 10.3390/biology11050710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
Abstract
Transposable elements (TEs) are mobile DNA sequences that can jump from one genomic locus to another and that have colonized the genomes of all living organisms. TE mobilization and accumulation are an important source of genomic innovations that greatly contribute to the host species evolution. To ensure their maintenance and amplification, TE transposition must occur in the germ cell genome. As TE transposition is also a major threat to genome integrity, the outcome of TE mobility in germ cell genomes could be highly dangerous because such mutations are inheritable. Thus, organisms have developed specialized strategies to protect the genome integrity from TE transposition, particularly in germ cells. Such effective TE silencing, together with ongoing mutations and negative selection, should result in the complete elimination of functional TEs from genomes. However, TEs have developed efficient strategies for their maintenance and spreading in populations, particularly by using horizontal transfer to invade the genome of novel species. Here, we discuss how TEs manage to bypass the host's silencing machineries to propagate in its genome and how hosts engage in a fightback against TE invasion and propagation. This shows how TEs and their hosts have been evolving together to achieve a fine balance between transposition and repression.
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Affiliation(s)
| | | | - Emilie Brasset
- iGReD, CNRS, INSERM, Faculté de Médecine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (M.Y.); (S.J.)
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Peral-Sanchez I, Hojeij B, Ojeda DA, Steegers-Theunissen RPM, Willaime-Morawek S. Epigenetics in the Uterine Environment: How Maternal Diet and ART May Influence the Epigenome in the Offspring with Long-Term Health Consequences. Genes (Basel) 2021; 13:31. [PMID: 35052371 PMCID: PMC8774448 DOI: 10.3390/genes13010031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
The societal burden of non-communicable disease is closely linked with environmental exposures and lifestyle behaviours, including the adherence to a poor maternal diet from the earliest preimplantation period of the life course onwards. Epigenetic variations caused by a compromised maternal nutritional status can affect embryonic development. This review summarises the main epigenetic modifications in mammals, especially DNA methylation, histone modifications, and ncRNA. These epigenetic changes can compromise the health of the offspring later in life. We discuss different types of nutritional stressors in human and animal models, such as maternal undernutrition, seasonal diets, low-protein diet, high-fat diet, and synthetic folic acid supplement use, and how these nutritional exposures epigenetically affect target genes and their outcomes. In addition, we review the concept of thrifty genes during the preimplantation period, and some examples that relate to epigenetic change and diet. Finally, we discuss different examples of maternal diets, their effect on outcomes, and their relationship with assisted reproductive technology (ART), including their implications on epigenetic modifications.
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Affiliation(s)
- Irene Peral-Sanchez
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.A.O.); (S.W.-M.)
| | - Batoul Hojeij
- Department Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3000 CA Rotterdam, The Netherlands; (B.H.); (R.P.M.S.-T.)
| | - Diego A. Ojeda
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.A.O.); (S.W.-M.)
| | - Régine P. M. Steegers-Theunissen
- Department Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3000 CA Rotterdam, The Netherlands; (B.H.); (R.P.M.S.-T.)
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Casier K, Boivin A, Carré C, Teysset L. Environmentally-Induced Transgenerational Epigenetic Inheritance: Implication of PIWI Interacting RNAs. Cells 2019; 8:cells8091108. [PMID: 31546882 PMCID: PMC6770481 DOI: 10.3390/cells8091108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/11/2022] Open
Abstract
Environmentally-induced transgenerational epigenetic inheritance is an emerging field. The understanding of associated epigenetic mechanisms is currently in progress with open questions still remaining. In this review, we present an overview of the knowledge of environmentally-induced transgenerational inheritance and associated epigenetic mechanisms, mainly in animals. The second part focuses on the role of PIWI-interacting RNAs (piRNAs), a class of small RNAs involved in the maintenance of the germline genome, in epigenetic memory to put into perspective cases of environmentally-induced transgenerational inheritance involving piRNA production. Finally, the last part addresses how genomes are facing production of new piRNAs, and from a broader perspective, how this process might have consequences on evolution and on sporadic disease development.
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Affiliation(s)
- Karine Casier
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France.
| | - Antoine Boivin
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France.
| | - Clément Carré
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France.
| | - Laure Teysset
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France.
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The Integrity of piRNA Clusters is Abolished by Insulators in the Drosophila Germline. Genes (Basel) 2019; 10:genes10030209. [PMID: 30862119 PMCID: PMC6471301 DOI: 10.3390/genes10030209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/13/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the retrotransposon gypsy. To understand how insulators contribute to piRNA cluster activity, we studied the effects of transgenes containing gypsy insulators on local organization of endogenous piRNA clusters. We show that transgene insertions interfere with piRNA precursor transcription, small RNA production and the formation of piRNA cluster-specific chromatin, a hallmark of which is Rhino, the germline homolog of the heterochromatin protein 1 (HP1). The mutations of Su(Hw) restored the integrity of piRNA clusters in transgenic strains. Surprisingly, Su(Hw) depletion enhanced the production of piRNAs by the domesticated telomeric retrotransposon TART, indicating that Su(Hw)-dependent elements protect TART transcripts from piRNA processing machinery in telomeres. A genome-wide analysis revealed that Su(Hw)-binding sites are depleted in endogenous germline piRNA clusters, suggesting that their functional integrity is under strict evolutionary constraints.
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Radion E, Morgunova V, Ryazansky S, Akulenko N, Lavrov S, Abramov Y, Komarov PA, Glukhov SI, Olovnikov I, Kalmykova A. Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline. Epigenetics Chromatin 2018; 11:40. [PMID: 30001204 PMCID: PMC6043984 DOI: 10.1186/s13072-018-0210-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Telomeric small RNAs related to PIWI-interacting RNAs (piRNAs) have been described in various eukaryotes; however, their role in germline-specific telomere function remains poorly understood. Using a Drosophila model, we performed an in-depth study of the biogenesis of telomeric piRNAs and their function in telomere homeostasis in the germline. RESULTS To fully characterize telomeric piRNA clusters, we integrated the data obtained from analysis of endogenous telomeric repeats, as well as transgenes inserted into different telomeric and subtelomeric regions. The small RNA-seq data from strains carrying telomeric transgenes demonstrated that all transgenes belong to a class of dual-strand piRNA clusters; however, their capacity to produce piRNAs varies significantly. Rhino, a paralog of heterochromatic protein 1 (HP1) expressed exclusively in the germline, is associated with all telomeric transgenes, but its enrichment correlates with the abundance of transgenic piRNAs. It is likely that this heterogeneity is determined by the sequence peculiarities of telomeric retrotransposons. In contrast to the heterochromatic non-telomeric germline piRNA clusters, piRNA loss leads to a dramatic decrease in HP1, Rhino, and trimethylated histone H3 lysine 9 in telomeric regions. Therefore, the presence of piRNAs is required for the maintenance of telomere chromatin in the germline. Moreover, piRNA loss causes telomere translocation from the nuclear periphery toward the nuclear interior but does not affect telomere end capping. Analysis of the telomere-associated sequences (TASs) chromatin revealed strong tissue specificity. In the germline, TASs are enriched with HP1 and Rhino, in contrast to somatic tissues, where they are repressed by Polycomb group proteins. CONCLUSIONS piRNAs play an essential role in the assembly of telomeric chromatin, as well as in nuclear telomere positioning in the germline. Telomeric arrays and TASs belong to a unique type of Rhino-dependent piRNA clusters with transcripts that serve simultaneously as piRNA precursors and as their only targets. Telomeric chromatin is highly sensitive to piRNA loss, implying the existence of a novel developmental checkpoint that depends on telomere integrity in the germline.
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Affiliation(s)
- Elizaveta Radion
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Sergey Lavrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Yuri Abramov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Pavel A Komarov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182.,Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Sergey I Glukhov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow, Russia, 123182.
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7
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Teo RYW, Anand A, Sridhar V, Okamura K, Kai T. Heterochromatin protein 1a functions for piRNA biogenesis predominantly from pericentric and telomeric regions in Drosophila. Nat Commun 2018; 9:1735. [PMID: 29728561 PMCID: PMC5935673 DOI: 10.1038/s41467-018-03908-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023] Open
Abstract
In metazoan germline, Piwi-interacting RNAs (piRNAs) provide defence against transposons. Piwi-piRNA complex mediates transcriptional silencing of transposons in nucleus. Heterochromatin protein 1a (HP1a) has been proposed to function downstream of Piwi-piRNA complex in Drosophila. Here we show that HP1a germline knockdown (HP1a-GLKD) leads to a reduction in the total and Piwi-bound piRNAs mapping to clusters and transposons insertions, predominantly in the regions close to telomeres and centromeres, resulting in derepression of a limited number of transposons from these regions. In addition, HP1a-GLKD increases the splicing of transcripts arising from clusters in above regions, suggesting HP1a also functions upstream to piRNA processing. Evolutionarily old transposons enriched in the pericentric regions exhibit significant loss in piRNAs targeting these transposons upon HP1a-GLKD. Our study suggests that HP1a functions to repress transposons in a chromosomal compartmentalised manner.
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Affiliation(s)
- Ryan Yee Wei Teo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, 117543, Singapore, Singapore
- Department of Pathology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | - Amit Anand
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore.
| | - Vishweshwaren Sridhar
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore
| | - Toshie Kai
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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Rogers AK, Situ K, Perkins EM, Toth KF. Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery. Genes Dev 2017; 31:1858-1869. [PMID: 29021243 PMCID: PMC5695087 DOI: 10.1101/gad.303214.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/13/2017] [Indexed: 11/24/2022]
Abstract
Here, Rogers et al. investigated how piRNA precursors are selected and channeled into the endonuclease Zucchini (Zuc)-dependent processing pathway in Drosophila germ cells. They engineered a modular system that can induce primary piRNA biogenesis at an arbitrary locus even in the absence of native piRNA precursors. They also established a subcellular compartmentalization as a key factor in RNA processing. The piRNA pathway represses transposable elements in the gonads and thereby plays a vital role in protecting the integrity of germline genomes of animals. Mature piRNAs are processed from longer transcripts, piRNA precursors (pre-piRNAs). In Drosophila, processing of pre-piRNAs is initiated by piRNA-guided Slicer cleavage or the endonuclease Zucchini (Zuc). As Zuc does not have any sequence or structure preferences in vitro, it is not known how piRNA precursors are selected and channeled into the Zuc-dependent processing pathway. We show that a heterologous RNA that lacks complementary piRNAs is processed into piRNAs upon recruitment of several piRNA pathway factors. This processing requires Zuc and the helicase Armitage (Armi). Aubergine (Aub), Argonaute 3 (Ago3), and components of the nuclear RDC complex, which are required for normal piRNA biogenesis in germ cells, are dispensable. Our approach allows discrimination of proteins involved in the transcription and export of piRNA precursors from components required for the cytoplasmic processing steps. piRNA processing correlates with localization of the substrate RNA to nuage, a distinct membraneless cytoplasmic compartment, which surrounds the nucleus of germ cells, suggesting that sequestration of RNA to this subcellular compartment is both necessary and sufficient for selecting piRNA biogenesis substrates.
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Affiliation(s)
- Alicia K Rogers
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Kathy Situ
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Edward M Perkins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Katalin Fejes Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Asif-Laidin A, Delmarre V, Laurentie J, Miller WJ, Ronsseray S, Teysset L. Short and long-term evolutionary dynamics of subtelomeric piRNA clusters in Drosophila. DNA Res 2017; 24:459-472. [PMID: 28459978 PMCID: PMC5737368 DOI: 10.1093/dnares/dsx017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
Two Telomeric Associated Sequences, TAS-R and TAS-L, form the principal subtelomeric repeat families identified in Drosophila melanogaster. They are PIWI-interacting RNA (piRNA) clusters involved in repression of Transposable Elements. In this study, we revisited TAS structural and functional dynamics in D. melanogaster and in related species. In silico analysis revealed that TAS-R family members are composed of previously uncharacterized domains. This analysis also showed that TAS-L repeats are composed of arrays of a region we have named "TAS-L like" (TLL) identified specifically in one TAS-R family member, X-TAS. TLL were also present in other species of the melanogaster subgroup. Therefore, it is possible that TLL represents an ancestral subtelomeric piRNA core-cluster. Furthermore, all D. melanogaster genomes tested possessed at least one TAS-R locus, whereas TAS-L can be absent. A screen of 110 D. melanogaster lines showed that X-TAS is always present in flies living in the wild, but often absent in long-term laboratory stocks and that natural populations frequently lost their X-TAS within 2 years upon lab conditioning. Therefore, the unexpected structural and temporal dynamics of subtelomeric piRNA clusters demonstrated here suggests that genome organization is subjected to distinct selective pressures in the wild and upon domestication in the laboratory.
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Affiliation(s)
- Amna Asif-Laidin
- Sorbonne Universités, UPMC University of Paris 06, CNRS, Biologie du Développement Paris-Seine, Institut de Biologie Paris-Seine (LBD-IBPS), 75005 Paris, France
| | - Valérie Delmarre
- Sorbonne Universités, UPMC University of Paris 06, CNRS, Biologie du Développement Paris-Seine, Institut de Biologie Paris-Seine (LBD-IBPS), 75005 Paris, France
| | - Jeanne Laurentie
- Sorbonne Universités, UPMC University of Paris 06, CNRS, Biologie du Développement Paris-Seine, Institut de Biologie Paris-Seine (LBD-IBPS), 75005 Paris, France
| | - Wolfgang J. Miller
- Lab Genome Dynamics, Department for Cell & Developmental Biology, Center of Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Stéphane Ronsseray
- Sorbonne Universités, UPMC University of Paris 06, CNRS, Biologie du Développement Paris-Seine, Institut de Biologie Paris-Seine (LBD-IBPS), 75005 Paris, France
| | - Laure Teysset
- Sorbonne Universités, UPMC University of Paris 06, CNRS, Biologie du Développement Paris-Seine, Institut de Biologie Paris-Seine (LBD-IBPS), 75005 Paris, France
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From Embryo to Adult: piRNA-Mediated Silencing throughout Germline Development in Drosophila. G3-GENES GENOMES GENETICS 2017; 7:505-516. [PMID: 27932388 PMCID: PMC5295597 DOI: 10.1534/g3.116.037291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In metazoan germ cells, transposable element activity is repressed by small noncoding PIWI-associated RNAs (piRNAs). Numerous studies in Drosophila have elucidated the mechanism of this repression in the adult germline. However, when and how transposable element repression is established during germline development has not been addressed. Here, we show that homology-dependent trans silencing is active in female primordial germ cells from late embryogenesis through pupal stages, and that genes related to the adult piRNA pathway are required for silencing during development. In larval gonads, we detect rhino-dependent piRNAs indicating de novo biogenesis of functional piRNAs during development. Those piRNAs exhibit the molecular signature of the “ping-pong” amplification step. Moreover, we show that Heterochromatin Protein 1a is required for the production of piRNAs coming from telomeric transposable elements. Furthermore, as in adult ovaries, incomplete, bimodal, and stochastic repression resembling variegation can occur at all developmental stages. Clonal analysis indicates that the repression status established in embryonic germ cells is maintained until the adult stage, suggesting the implication of a cellular memory mechanism. Taken together, data presented here show that piRNAs and their associated proteins are epigenetic components of a continuous repression system throughout germ cell development.
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Chang YC, Chiu CC, Yuo CY, Chan WL, Chang YS, Chang WH, Wu SM, Chou HL, Liu TC, Lu CY, Yang WK, Chang JG. An XIST-related small RNA regulates KRAS G-quadruplex formation beyond X-inactivation. Oncotarget 2016; 7:86713-86729. [PMID: 27880931 PMCID: PMC5349948 DOI: 10.18632/oncotarget.13433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022] Open
Abstract
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex. Moreover, the microarray data showed the knockdown of XPi2 down-regulated the KRAS pathway. Consistently, we tested the expression of ten genes, including KRAS, which was correlated with a G-quadruplex formation and found the knockdown of XPi2 caused a dramatic decrease in the transcription level of KRAS among the ten genes. The results of CD/NMR assay also supported the interaction of XPi2 and the polypurine-polypyrimidine element of KRAS. Accordingly, XPi2 may stimulate the KRAS expression by attenuating G-quadruplex formation. Our present work sheds light on the novel role of small RNA XPi2 in modulating the G-quadruplex formation which may play some essential roles in the KRAS- associated carcinogenesis.
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Affiliation(s)
- Yuli C. Chang
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chien-Chih Chiu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Yee Yuo
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Ling Chan
- Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University
| | - Ya-Sian Chang
- Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Wen-Hsin Chang
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shou-Mei Wu
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Han-Lin Chou
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ta-Chih Liu
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Wen-Kuang Yang
- Cell/Gene Therapy Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
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12
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Chen YCA, Stuwe E, Luo Y, Ninova M, Le Thomas A, Rozhavskaya E, Li S, Vempati S, Laver JD, Patel DJ, Smibert CA, Lipshitz HD, Toth KF, Aravin AA. Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. Mol Cell 2016; 63:97-109. [PMID: 27292797 DOI: 10.1016/j.molcel.2016.05.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/04/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
Abstract
Small non-coding RNAs called piRNAs serve as guides for an adaptable immune system that represses transposable elements in germ cells of Metazoa. In Drosophila the RDC complex, composed of Rhino, Deadlock and Cutoff (Cuff) bind chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is required for transcription of piRNA precursors, though the mechanism by which it licenses transcription remained unknown. Here, we show that Cuff prevents premature termination of RNA polymerase II. Cuff prevents cleavage of nascent RNA at poly(A) sites by interfering with recruitment of the cleavage and polyadenylation specificity factor (CPSF) complex. Cuff also protects processed transcripts from degradation by the exonuclease Rat1. Our work reveals a conceptually different mechanism of transcriptional enhancement. In contrast to other factors that regulate termination by binding to specific signals on nascent RNA, the RDC complex inhibits termination in a chromatin-dependent and sequence-independent manner.
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Affiliation(s)
- Yung-Chia Ariel Chen
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Evelyn Stuwe
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA.,Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Yicheng Luo
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Maria Ninova
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Adrien Le Thomas
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Ekaterina Rozhavskaya
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Sisi Li
- Memorial Sloan-Kettering Cancer Center, Structural Biology Program, 1275 York Avenue, New York, NY, 10021 USA
| | - Sivani Vempati
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Dinshaw J Patel
- Memorial Sloan-Kettering Cancer Center, Structural Biology Program, 1275 York Avenue, New York, NY, 10021 USA
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Katalin Fejes Toth
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
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13
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Hermant C, Boivin A, Teysset L, Delmarre V, Asif-Laidin A, van den Beek M, Antoniewski C, Ronsseray S. Paramutation in Drosophila Requires Both Nuclear and Cytoplasmic Actors of the piRNA Pathway and Induces Cis-spreading of piRNA Production. Genetics 2015; 201:1381-96. [PMID: 26482790 PMCID: PMC4676525 DOI: 10.1534/genetics.115.180307] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/05/2015] [Indexed: 01/24/2023] Open
Abstract
Transposable element activity is repressed in the germline in animals by PIWI-interacting RNAs (piRNAs), a class of small RNAs produced by genomic loci mostly composed of TE sequences. The mechanism of induction of piRNA production by these loci is still enigmatic. We have shown that, in Drosophila melanogaster, a cluster of tandemly repeated P-lacZ-white transgenes can be activated for piRNA production by maternal inheritance of a cytoplasm containing homologous piRNAs. This activated state is stably transmitted over generations and allows trans-silencing of a homologous transgenic target in the female germline. Such an epigenetic conversion displays the functional characteristics of a paramutation, i.e., a heritable epigenetic modification of one allele by the other. We report here that piRNA production and trans-silencing capacities of the paramutated cluster depend on the function of the rhino, cutoff, and zucchini genes involved in primary piRNA biogenesis in the germline, as well as on that of the aubergine gene implicated in the ping-pong piRNA amplification step. The 21-nt RNAs, which are produced by the paramutated cluster, in addition to 23- to 28-nt piRNAs are not necessary for paramutation to occur. Production of these 21-nt RNAs requires Dicer-2 but also all the piRNA genes tested. Moreover, cytoplasmic transmission of piRNAs homologous to only a subregion of the transgenic locus can generate a strong paramutated locus that produces piRNAs along the whole length of the transgenes. Finally, we observed that maternally inherited transgenic small RNAs can also impact transgene expression in the soma. In conclusion, paramutation involves both nuclear (Rhino, Cutoff) and cytoplasmic (Aubergine, Zucchini) actors of the piRNA pathway. In addition, since it is observed between nonfully homologous loci located on different chromosomes, paramutation may play a crucial role in epigenome shaping in Drosophila natural populations.
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Affiliation(s)
- Catherine Hermant
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Antoine Boivin
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Laure Teysset
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Valérie Delmarre
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Amna Asif-Laidin
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Marius van den Beek
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Drosophila Genetics and Epigenetics," F-75005, Paris, France CNRS, FR3631, Institut de Biologie Paris-Seine, ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
| | - Christophe Antoniewski
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Drosophila Genetics and Epigenetics," F-75005, Paris, France CNRS, FR3631, Institut de Biologie Paris-Seine, ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
| | - Stéphane Ronsseray
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
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14
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Lim RSM, Kai T. A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners. Semin Cell Dev Biol 2015; 47-48:17-31. [PMID: 26582251 DOI: 10.1016/j.semcdb.2015.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.
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Affiliation(s)
- Robyn S M Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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15
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Ronsseray S. Paramutation phenomena in non-vertebrate animals. Semin Cell Dev Biol 2015; 44:39-46. [PMID: 26318740 DOI: 10.1016/j.semcdb.2015.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/18/2015] [Indexed: 01/23/2023]
Abstract
Paramutation was initially described in maize and was defined as an epigenetic interaction between two alleles of a locus, through which one allele induces a heritable modification of the other allele without modifying the DNA sequence [1,2]. Thus it implies that the paramutated allele conserves its new properties on the long term over generations even in the absence of the paramutagenic allele and that it turns paramutagenic itself, without undergoing any changes in the DNA sequence. Some epigenetic interactions have been described in two non-vertebrate animal models, which appear to exhibit similar properties. Both systems are linked to trans-generational transmission of non-coding small RNAs. In Drosophila melanogaster, paramutation is correlated with transmission of PIWI-Interacting RNAs (piRNAs), a class of small non-coding RNAs that repress mobile DNA in the germline. A tandem repeated transgenic locus producing abundant ovarian piRNAs can activate piRNA production and associated homology-dependent silencing at a locus that was previously stably devoid of such capacities. The newly converted locus is then perfectly stable in absence of the inducer locus (>100 generations) and becomes fully paramutagenic. In Caenorhabditis elegans, paramutation is correlated with transmission of siRNAs, which are produced by transgenes targeted by piRNAs in the germline. Indeed, a transgenic locus, targeted by the piRNA machinery, produces siRNAs that can induce silencing of homologous transgenes, which can be further transmitted in a repressed state over generations despite the absence of the inducer transgenic locus. As in fly, the paramutated locus can become fully paramutagenic, and paramutation can be mediated by cytoplasmic inheritance without transmission of the paramutagenic locus itself. Nevertheless, in contrast to flies where the induction is only maternally inherited, both parents can transmit it in worms. In addition, a reciprocal phenomenon - (from off toward on) - appears to be also possible in worms as some activated transgenes can reactivate silent transgenes in the germline, and this modification can also be transmitted to next generations, even so it appears to be only partially stable. Thus, in a given system, opposite paramutation-like phenomena could exist, mediated by antagonist active pathways. As in plants, paramutation in flies and worms correlates with chromatin structure modification of the paramutated locus. In flies, inheritance of small RNAs from one generation to the next transmits a memory mainly targeting loci for repression whereas in worms, small RNAs can target loci either for repression or expression. Nevertheless, in the two species, paramutation can play an important role in the epigenome establishment.
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Affiliation(s)
- Stéphane Ronsseray
- Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR 7622, Developmental Biology, 9 quai Saint-Bernard, F-75005 Paris, France; CNRS, IBPS, UMR 7622, Developmental Biology, 9 quai Saint-Bernard, F-75005 Paris, France.
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16
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Majumdar S, Rio DC. P Transposable Elements in Drosophila and other Eukaryotic Organisms. Microbiol Spectr 2015; 3:MDNA3-0004-2014. [PMID: 26104714 PMCID: PMC4399808 DOI: 10.1128/microbiolspec.mdna3-0004-2014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 11/20/2022] Open
Abstract
P transposable elements were discovered in Drosophila as the causative agents of a syndrome of genetic traits called hybrid dysgenesis. Hybrid dysgenesis exhibits a unique pattern of maternal inheritance linked to the germline-specific small RNA piwi-interacting (piRNA) pathway. The use of P transposable elements as vectors for gene transfer and as genetic tools revolutionized the field of Drosophila molecular genetics. P element transposons have served as a useful model to investigate mechanisms of cut-and-paste transposition in eukaryotes. Biochemical studies have revealed new and unexpected insights into how eukaryotic DNA-based transposons are mobilized. For example, the P element transposase makes unusual 17nt-3' extended double-strand DNA breaks at the transposon termini and uses guanosine triphosphate (GTP) as a cofactor to promote synapsis of the two transposon ends early in the transposition pathway. The N-terminal DNA binding domain of the P element transposase, called a THAP domain, contains a C2CH zinc-coordinating motif and is the founding member of a large family of animal-specific site-specific DNA binding proteins. Over the past decade genome sequencing efforts have revealed the presence of P element-like transposable elements or P element transposase-like genes (called THAP9) in many eukaryotic genomes, including vertebrates, such as primates including humans, zebrafish and Xenopus, as well as the human parasite Trichomonas vaginalis, the sea squirt Ciona, sea urchin and hydra. Surprisingly, the human and zebrafish P element transposase-related THAP9 genes promote transposition of the Drosophila P element transposon DNA in human and Drosophila cells, indicating that the THAP9 genes encode active P element "transposase" proteins.
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Affiliation(s)
| | - Donald C. Rio
- Department of Molecular and Cell Biology University of California, Berkeley Berkeley, CA 94720-3204
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17
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Schott D, Yanai I, Hunter CP. Natural RNA interference directs a heritable response to the environment. Sci Rep 2014; 4:7387. [PMID: 25552271 PMCID: PMC4894413 DOI: 10.1038/srep07387] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/20/2014] [Indexed: 11/14/2022] Open
Abstract
RNA interference can induce heritable gene silencing, but it remains unexplored whether similar mechanisms play a general role in responses to cues that occur in the wild. We show that transient, mild heat stress in the nematode Caenorhabditis elegans results in changes in messenger RNA levels that last for more than one generation. The affected transcripts are enriched for genes targeted by germline siRNAs downstream of the piRNA pathway, and worms defective for germline RNAi are defective for these heritable effects. Our results demonstrate that a specific siRNA pathway transmits information about variable environmental conditions between generations.
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Affiliation(s)
- Daniel Schott
- Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Itai Yanai
- Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Craig P Hunter
- Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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18
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Baranasic D, Oppermann T, Cheaib M, Cullum J, Schmidt H, Simon M. Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia. mBio 2014; 5:e01328. [PMID: 25389173 PMCID: PMC4235209 DOI: 10.1128/mbio.01328-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 06/24/2014] [Indexed: 12/02/2022] Open
Abstract
UNLABELLED Antigenic or phenotypic variation is a widespread phenomenon of expression of variable surface protein coats on eukaryotic microbes. To clarify the mechanism behind mutually exclusive gene expression, we characterized the genetic properties of the surface antigen multigene family in the ciliate Paramecium tetraurelia and the epigenetic factors controlling expression and silencing. Genome analysis indicated that the multigene family consists of intrachromosomal and subtelomeric genes; both classes apparently derive from different gene duplication events: whole-genome and intrachromosomal duplication. Expression analysis provides evidence for telomere position effects, because only subtelomeric genes follow mutually exclusive transcription. Microarray analysis of cultures deficient in Rdr3, an RNA-dependent RNA polymerase, in comparison to serotype-pure wild-type cultures, shows cotranscription of a subset of subtelomeric genes, indicating that the telomere position effect is due to a selective occurrence of Rdr3-mediated silencing in subtelomeric regions. We present a model of surface antigen evolution by intrachromosomal gene duplication involving the maintenance of positive selection of structurally relevant regions. Further analysis of chromosome heterogeneity shows that alternative telomere addition regions clearly affect transcription of closely related genes. Consequently, chromosome fragmentation appears to be of crucial importance for surface antigen expression and evolution. Our data suggest that RNAi-mediated control of this genetic network by trans-acting RNAs allows rapid epigenetic adaptation by phenotypic variation in combination with long-term genetic adaptation by Darwinian evolution of antigen genes. IMPORTANCE Alternating surface protein structures have been described for almost all eukaryotic microbes, and a broad variety of functions have been described, such as virulence factors, adhesion molecules, and molecular camouflage. Mechanisms controlling gene expression of variable surface proteins therefore represent a powerful tool for rapid phenotypic variation across kingdoms in pathogenic as well as free-living eukaryotic microbes. However, the epigenetic mechanisms controlling synchronous expression and silencing of individual genes are hardly understood. Using the ciliate Paramecium tetraurelia as a (epi)genetic model, we showed that a subtelomeric gene position effect is associated with the selective occurrence of RNAi-mediated silencing of silent surface protein genes, suggesting small interfering RNA (siRNA)-mediated epigenetic cross talks between silent and active surface antigen genes. Our integrated genomic and molecular approach discloses the correlation between gene position effects and siRNA-mediated trans-silencing, thus providing two new parameters for regulation of mutually exclusive gene expression and the genomic organization of variant gene families.
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Affiliation(s)
| | - Timo Oppermann
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - John Cullum
- Department for Genetics, Faculty of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Helmut Schmidt
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Martin Simon
- Saarland University, Centre for Human and Molecular Biology, Molecular Cellular Dynamics, Saarbrücken, Germany
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19
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Le Thomas A, Stuwe E, Li S, Du J, Marinov G, Rozhkov N, Chen YCA, Luo Y, Sachidanandam R, Toth KF, Patel D, Aravin AA. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev 2014; 28:1667-80. [PMID: 25085419 PMCID: PMC4117942 DOI: 10.1101/gad.245514.114] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
piRNAs guide the repression of diverse transposable elements in metazoan germ cells. Le Thomas et al. show that piRNA biogenesis in Drosophila germ cells depends on the inheritance of homologous piRNAs from the previous generation. Transgenerationally inherited piRNAs trigger piRNA biogenesis in the progeny by two different mechanisms. First, inherited piRNAs guide post-transcriptional processing of precursors into mature piRNAs. Second, inherited piRNAs direct the modification of the chromatin state of cluster sequences. This study provides key insights into the transgenerational mechanism that specifies piRNA biogenesis in the germline. Small noncoding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. We found that transgenerationally inherited piRNAs provide the critical trigger for piRNA production from homologous genomic regions in the next generation by two different mechanisms. First, inherited piRNAs enhance processing of homologous transcripts into mature piRNAs by initiating the ping-pong cycle in the cytoplasm. Second, inherited piRNAs induce installment of the histone 3 Lys9 trimethylation (H3K9me3) mark on genomic piRNA cluster sequences. The heterochromatin protein 1 (HP1) homolog Rhino binds to the H3K9me3 mark through its chromodomain and is enriched over piRNA clusters. Rhino recruits the piRNA biogenesis factor Cutoff to piRNA clusters and is required for efficient transcription of piRNA precursors. We propose that transgenerationally inherited piRNAs act as an epigenetic memory for identification of substrates for piRNA biogenesis on two levels: by inducing a permissive chromatin environment for piRNA precursor synthesis and by enhancing processing of these precursors.
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Affiliation(s)
- Adrien Le Thomas
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA; Ecole Doctorale Complexité du Vivant, Université Pierre et Marie Curie, 75005 Paris, France
| | - Evelyn Stuwe
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA; Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Sisi Li
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Jiamu Du
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA;
| | - Georgi Marinov
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Nikolay Rozhkov
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yung-Chia Ariel Chen
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Yicheng Luo
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Ravi Sachidanandam
- Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Katalin Fejes Toth
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Dinshaw Patel
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Alexei A Aravin
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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20
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A transgenerational process defines piRNA biogenesis in Drosophila virilis. Cell Rep 2014; 8:1617-1623. [PMID: 25199836 DOI: 10.1016/j.celrep.2014.08.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 05/22/2014] [Accepted: 08/06/2014] [Indexed: 11/23/2022] Open
Abstract
Piwi-interacting (pi)RNAs repress diverse transposable elements in germ cells of Metazoa and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two D. virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the transgenerational inheritance of an epigenetic signal, presumably in the form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis through the installment of H3K9me3 on piRNA clusters.
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21
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Molla-Herman A, Matias NR, Huynh JR. Chromatin modifications regulate germ cell development and transgenerational information relay. CURRENT OPINION IN INSECT SCIENCE 2014; 1:10-18. [PMID: 32846502 DOI: 10.1016/j.cois.2014.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/23/2014] [Accepted: 04/23/2014] [Indexed: 06/11/2023]
Abstract
Germ cells transmit genetic, cytoplasmic and epigenetic information to the next generation. Recent reports describe the importance of chromatin modifiers and small RNAs for germ cells development in Drosophila. We also review exciting progress in our understanding of piRNAs functions, which demonstrate that this class of small RNAs is both an adaptive and inheritable epigenetic memory.
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Affiliation(s)
- Anahi Molla-Herman
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France; CNRS UMR3215, Inserm U934, F-75248 Paris, France
| | - Neuza R Matias
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France; CNRS UMR3215, Inserm U934, F-75248 Paris, France
| | - Jean-René Huynh
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France; CNRS UMR3215, Inserm U934, F-75248 Paris, France.
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22
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Basquin D, Spierer A, Begeot F, Koryakov DE, Todeschini AL, Ronsseray S, Vieira C, Spierer P, Delattre M. The Drosophila Su(var)3-7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing. PLoS One 2014; 9:e96802. [PMID: 24820312 PMCID: PMC4018442 DOI: 10.1371/journal.pone.0096802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/11/2014] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin is made of repetitive sequences, mainly transposable elements (TEs), the regulation of which is critical for genome stability. We have analyzed the role of the heterochromatin-associated Su(var)3-7 protein in Drosophila ovaries. We present evidences that Su(var)3-7 is required for correct oogenesis and female fertility. It accumulates in heterochromatic domains of ovarian germline and somatic cells nuclei, where it co-localizes with HP1. Homozygous mutant females display ovaries with frequent degenerating egg-chambers. Absence of Su(var)3-7 in embryos leads to defects in meiosis and first mitotic divisions due to chromatin fragmentation or chromosome loss, showing that Su(var)3-7 is required for genome integrity. Females homozygous for Su(var)3-7 mutations strongly impair repression of P-transposable element induced gonadal dysgenesis but have minor effects on other TEs. Su(var)3-7 mutations reduce piRNA cluster transcription and slightly impact ovarian piRNA production. However, this modest piRNA reduction does not correlate with transposon de-silencing, suggesting that the moderate effect of Su(var)3-7 on some TE repression is not linked to piRNA production. Strikingly, Su(var)3-7 genetically interacts with the piwi and aubergine genes, key components of the piRNA pathway, by strongly impacting female fertility without impairing transposon silencing. These results lead us to propose that the interaction between Su(var)3-7 and piwi or aubergine controls important developmental processes independently of transposon silencing.
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Affiliation(s)
- Denis Basquin
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Anne Spierer
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Flora Begeot
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Anne-Laure Todeschini
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, Paris, France
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, Paris, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon1, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Pierre Spierer
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Marion Delattre
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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Olovnikov IA, Kalmykova AI. piRNA clusters as a main source of small RNAs in the animal germline. BIOCHEMISTRY (MOSCOW) 2014; 78:572-84. [PMID: 23980884 DOI: 10.1134/s0006297913060035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PIWI subfamily Argonaute proteins and small RNAs bound to them (PIWI interacting RNA, piRNA) control mobilization of transposable elements (TE) in the animal germline. piRNAs are generated by distinct genomic regions termed piRNA clusters. piRNA clusters are often extensive loci enriched in damaged fragments of TEs. New TE integration into piRNA clusters causes production of TE-specific piRNAs and repression of cognate sequences. piRNAs are thought to be generated from long single-stranded precursors encoded by piRNA clusters. Special chromatin structures might be essential to distinguish these genomic loci as a source for piRNAs. In this review, we present recent findings on the structural organization of piRNA clusters and piRNA biogenesis in Drosophila and other organisms, which are important for understanding a key epigenetic mechanism that provides defense against TE expansion.
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Affiliation(s)
- I A Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
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de Vanssay A, Bougé AL, Boivin A, Hermant C, Teysset L, Delmarre V, Antoniewski C, Ronsseray S. piRNAs and epigenetic conversion in Drosophila. Fly (Austin) 2013; 7:237-41. [PMID: 24088599 DOI: 10.4161/fly.26522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transposable element (TE) activity is repressed in the Drosophila germline by Piwi-Interacting RNAs (piRNAs), a class of small non-coding RNAs. These piRNAs are produced by discrete genomic loci containing TE fragments. In a recent publication, we tested for the existence of a strict epigenetic induction of piRNA production capacity by a locus in the D. melanogaster genome. We used 2 lines carrying a transgenic 7-copy tandem cluster (P-lacZ-white) at the same genomic site. This cluster generates in both lines a local heterochromatic sector. One line (T-1) produces high levels of ovarian piRNAs homologous to the P-lacZ-white transgenes and shows a strong capacity to repress homologous sequences in trans, whereas the other line (BX2) is devoid of both of these capacities. The properties of these 2 lines are perfectly stable over generations. We have shown that the maternal transmission of a cytoplasm carrying piRNAs from the first line can confer to the inert transgenic locus of the second, a totally de novo capacity to produce high levels of piRNAs as well as the ability to induce homology-dependent silencing in trans. These new properties are stably inherited over generations (n>50). Furthermore, the converted locus has itself become able to convert an inert transgenic locus via cytoplasmic maternal inheritance. This results in a stable epigenetic conversion process, which can be performed recurrently--a phenomenon termed paramutation and discovered in Maize 60 y ago. Paramutation in Drosophila corresponds to the first stable paramutation in animals and provides a model system to investigate the epigenetically induced emergence of a piRNA-producing locus, a crucial step in epigenome shaping. In this Extra View, we discuss some additional functional aspects and the possible molecular mechanism of this piRNA-linked paramutation.
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Affiliation(s)
- Augustin de Vanssay
- Epigenetic Repression and Mobile DNA; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
| | - Anne-Laure Bougé
- Drosophila Genetics and Epigenetics; CNRS URA2578; Institut Pasteur; Paris, France
| | - Antoine Boivin
- Epigenetic Repression and Mobile DNA; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
| | - Catherine Hermant
- Epigenetic Repression and Mobile DNA; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
| | - Laure Teysset
- Epigenetic Repression and Mobile DNA; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
| | - Valérie Delmarre
- Epigenetic Repression and Mobile DNA; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
| | | | - Stéphane Ronsseray
- Epigenetic Repression and Mobile DNA; Laboratoire Biologie du Développement; UMR7622; CNRS-Université Pierre et Marie Curie; Paris, France
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25
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Kawaoka S, Hara K, Shoji K, Kobayashi M, Shimada T, Sugano S, Tomari Y, Suzuki Y, Katsuma S. The comprehensive epigenome map of piRNA clusters. Nucleic Acids Res 2012; 41:1581-90. [PMID: 23258708 PMCID: PMC3561999 DOI: 10.1093/nar/gks1275] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PIWI-interacting RNA (piRNA) clusters act as anti-transposon/retrovirus centers. Integration of selfish jumping elements into piRNA clusters generates de novo piRNAs, which in turn exert trans-silencing activity against these elements in animal gonads. To date, neither genome-wide chromatin modification states of piRNA clusters nor a mode for piRNA precursor transcription have been well understood. Here, to understand the chromatin landscape of piRNA clusters and how piRNA precursors are generated, we analyzed the transcriptome, transcription start sites (TSSs) and the chromatin landscape of the BmN4 cell line, which harbors the germ-line piRNA pathway. Notably, our epigenomic map demonstrated the highly euchromatic nature of unique piRNA clusters. RNA polymerase II was enriched for TSSs that transcribe piRNA precursors. piRNA precursors possessed 5'-cap structures as well as 3'-poly A-tails. Collectively, we envision that the euchromatic, opened nature of unique piRNA clusters or piRNA cluster-associated TSSs allows piRNA clusters to capture new insertions efficiently.
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Affiliation(s)
- Shinpei Kawaoka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Tokyo, Japan.
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26
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de Vanssay A, Bougé AL, Boivin A, Hermant C, Teysset L, Delmarre V, Antoniewski C, Ronsseray S. Paramutation in Drosophila linked to emergence of a piRNA-producing locus. Nature 2012; 490:112-5. [PMID: 22922650 DOI: 10.1038/nature11416] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 07/16/2012] [Indexed: 11/10/2022]
Abstract
A paramutation is an epigenetic interaction between two alleles of a locus, through which one allele induces a heritable modification in the other allele without modifying the DNA sequence. The paramutated allele itself becomes paramutagenic, that is, capable of epigenetically converting a new paramutable allele. Here we describe a case of paramutation in animals showing long-term transmission over generations. We previously characterized a homology-dependent silencing mechanism referred to as the trans-silencing effect (TSE), involved in P-transposable-element repression in the germ line. We now show that clusters of P-element-derived transgenes that induce strong TSE can convert other homologous transgene clusters incapable of TSE into strong silencers, which transmit the acquired silencing capacity through 50 generations. The paramutation occurs without any need for chromosome pairing between the paramutagenic and the paramutated loci, and is mediated by maternal inheritance of cytoplasm carrying Piwi-interacting RNAs (piRNAs) homologous to the transgenes. The repression capacity of the paramutated locus is abolished by a loss-of-function mutation of the aubergine gene involved in piRNA biogenesis, but not by a loss-of-function mutation of the Dicer-2 gene involved in siRNA production. The paramutated cluster, previously producing barely detectable levels of piRNAs, is converted into a stable, strong piRNA-producing locus by the paramutation and becomes fully paramutagenic itself. Our work provides a genetic model for the emergence of piRNA loci, as well as for RNA-mediated trans-generational repression of transposable elements.
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Affiliation(s)
- Augustin de Vanssay
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, 9 quai Saint Bernard, 75005 Paris, France
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27
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Wang J, Wu Z, Li D, Li N, Dindot SV, Satterfield MC, Bazer FW, Wu G. Nutrition, epigenetics, and metabolic syndrome. Antioxid Redox Signal 2012; 17:282-301. [PMID: 22044276 PMCID: PMC3353821 DOI: 10.1089/ars.2011.4381] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 01/21/2023]
Abstract
SIGNIFICANCE Epidemiological and animal studies have demonstrated a close link between maternal nutrition and chronic metabolic disease in children and adults. Compelling experimental results also indicate that adverse effects of intrauterine growth restriction on offspring can be carried forward to subsequent generations through covalent modifications of DNA and core histones. RECENT ADVANCES DNA methylation is catalyzed by S-adenosylmethionine-dependent DNA methyltransferases. Methylation, demethylation, acetylation, and deacetylation of histone proteins are performed by histone methyltransferase, histone demethylase, histone acetyltransferase, and histone deacetyltransferase, respectively. Histone activities are also influenced by phosphorylation, ubiquitination, ADP-ribosylation, sumoylation, and glycosylation. Metabolism of amino acids (glycine, histidine, methionine, and serine) and vitamins (B6, B12, and folate) plays a key role in provision of methyl donors for DNA and protein methylation. CRITICAL ISSUES Disruption of epigenetic mechanisms can result in oxidative stress, obesity, insulin resistance, diabetes, and vascular dysfunction in animals and humans. Despite a recognized role for epigenetics in fetal programming of metabolic syndrome, research on therapies is still in its infancy. Possible interventions include: 1) inhibition of DNA methylation, histone deacetylation, and microRNA expression; 2) targeting epigenetically disturbed metabolic pathways; and 3) dietary supplementation with functional amino acids, vitamins, and phytochemicals. FUTURE DIRECTIONS Much work is needed with animal models to understand the basic mechanisms responsible for the roles of specific nutrients in fetal and neonatal programming. Such new knowledge is crucial to design effective therapeutic strategies for preventing and treating metabolic abnormalities in offspring born to mothers with a previous experience of malnutrition.
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Affiliation(s)
- Junjun Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Defa Li
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Ning Li
- State Key Laboratory of AgroBiotechnology, China Agricultural University, Beijing, China
| | - Scott V. Dindot
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas
| | - M. Carey Satterfield
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
| | - Fuller W. Bazer
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
| | - Guoyao Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
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28
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Olovnikov I, Aravin AA, Toth KF. Small RNA in the nucleus: the RNA-chromatin ping-pong. Curr Opin Genet Dev 2012; 22:164-71. [PMID: 22349141 PMCID: PMC3345048 DOI: 10.1016/j.gde.2012.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 11/23/2022]
Abstract
Eukaryotes use several classes of small RNA molecules to guide diverse protein machineries to target messenger RNA. The role of small RNA in post-transcriptional regulation of mRNA stability and translation is now well established. Small RNAs can also guide sequence-specific modification of chromatin structure and thus contribute to establishment and maintenance of distinct chromatin domains. In this review we summarize the model for the inter-dependent interaction between small RNA and chromatin that has emerged from studies on fission yeast and plants. We focus on recent results that link a distinct class of small RNAs, the piRNAs, to chromatin regulation in animals.
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Affiliation(s)
- Ivan Olovnikov
- California Institute of Technology Division of Biology, 147-75 1200E California Blvd. Pasadena, CA 91125, USA
- Institute of Molecular Genetics Russian Academy of Sciences Kurchatov sq. 2 Moscow, 123182, Russia
| | - Alexei A. Aravin
- California Institute of Technology Division of Biology, 147-75 1200E California Blvd. Pasadena, CA 91125, USA
| | - Katalin Fejes Toth
- California Institute of Technology Division of Biology, 147-75 1200E California Blvd. Pasadena, CA 91125, USA
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29
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Pöyhönen M, de Vanssay A, Delmarre V, Hermant C, Todeschini AL, Teysset L, Ronsseray S. Homology-dependent silencing by an exogenous sequence in the Drosophila germline. G3 (BETHESDA, MD.) 2012; 2:331-8. [PMID: 22413086 PMCID: PMC3291502 DOI: 10.1534/g3.111.001925] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/24/2011] [Indexed: 11/25/2022]
Abstract
The study of P transposable element repression in Drosophila melanogaster led to the discovery of the trans-silencing effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences) represses in trans, in the female germline, a homologous P-lacZ transgene inserted in euchromatin. TSE shows variegation in ovaries and displays a maternal effect as well as epigenetic transmission through meiosis. In addition, TSE is highly sensitive to mutations affecting heterochromatin components (including HP1) and the Piwi-interacting RNA silencing pathway (piRNA), a homology-dependent silencing mechanism that functions in the germline. TSE appears thus to involve the piRNA-based silencing proposed to play a major role in P repression. Under this hypothesis, TSE may also be established when homology between the telomeric and target loci involves sequences other than P elements, including sequences exogenous to the D. melanogaster genome. We have tested whether TSE can be induced via lacZ sequence homology. We generated a piggyBac-otu-lacZ transgene in which lacZ is under the control of the germline ovarian tumor promoter, resulting in strong expression in nurse cells and the oocyte. We show that all piggyBac-otu-lacZ transgene insertions are strongly repressed by maternally inherited telomeric P-lacZ transgenes. This repression shows variegation between egg chambers when it is incomplete and presents a maternal effect, two of the signatures of TSE. Finally, this repression is sensitive to mutations affecting aubergine, a key player of the piRNA pathway. These data show that TSE can occur when silencer and target loci share solely a sequence exogenous to the D. melanogaster genome. This functionally supports the hypothesis that TSE represents a general repression mechanism which can be co-opted by new transposable elements to regulate their activity after a transfer to the D. melanogaster genome.
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Affiliation(s)
| | | | - Valérie Delmarre
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
| | - Catherine Hermant
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
| | | | - Laure Teysset
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622, CNRS–Université Pierre et Marie Curie, 9 quai Saint-Bernard, 75005 Paris, France
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30
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Kawaoka S, Mitsutake H, Kiuchi T, Kobayashi M, Yoshikawa M, Suzuki Y, Sugano S, Shimada T, Kobayashi J, Tomari Y, Katsuma S. A role for transcription from a piRNA cluster in de novo piRNA production. RNA (NEW YORK, N.Y.) 2012; 18:265-73. [PMID: 22194309 PMCID: PMC3264913 DOI: 10.1261/rna.029777.111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are at the heart of the nucleic acid-based adaptive immune system against transposons in animal gonads. To date, how the piRNA pathway senses an element as a substrate and how de novo piRNA production is initiated remain elusive. Here, by utilizing a GFP transgene, we screened and obtained clonal silkworm BmN4 cell lines producing massively amplified GFP-derived piRNAs capable of silencing GFP in trans. In multiple independent cell lines where GFP expression was silenced by the piRNA pathway, we detected a common transcript from an endogenous piRNA cluster, in which a part of the cluster is uniquely fused with an antisense GFP sequence. Bioinformatic analyses suggest that the fusion transcript is a source of GFP primary piRNAs. Our data implicate a role for transcription from a piRNA cluster in initiating de novo piRNA production against a new insertion.
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Affiliation(s)
- Shinpei Kawaoka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroshi Mitsutake
- The United Graduate School of Agricultural Sciences, Tottori University, Koyama-cho, Minami 4-101, Tottori 680-8553, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Maki Kobayashi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mayu Yoshikawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toru Shimada
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun Kobayashi
- The United Graduate School of Agricultural Sciences, Tottori University, Koyama-cho, Minami 4-101, Tottori 680-8553, Japan
- Faculty of Agriculture, Yamaguchi University, Yoshida 1677-1, Yamaguchi 753-8515, Japan
- Corresponding authors.E-mail .E-mail .E-mail .
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding authors.E-mail .E-mail .E-mail .
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Corresponding authors.E-mail .E-mail .E-mail .
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Muerdter F, Olovnikov I, Molaro A, Rozhkov NV, Czech B, Gordon A, Hannon GJ, Aravin AA. Production of artificial piRNAs in flies and mice. RNA (NEW YORK, N.Y.) 2012; 18:42-52. [PMID: 22096018 PMCID: PMC3261743 DOI: 10.1261/rna.029769.111] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In animals a discrete class of small RNAs, the piwi-interacting RNAs (piRNAs), guard germ cell genomes against the activity of mobile genetic elements. piRNAs are generated, via an unknown mechanism, from apparently single-stranded precursors that arise from discrete genomic loci, termed piRNA clusters. Presently, little is known about the signals that distinguish a locus as a source of piRNAs. It is also unknown how individual piRNAs are selected from long precursor transcripts. To address these questions, we inserted new artificial sequence information into piRNA clusters and introduced these marked clusters as transgenes into heterologous genomic positions in mice and flies. Profiling of piRNA from transgenic animals demonstrated that artificial sequences were incorporated into the piRNA repertoire. Transgenic piRNA clusters are functional in non-native genomic contexts in both mice and flies, indicating that the signals that define piRNA generative loci must lie within the clusters themselves rather than being implicit in their genomic position. Comparison of transgenic animals that carry insertions of the same artificial sequence into different ectopic piRNA-generating loci showed that both local and long-range sequence environments inform the generation of individual piRNAs from precursor transcripts.
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Affiliation(s)
- Felix Muerdter
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Zentrum für Molekularbiologie der Pflanzen, Entwicklungsgenetik, University of Tübingen, 72076 Tübingen, Germany
| | - Ivan Olovnikov
- California Institute of Technology, Division of Biology, Pasadena, California 91125, USA
- Institute of Molecular Genetics, Russian Academy of Sciences, 123182 Moscow, Russia
| | - Antoine Molaro
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nikolay V. Rozhkov
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Benjamin Czech
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Zentrum für Molekularbiologie der Pflanzen, Entwicklungsgenetik, University of Tübingen, 72076 Tübingen, Germany
| | - Assaf Gordon
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gregory J. Hannon
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Corresponding authors.E-mail .E-mail .
| | - Alexei A. Aravin
- California Institute of Technology, Division of Biology, Pasadena, California 91125, USA
- Corresponding authors.E-mail .E-mail .
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32
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Ilnytskyy Y, Kovalchuk O. Non-targeted radiation effects-an epigenetic connection. Mutat Res 2011; 714:113-25. [PMID: 21784089 DOI: 10.1016/j.mrfmmm.2011.06.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 06/24/2011] [Accepted: 06/29/2011] [Indexed: 01/18/2023]
Abstract
Ionizing radiation (IR) is a pivotal diagnostic and treatment modality, yet it is also a potent genotoxic agent that causes genome instability and carcinogenesis. While modern cancer radiation therapy has led to increased patient survival rates, the risk of radiation treatment-related complications is becoming a growing problem. IR-induced genome instability has been well-documented in directly exposed cells and organisms. It has also been observed in distant 'bystander' cells. Enigmatically, increased instability is even observed in progeny of pre-conceptually exposed animals, including humans. The mechanisms by which it arises remain obscure and, recently, they have been proposed to be epigenetic in nature. Three major epigenetic phenomena include DNA methylation, histone modifications and small RNA-mediated silencing. This review focuses on the role of DNA methylation and small RNAs in directly exposed and bystander tissues and in IR-induced transgenerational effects. Here, we present evidence that IR-mediated effects are maintained by epigenetic mechanisms.
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Affiliation(s)
- Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge T1K 3M4, Alberta, Canada
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33
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Mattick JS. The central role of RNA in human development and cognition. FEBS Lett 2011; 585:1600-16. [DOI: 10.1016/j.febslet.2011.05.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 05/03/2011] [Indexed: 12/22/2022]
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