1
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Blumenstiel JP. From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements. Semin Cell Dev Biol 2025; 164:1-12. [PMID: 38823219 DOI: 10.1016/j.semcdb.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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2
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Rivera A, Lee JHR, Gupta S, Yang L, Goel RK, Zaia J, Lau NC. Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608167. [PMID: 39211177 PMCID: PMC11361183 DOI: 10.1101/2024.08.15.608167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Flamenco (Flam) is the most prominent piRNA cluster locus expressed in Drosophila ovarian follicle cells, and it is required for female fertility to silence gypsy/mdg4 transposons. To determine how Flam is regulated, we used promoter-bashing reporter assays in OSS cells to uncover novel enhancer sequences within the first exons of Flam . We confirmed the enhancer sequence relevance in vivo with new Drosophila Flam deletion mutants of these regions that compromised Flam piRNA expression and lowered female fertility from activated transposons. Our proteomic analysis of proteins associated with these enhancer sequences discovered the transcription factor Traffic Jam (TJ). Tj knockdowns in OSS cells caused a decrease in Flam transcripts, Flam piRNAs, and multiple Piwi pathway genes. A TJ ChIP-seq analysis from whole flies and OSS cells confirmed TJ binding exactly at the enhancer that was deleted in the new Flam mutant as well as at multiple Piwi pathway gene enhancers. Interestingly, TJ also bound the Long Terminal Repeats of transposons that had decreased expression after Tj knockdowns in OSS cells. Our study reveals the integral role TJ plays in the on-going arms race between selfish transposons and their suppression by the host Piwi pathway and the Flam piRNA cluster locus.
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3
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Shao Z, Hu J, Jandura A, Wilk R, Jachimowicz M, Ma L, Hu C, Sundquist A, Das I, Samuel-Larbi P, Brill JA, Krause HM. Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution. Nat Commun 2024; 15:3806. [PMID: 38714658 PMCID: PMC11076287 DOI: 10.1038/s41467-024-47346-w] [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: 07/26/2023] [Accepted: 03/25/2024] [Indexed: 05/10/2024] Open
Abstract
Unlike coding genes, the number of lncRNA genes in organism genomes is relatively proportional to organism complexity. From plants to humans, the tissues with highest numbers and levels of lncRNA gene expression are the male reproductive organs. To learn why, we initiated a genome-wide analysis of Drosophila lncRNA spatial expression patterns in these tissues. The numbers of genes and levels of expression observed greatly exceed those previously reported, due largely to a preponderance of non-polyadenylated transcripts. In stark contrast to coding genes, the highest numbers of lncRNAs expressed are in post-meiotic spermatids. Correlations between expression levels, localization and previously performed genetic analyses indicate high levels of function and requirement. More focused analyses indicate that lncRNAs play major roles in evolution by controlling transposable element activities, Y chromosome gene expression and sperm construction. A new type of lncRNA-based particle found in seminal fluid may also contribute to reproductive outcomes.
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Affiliation(s)
- Zhantao Shao
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
| | - Jack Hu
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
| | - Allison Jandura
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ronit Wilk
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
| | - Matthew Jachimowicz
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lingfeng Ma
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chun Hu
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
| | - Abby Sundquist
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
| | - Indrani Das
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada
| | | | - Julie A Brill
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Henry M Krause
- Donnelly Ctr., 160 College St., University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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4
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van Lopik J, Alizada A, Trapotsi MA, Hannon GJ, Bornelöv S, Czech Nicholson B. Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus. Nat Commun 2023; 14:7337. [PMID: 37957172 PMCID: PMC10643416 DOI: 10.1038/s41467-023-42787-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway prevents endogenous genomic parasites, i.e. transposable elements, from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, are thought to define each species' piRNA repertoire and therefore its capacity to recognize and silence specific transposon families. The unistrand cluster flamenco (flam) is essential in the somatic compartment of the Drosophila ovary to restrict Gypsy-family transposons from infecting the neighbouring germ cells. Disruption of flam results in transposon de-repression and sterility, yet it remains unknown whether this silencing mechanism is present more widely. Here, we systematically characterise 119 Drosophila species and identify five additional flam-like clusters separated by up to 45 million years of evolution. Small RNA-sequencing validated these as bona-fide unistrand piRNA clusters expressed in somatic cells of the ovary, where they selectively target transposons of the Gypsy family. Together, our study provides compelling evidence of a widely conserved transposon silencing mechanism that co-evolved with virus-like Gypsy-family transposons.
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Affiliation(s)
- Jasper van Lopik
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Azad Alizada
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Maria-Anna Trapotsi
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
| | - Benjamin Czech Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
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5
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Yoth M, Maupetit-Méhouas S, Akkouche A, Gueguen N, Bertin B, Jensen S, Brasset E. Reactivation of a somatic errantivirus and germline invasion in Drosophila ovaries. Nat Commun 2023; 14:6096. [PMID: 37773253 PMCID: PMC10541861 DOI: 10.1038/s41467-023-41733-5] [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: 12/15/2022] [Accepted: 09/15/2023] [Indexed: 10/01/2023] Open
Abstract
Most Drosophila transposable elements are LTR retrotransposons, some of which belong to the genus Errantivirus and share structural and functional characteristics with vertebrate endogenous retroviruses. Like endogenous retroviruses, it is unclear whether errantiviruses retain some infectivity and transposition capacity. We created conditions where control of the Drosophila ZAM errantivirus through the piRNA pathway was abolished leading to its de novo reactivation in somatic gonadal cells. After reactivation, ZAM invaded the oocytes and severe fertility defects were observed. While ZAM expression persists in the somatic gonadal cells, the germline then set up its own adaptive genomic immune response by producing piRNAs against the constantly invading errantivirus, restricting invasion. Our results suggest that although errantiviruses are continuously repressed by the piRNA pathway, they may retain their ability to infect the germline and transpose, thus allowing them to efficiently invade the germline if they are expressed.
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Affiliation(s)
- Marianne Yoth
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | | | - Abdou Akkouche
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Nathalie Gueguen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Benjamin Bertin
- LIMAGRAIN EUROPE, Centre de recherche, 63720, Chappes, France
| | - Silke Jensen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
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6
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Loubalova Z, Konstantinidou P, Haase AD. Themes and variations on piRNA-guided transposon control. Mob DNA 2023; 14:10. [PMID: 37660099 PMCID: PMC10474768 DOI: 10.1186/s13100-023-00298-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are responsible for preventing the movement of transposable elements in germ cells and protect the integrity of germline genomes. In this review, we examine the common elements of piRNA-guided silencing as well as the differences observed between species. We have categorized the mechanisms of piRNA biogenesis and function into modules. Individual PIWI proteins combine these modules in various ways to produce unique PIWI-piRNA pathways, which nevertheless possess the ability to perform conserved functions. This modular model incorporates conserved core mechanisms and accommodates variable co-factors. Adaptability is a hallmark of this RNA-based immune system. We believe that considering the differences in germ cell biology and resident transposons in different organisms is essential for placing the variations observed in piRNA biology into context, while still highlighting the conserved themes that underpin this process.
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Affiliation(s)
- Zuzana Loubalova
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Parthena Konstantinidou
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Astrid D Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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7
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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8
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Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R, Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet 2023; 19:e1010914. [PMID: 37643184 PMCID: PMC10495008 DOI: 10.1371/journal.pgen.1010914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. In D. melanogaster, the flamenco locus is a master suppressor of TEs, preventing the mobilization of certain endogenous retrovirus-like TEs from somatic ovarian support cells to the germline. It is transcribed by Pol II as a long (100s of kb), single-stranded, primary transcript, and metabolized into ~24-32 nt Piwi-interacting RNAs (piRNAs) that target active TEs via antisense complementarity. flamenco is thought to operate as a trap, owing to its high content of recent horizontally transferred TEs that are enriched in antisense orientation. Using newly-generated long read genome data, which is critical for accurate assembly of repetitive sequences, we find that flamenco has undergone radical transformations in sequence content and even copy number across simulans clade Drosophilid species. Drosophila simulans flamenco has duplicated and diverged, and neither copy exhibits synteny with D. melanogaster beyond the core promoter. Moreover, flamenco organization is highly variable across D. simulans individuals. Next, we find that D. simulans and D. mauritiana flamenco display signatures of a dual-stranded cluster, with ping-pong signals in the testis and/or embryo. This is accompanied by increased copy numbers of germline TEs, consistent with these regions operating as functional dual-stranded clusters. Overall, the physical and functional diversity of flamenco orthologs is testament to the extremely dynamic consequences of TE arms races on genome organization, not only amongst highly related species, but even amongst individuals.
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Affiliation(s)
- Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, Texas, United States of America
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Eric C. Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
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9
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Chary S, Hayashi R. The absence of core piRNA biogenesis factors does not impact efficient transposon silencing in Drosophila. PLoS Biol 2023; 21:e3002099. [PMID: 37279192 DOI: 10.1371/journal.pbio.3002099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/30/2023] [Indexed: 06/08/2023] Open
Abstract
Organisms require mechanisms to distinguish self and non-self-RNA. This distinction is crucial to initiate the biogenesis of Piwi-interacting RNAs (piRNAs). In Drosophila ovaries, PIWI-guided slicing and the recognition of piRNA precursor transcripts by the DEAD-box RNA helicase Yb are the 2 known mechanisms to licence an RNA for piRNA biogenesis in the germline and the soma, respectively. Both the PIWI proteins and Yb are highly conserved across most Drosophila species and are thought to be essential to the piRNA pathway and for silencing transposons. However, we find that species closely related to Drosophila melanogaster have lost the yb gene, as well as the PIWI gene Ago3. We show that the precursor RNA is still selected in the absence of Yb to abundantly generate transposon antisense piRNAs in the soma. We further demonstrate that Drosophila eugracilis, which lacks Ago3, is completely devoid of ping-pong piRNAs and exclusively produces phased piRNAs in the absence of slicing. Thus, core piRNA pathway genes can be lost in evolution while still maintaining efficient transposon silencing.
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Affiliation(s)
- Shashank Chary
- John Curtin School of Medical Research, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Rippei Hayashi
- John Curtin School of Medical Research, The Australian National University, Acton, Australian Capital Territory, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Acton, Australian Capital Territory, Australia
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10
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Chen P, Aravin AA. Genetic control of a sex-specific piRNA program. Curr Biol 2023; 33:1825-1835.e3. [PMID: 37059098 PMCID: PMC10431932 DOI: 10.1016/j.cub.2023.03.057] [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] [Revised: 02/15/2023] [Accepted: 03/17/2023] [Indexed: 04/16/2023]
Abstract
Sexually dimorphic traits in morphologies are widely studied,1,2,3,4 but those in essential molecular pathways remain largely unexplored. Previous work showed substantial sex differences in Drosophila gonadal piRNAs,5 which guide PIWI proteins to silence selfish genetic elements, thereby safeguarding fertility.6,7,8 However, the genetic control mechanisms of piRNA sexual dimorphism remain unknown. Here, we showed that most sex differences in the piRNA program originate from the germ line rather than the gonadal somatic cells. Building on this, we dissected the contribution of sex chromosomes and cellular sexual identity toward the sex-specific germline piRNA program. We found that the presence of the Y chromosome is sufficient to recapitulate some aspects of the male piRNA program in a female cellular environment. Meanwhile, sexual identity controls the sexually divergent piRNA production from X-linked and autosomal loci, revealing a crucial input from sex determination into piRNA biogenesis. Sexual identity regulates piRNA biogenesis through Sxl, and this effect is mediated, in part, through chromatin proteins Phf7 and Kipferl. Together, our work delineated the genetic control of a sex-specific piRNA program, where sex chromosomes and sexual identity collectively sculpt an essential molecular trait.
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Affiliation(s)
- Peiwei Chen
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA.
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11
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Wang L, Tracy L, Su W, Yang F, Feng Y, Silverman N, Zhang ZZZ. Retrotransposon activation during Drosophila metamorphosis conditions adult antiviral responses. Nat Genet 2022; 54:1933-1945. [PMID: 36396707 PMCID: PMC9795486 DOI: 10.1038/s41588-022-01214-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/29/2022] [Indexed: 11/18/2022]
Abstract
Retrotransposons are one type of mobile genetic element that abundantly reside in the genomes of nearly all animals. Their uncontrolled activation is linked to sterility, cancer and other pathologies, thereby being largely considered detrimental. Here we report that, within a specific time window of development, retrotransposon activation can license the host's immune system for future antiviral responses. We found that the mdg4 (also known as Gypsy) retrotransposon selectively becomes active during metamorphosis at the Drosophila pupal stage. At this stage, mdg4 activation educates the host's innate immune system by inducing the systemic antiviral function of the nuclear factor-κB protein Relish in a dSTING-dependent manner. Consequently, adult flies with mdg4, Relish or dSTING silenced at the pupal stage are unable to clear exogenous viruses and succumb to viral infection. Altogether, our data reveal that hosts can establish a protective antiviral response that endows a long-term benefit in pathogen warfare due to the developmental activation of mobile genetic elements.
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Affiliation(s)
- Lu Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
| | - Lauren Tracy
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Weijia Su
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Fu Yang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yu Feng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Neal Silverman
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Z Z Zhao Zhang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA.
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12
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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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13
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Haase AD. An introduction to PIWI-interacting RNAs (piRNAs) in the context of metazoan small RNA silencing pathways. RNA Biol 2022; 19:1094-1102. [PMID: 36217279 PMCID: PMC9559041 DOI: 10.1080/15476286.2022.2132359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022] Open
Abstract
PIWI proteins and their associated PIWI-interacting RNAs (piRNAs) constitute a small RNA-based adaptive immune system that restricts the deleterious activity of mobile genetic elements to protect genome integrity. Self/nonself discrimination is at the very core of successful defence and relies on complementary base-pairing in RNA-guided immunity. How the millions of piRNA sequences faithfully discriminate between self and nonself and how they adapt to novel genomic invaders remain key outstanding questions in genome biology. This review aims to introduce principles of piRNA silencing in the context of metazoan small RNA pathways. A distinct feature of piRNAs is their origin from single-stranded instead of double-stranded RNA precursors, and piRNAs require a unique set of processing factors. Novel nucleases, helicases and RNA binding proteins have been identified in piRNA biology, and while we are starting to understand some mechanisms of piRNA biogenesis and function, this diverse and prolific class of small RNAs remains full of surprises.
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Affiliation(s)
- Astrid D. Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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14
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Retrotransposons Down- and Up-Regulation in Aging Somatic Tissues. Cells 2021; 11:cells11010079. [PMID: 35011640 PMCID: PMC8750722 DOI: 10.3390/cells11010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 01/19/2023] Open
Abstract
The transposon theory of aging hypothesizes the activation of transposable elements (TEs) in somatic tissues with age, leading to a shortening of the lifespan. It is thought that TE activation in aging produces an increase in DNA double-strand breaks, contributing to genome instability and promoting the activation of inflammatory responses. To investigate how TE regulation changes in somatic tissues during aging, we analyzed the expression of some TEs, as well as a source of small RNAs that specifically silence the analyzed TEs; the Drosophila cluster named flamenco. We found significant variations in the expression levels of all the analyzed TEs during aging, with a trend toward reduction in middle-aged adults and reactivation in older individuals that suggests dynamic regulation during the lifespan.
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15
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Lawlor MA, Cao W, Ellison CE. A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis. Nat Commun 2021; 12:6854. [PMID: 34824217 PMCID: PMC8617248 DOI: 10.1038/s41467-021-27136-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/04/2021] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) must replicate in germline cells to pass novel insertions to offspring. In Drosophila melanogaster ovaries, TEs can exploit specific developmental windows of opportunity to evade host silencing and increase their copy numbers. However, TE activity and host silencing in the distinct cell types of Drosophila testis are not well understood. Here, we reanalyze publicly available single-cell RNA-seq datasets to quantify TE expression in the distinct cell types of the Drosophila testis. We develop a method for identification of TE and host gene expression modules and find that a distinct population of early spermatocytes expresses a large number of TEs at much higher levels than other germline and somatic components of the testes. This burst of TE expression coincides with the activation of Y chromosome fertility factors and spermatocyte-specific transcriptional regulators, as well as downregulation of many components of the piRNA pathway. The TEs expressed by this cell population are specifically enriched on the Y chromosome and depleted on the X chromosome, relative to other active TEs. These data suggest that some TEs may achieve high insertional activity in males by exploiting a window of opportunity for mobilization created by the activation of spermatocyte-specific and Y chromosome-specific transcriptional programs.
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Affiliation(s)
- Matthew A Lawlor
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA.
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16
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Gebert D, Neubert LK, Lloyd C, Gui J, Lehmann R, Teixeira FK. Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation. Mol Cell 2021; 81:3965-3978.e5. [PMID: 34352205 PMCID: PMC8516431 DOI: 10.1016/j.molcel.2021.07.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/23/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022]
Abstract
PIWI proteins and their guiding Piwi-interacting small RNAs (piRNAs) are crucial for fertility and transposon defense in the animal germline. In most species, the majority of piRNAs are produced from distinct large genomic loci, called piRNA clusters. It is assumed that germline-expressed piRNA clusters, particularly in Drosophila, act as principal regulators to control transposons dispersed across the genome. Here, using synteny analysis, we show that large clusters are evolutionarily labile, arise at loci characterized by recurrent chromosomal rearrangements, and are mostly species-specific across the Drosophila genus. By engineering chromosomal deletions in D. melanogaster, we demonstrate that the three largest germline clusters, which account for the accumulation of >40% of all transposon-targeting piRNAs in ovaries, are neither required for fertility nor for transposon regulation in trans. We provide further evidence that dispersed elements, rather than the regulatory action of large Drosophila germline clusters in trans, may be central for transposon defense.
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Affiliation(s)
- Daniel Gebert
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Lena K Neubert
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Catrin Lloyd
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Jinghua Gui
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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17
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Abstract
More than a century ago, August Weissman defined a distinction between the germline (responsible for propagating heritable information from generation to generation) and the perishable soma. A central motivation for this distinction was to argue against the inheritance of acquired characters, as the germline was partly defined by its protection from external conditions. However, recent decades have seen an explosion of studies documenting the intergenerational and transgenerational effects of environmental conditions, forcing a re-evaluation of how external signals are sensed by, or communicated to, the germline epigenome. Here, motivated by the centrality of small RNAs in paradigms of epigenetic inheritance, we review across species the myriad examples of intercellular RNA trafficking from nurse cells or somatic tissues to developing gametes.
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18
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Onishi R, Yamanaka S, Siomi MC. piRNA- and siRNA-mediated transcriptional repression in Drosophila, mice, and yeast: new insights and biodiversity. EMBO Rep 2021; 22:e53062. [PMID: 34347367 PMCID: PMC8490990 DOI: 10.15252/embr.202153062] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The PIWI‐interacting RNA (piRNA) pathway acts as a self‐defense mechanism against transposons to maintain germline genome integrity. Failures in the piRNA pathway cause DNA damage in the germline genome, disturbing inheritance of “correct” genetic information by the next generations and leading to infertility. piRNAs execute transposon repression in two ways: degrading their RNA transcripts and compacting the genomic loci via heterochromatinization. The former event is mechanistically similar to siRNA‐mediated RNA cleavage that occurs in the cytoplasm and has been investigated in many species including nematodes, fruit flies, and mammals. The latter event seems to be mechanistically parallel to siRNA‐centered kinetochore assembly and subsequent chromosome segregation, which has so far been studied particularly in fission yeast. Despite the interspecies conservations, the overall schemes of the nuclear events show clear biodiversity across species. In this review, we summarize the recent progress regarding piRNA‐mediated transcriptional silencing in Drosophila and discuss the biodiversity by comparing it with the equivalent piRNA‐mediated system in mice and the siRNA‐mediated system in fission yeast.
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Affiliation(s)
- Ryo Onishi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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19
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Baptista B, Riscado M, Queiroz J, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021. [DOI: 10.1016/j.bcp.2021.114469 order by 22025--] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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20
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Tiedeman Z, Signor S. The transposable elements of the Drosophila serrata reference panel. Genome Biol Evol 2021; 13:6265467. [PMID: 33950180 PMCID: PMC8434751 DOI: 10.1093/gbe/evab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are an important component of the complex genomic ecosystem. Understanding the tempo and mode of TE proliferation, that is whether it is in maintained in transposition selection balance, or is induced periodically by environmental stress or other factors, is important for understanding the evolution of organismal genomes through time. Although TEs have been characterized in individuals or limited samples, a true understanding of the population genetics of TEs, and therefore the tempo and mode of transposition, is still lacking. Here, we characterize the TE landscape in an important model Drosophila, Drosophila serrata using the D. serrata reference panel, which is comprised of 102 sequenced inbred genotypes. We annotate the families of TEs in the D. serrata genome and investigate variation in TE copy number between genotypes. We find that many TEs have low copy number in the population, but this varies by family and includes a single TE making up to 50% of the genome content of TEs. We find that some TEs proliferate in particular genotypes compared with population levels. In addition, we characterize variation in each TE family allowing copy number to vary in each genotype and find that some TEs have diversified very little between individuals suggesting recent spread. TEs are important sources of spontaneous mutations in Drosophila, making up a large fraction of the total number of mutations in particular genotypes. Understanding the dynamics of TEs within populations will be an important step toward characterizing the origin of variation within and between species.
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Affiliation(s)
- Zachery Tiedeman
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, U.S.A
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, U.S.A
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21
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Munafò M, Lawless VR, Passera A, MacMillan S, Bornelöv S, Haussmann IU, Soller M, Hannon GJ, Czech B. Channel nuclear pore complex subunits are required for transposon silencing in Drosophila. eLife 2021; 10:e66321. [PMID: 33856346 PMCID: PMC8133776 DOI: 10.7554/elife.66321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
The nuclear pore complex (NPC) is the principal gateway between nucleus and cytoplasm that enables exchange of macromolecular cargo. Composed of multiple copies of ~30 different nucleoporins (Nups), the NPC acts as a selective portal, interacting with factors which individually license passage of specific cargo classes. Here we show that two Nups of the inner channel, Nup54 and Nup58, are essential for transposon silencing via the PIWI-interacting RNA (piRNA) pathway in the Drosophila ovary. In ovarian follicle cells, loss of Nup54 and Nup58 results in compromised piRNA biogenesis exclusively from the flamenco locus, whereas knockdowns of other NPC subunits have widespread consequences. This provides evidence that some Nups can acquire specialised roles in tissue-specific contexts. Our findings consolidate the idea that the NPC has functions beyond simply constituting a barrier to nuclear/cytoplasmic exchange as genomic loci subjected to strong selective pressure can exploit NPC subunits to facilitate their expression.
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Affiliation(s)
- Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Victoria R Lawless
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Alessandro Passera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Serena MacMillan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Irmgard U Haussmann
- Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City UniversityBirminghamUnited Kingdom
- School of Biosciences, College of Life and Environmental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of BirminghamBirminghamUnited Kingdom
- Birmingham Center for Genome Biology, University of BirminghamBirminghamUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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22
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Keegan RM, Talbot LR, Chang YH, Metzger MJ, Dubnau J. Intercellular viral spread and intracellular transposition of Drosophila gypsy. PLoS Genet 2021; 17:e1009535. [PMID: 33886543 PMCID: PMC8096092 DOI: 10.1371/journal.pgen.1009535] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 05/04/2021] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
It has become increasingly clear that retrotransposons (RTEs) are more widely expressed in somatic tissues than previously appreciated. RTE expression has been implicated in a myriad of biological processes ranging from normal development and aging, to age related diseases such as cancer and neurodegeneration. Long Terminal Repeat (LTR)-RTEs are evolutionary ancestors to, and share many features with, exogenous retroviruses. In fact, many organisms contain endogenous retroviruses (ERVs) derived from exogenous retroviruses that integrated into the germ line. These ERVs are inherited in Mendelian fashion like RTEs, and some retain the ability to transmit between cells like viruses, while others develop the ability to act as RTEs. The process of evolutionary transition between LTR-RTE and retroviruses is thought to involve multiple steps by which the element loses or gains the ability to transmit copies between cells versus the ability to replicate intracellularly. But, typically, these two modes of transmission are incompatible because they require assembly in different sub-cellular compartments. Like murine IAP/IAP-E elements, the gypsy family of retroelements in arthropods appear to sit along this evolutionary transition. Indeed, there is some evidence that gypsy may exhibit retroviral properties. Given that gypsy elements have been found to actively mobilize in neurons and glial cells during normal aging and in models of neurodegeneration, this raises the question of whether gypsy replication in somatic cells occurs via intracellular retrotransposition, intercellular viral spread, or some combination of the two. These modes of replication in somatic tissues would have quite different biological implications. Here, we demonstrate that Drosophila gypsy is capable of both cell-associated and cell-free viral transmission between cultured S2 cells of somatic origin. Further, we demonstrate that the ability of gypsy to move between cells is dependent upon a functional copy of its viral envelope protein. This argues that the gypsy element has transitioned from an RTE into a functional endogenous retrovirus with the acquisition of its envelope gene. On the other hand, we also find that intracellular retrotransposition of the same genomic copy of gypsy can occur in the absence of the Env protein. Thus, gypsy exhibits both intracellular retrotransposition and intercellular viral transmission as modes of replicating its genome.
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Affiliation(s)
- Richard M. Keegan
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Lillian R. Talbot
- Medical Scientist Training Program, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
| | - Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
| | - Michael J. Metzger
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Josh Dubnau
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, New York City, New York, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, New York City, New York, United States of America
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
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23
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Baptista B, Riscado M, Queiroz JA, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021; 189:114469. [PMID: 33577888 DOI: 10.1016/j.bcp.2021.114469] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
The knowledge about non-coding RNAs (ncRNAs) is rapidly increasing with new data continuously emerging, regarding their diverse types, applications, and roles. Particular attention has been given to ncRNA with regulatory functions, which may have a critical role both in biological and pathological conditions. As a result of the diversity of ncRNAs and their ubiquitous involvement in several biologic processes, ncRNA started to be considered in the biomedical field, with immense potential to be exploited either as biomarkers or as therapeutic agents in certain pathologies. Indeed, ncRNA-based therapeutics have been proposed in many disorders and some even reached clinical trials. However, to prepare an RNA product suitable for pharmacological applications, certain criteria must be fulfilled, and it has to be guaranteed RNA purity, stability, and bioactivity. So, in this review, the different types of ncRNAs are identified and characterized, by describing their biogenesis, functions, and applications. A perspective on the main challenges and innovative approaches for the future and broad therapeutic application of RNA is also presented.
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Affiliation(s)
- B Baptista
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - M Riscado
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - J A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - C Pichon
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS & University of Orléans Orléans, France
| | - F Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal.
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24
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Ghanim GE, Rio DC, Teixeira FK. Mechanism and regulation of P element transposition. Open Biol 2020; 10:200244. [PMID: 33352068 PMCID: PMC7776569 DOI: 10.1098/rsob.200244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/26/2020] [Indexed: 12/05/2022] Open
Abstract
P elements were first discovered in the fruit fly Drosophila melanogaster as the causative agents of a syndrome of aberrant genetic traits called hybrid dysgenesis. This occurs when P element-carrying males mate with females that lack P elements and results in progeny displaying sterility, mutations and chromosomal rearrangements. Since then numerous genetic, developmental, biochemical and structural studies have culminated in a deep understanding of P element transposition: from the cellular regulation and repression of transposition to the mechanistic details of the transposase nucleoprotein complex. Recent studies have revealed how piwi-interacting small RNA pathways can act to control splicing of the P element pre-mRNA to modulate transposase production in the germline. A recent cryo-electron microscopy structure of the P element transpososome reveals an unusual DNA architecture at the transposon termini and shows that the bound GTP cofactor functions to position the transposon ends within the transposase active site. Genome sequencing efforts have shown that there are P element transposase-homologous genes (called THAP9) in other animal genomes, including humans. This review highlights recent and previous studies, which together have led to new insights, and surveys our current understanding of the biology, biochemistry, mechanism and regulation of P element transposition.
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Affiliation(s)
- George E. Ghanim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Donald C. Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
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25
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Gamez S, Srivastav S, Akbari OS, Lau NC. Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways. Cells 2020; 9:E2180. [PMID: 32992598 PMCID: PMC7601171 DOI: 10.3390/cells9102180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Animals face the dual threat of virus infections hijacking cellular function and transposons proliferating in germline genomes. For insects, the deeply conserved RNA interference (RNAi) pathways and other chromatin regulators provide an important line of defense against both viruses and transposons. For example, this innate immune system displays adaptiveness to new invasions by generating cognate small RNAs for targeting gene silencing measures against the viral and genomic intruders. However, within the Dipteran clade of insects, Drosophilid fruit flies and Culicids mosquitoes have evolved several unique mechanistic aspects of their RNAi defenses to combat invading transposons and viruses, with the Piwi-piRNA arm of the RNAi pathways showing the greatest degree of novel evolution. Whereas central features of Piwi-piRNA pathways are conserved between Drosophilids and Culicids, multiple lineage-specific innovations have arisen that may reflect distinct genome composition differences and specific ecological and physiological features dividing these two branches of Dipterans. This perspective review focuses on the most recent findings illuminating the Piwi/piRNA pathway distinctions between fruit flies and mosquitoes, and raises open questions that need to be addressed in order to ameliorate human diseases caused by pathogenic viruses that mosquitoes transmit as vectors.
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Affiliation(s)
- Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Satyam Srivastav
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA;
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Nelson C. Lau
- Department of Biochemistry and Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
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26
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Maghodia AB, Geisler C, Jarvis DL. A new nodavirus-negative Trichoplusia ni cell line for baculovirus-mediated protein production. Biotechnol Bioeng 2020; 117:3248-3264. [PMID: 32662870 DOI: 10.1002/bit.27494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 07/12/2020] [Indexed: 12/22/2022]
Abstract
Cell lines derived from Trichoplusia ni (Tn) are widely used as hosts in the baculovirus-insect cell system (BICS). One advantage of Tn cell lines is they can produce recombinant proteins at higher levels than cell lines derived from other insects. However, Tn cell lines are persistently infected with an alphanodavirus, Tn5 cell-line virus (TnCLV), which reduces their utility as a host for the BICS. Several groups have isolated TnCLV-negative Tn cell lines, but none were thoroughly characterized and shown to be free of other adventitious viruses. Thus, we isolated and extensively characterized a new TnCLV-negative line, Tn-nodavirus-negative (Tn-NVN). Tn-NVN cells have no detectable TnCLV, no other previously identified viral contaminants of lepidopteran insect cell lines, and no sequences associated with any replicating virus or other viral adventitious agents. Tn-NVN cells tested negative for >60 species of Mycoplasma, Acholeplasma, Spiroplasma, and Ureaplasma. Finally, Tn-NVN cells grow well as a single-cell suspension culture in serum-free medium, produce recombinant proteins at levels similar to High Five™ cells, and do not produce recombinant glycoproteins with immunogenic core α1,3-fucosylation. Thus, Tn-NVN is a new, well-characterized TnCLV-negative cell line with several other features enhancing its utility as a host for the BICS.
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Affiliation(s)
| | | | - Donald L Jarvis
- GlycoBac, LLC, Laramie, Wyoming.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
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27
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Wu PH, Fu Y, Cecchini K, Özata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD. The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nat Genet 2020; 52:728-739. [PMID: 32601478 PMCID: PMC7383350 DOI: 10.1038/s41588-020-0657-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/29/2020] [Indexed: 12/16/2022]
Abstract
Pachytene PIWI-interacting RNAs (piRNAs), which comprise >80% of small RNAs in the adult mouse testis, have been proposed to bind and regulate target RNAs like microRNAs, cleave targets like short interfering RNAs or lack biological function altogether. Although piRNA pathway protein mutants are male sterile, no biological function has been identified for any mammalian piRNA-producing locus. Here, we report that males lacking piRNAs from a conserved mouse pachytene piRNA locus on chromosome 6 (pi6) produce sperm with defects in capacitation and egg fertilization. Moreover, heterozygous embryos sired by pi6-/- fathers show reduced viability in utero. Molecular analyses suggest that pi6 piRNAs repress gene expression by cleaving messenger RNAs encoding proteins required for sperm function. pi6 also participates in a network of piRNA-piRNA precursor interactions that initiate piRNA production from a second piRNA locus on chromosome 10, as well as pi6 itself. Our data establish a direct role for pachytene piRNAs in spermiogenesis and embryo viability.
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Affiliation(s)
- Pei-Hsuan Wu
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Yu Fu
- Bioinformatics Program, Boston University, Boston, MA, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Oncology Drug Discovery Unit, Takeda Pharmaceuticals, Cambridge, MA, USA
| | - Katharine Cecchini
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Deniz M Özata
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amena Arif
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Tianxiong Yu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA.,School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cansu Colpan
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Phillip D Zamore
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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28
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Kukushkina IV, Makhnovskii PA, Nefedova LN, Milyaeva PA, Kuzmin IV, Lavrenov AR, Kim AI. Analysis of Transcriptome of Drosophila melanogaster Strains with Disrupted Control of gypsy Retrotransposon Transposition. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Kukushkina IV, Makhnovskii PA, Nefedova LN, Balakireva EA, Romanova NI, Kuzmin IV, Lavrenov AR, Kim AI. A Study of the Fertility of a Drosophila melanogaster MS Strain with Impaired Transposition Control of the gypsy Mobile Element. Mol Biol 2020. [DOI: 10.1134/s0026893320030097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.
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Affiliation(s)
- Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
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Sokolova OA, Mikhaleva EA, Kharitonov SL, Abramov YA, Gvozdev VA, Klenov MS. Special vulnerability of somatic niche cells to transposable element activation in Drosophila larval ovaries. Sci Rep 2020; 10:1076. [PMID: 31974416 PMCID: PMC6978372 DOI: 10.1038/s41598-020-57901-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/07/2020] [Indexed: 01/09/2023] Open
Abstract
In the Drosophila ovary, somatic escort cells (ECs) form a niche that promotes differentiation of germline stem cell (GSC) progeny. The piRNA (Piwi-interacting RNA) pathway, which represses transposable elements (TEs), is required in ECs to prevent the accumulation of undifferentiated germ cells (germline tumor phenotype). The soma-specific piRNA cluster flamenco (flam) produces a substantial part of somatic piRNAs. Here, we characterized the biological effects of somatic TE activation on germ cell differentiation in flam mutants. We revealed that the choice between normal and tumorous phenotypes of flam mutant ovaries depends on the number of persisting ECs, which is determined at the larval stage. Accordingly, we found much more frequent DNA breaks in somatic cells of flam larval ovaries than in adult ECs. The absence of Chk2 or ATM checkpoint kinases dramatically enhanced oogenesis defects of flam mutants, in contrast to the germline TE-induced defects that are known to be mostly suppressed by сhk2 mutation. These results demonstrate a crucial role of checkpoint kinases in protecting niche cells against deleterious TE activation and suggest substantial differences between DNA damage responses in ovarian somatic and germ cells.
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Affiliation(s)
- Olesya A Sokolova
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182, Moscow, Russian Federation
| | - Elena A Mikhaleva
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182, Moscow, Russian Federation
| | - Sergey L Kharitonov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182, Moscow, Russian Federation
- Laboratory of Postgenomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova St., 119991, Moscow, Russian Federation
| | - Yuri A Abramov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182, Moscow, Russian Federation
| | - Vladimir A Gvozdev
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182, Moscow, Russian Federation
| | - Mikhail S Klenov
- Department of Molecular Genetics of the Cell, Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182, Moscow, Russian Federation.
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Assembly and Function of Gonad-Specific Non-Membranous Organelles in Drosophila piRNA Biogenesis. Noncoding RNA 2019; 5:ncrna5040052. [PMID: 31698692 PMCID: PMC6958439 DOI: 10.3390/ncrna5040052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that repress transposons in animal germlines. This protects the genome from the invasive DNA elements. piRNA pathway failures lead to DNA damage, gonadal development defects, and infertility. Thus, the piRNA pathway is indispensable for the continuation of animal life. piRNA-mediated transposon silencing occurs in both the nucleus and cytoplasm while piRNA biogenesis is a solely cytoplasmic event. piRNA production requires a number of proteins, the majority of which localize to non-membranous organelles that specifically appear in the gonads. Other piRNA factors are localized on outer mitochondrial membranes. In situ RNA hybridization experiments show that piRNA precursors are compartmentalized into other non-membranous organelles. In this review, we summarize recent findings about the function of these organelles in the Drosophila piRNA pathway by focusing on their assembly and function.
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Dennis C, Brasset E, Vaury C. flam piRNA precursors channel from the nucleus to the cytoplasm in a temporally regulated manner along Drosophila oogenesis. Mob DNA 2019; 10:28. [PMID: 31312260 PMCID: PMC6612187 DOI: 10.1186/s13100-019-0170-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/25/2019] [Indexed: 02/08/2023] Open
Abstract
Background PIWI-interacting RNAs (piRNAs) are the effectors of transposable element silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from long RNA precursors presumably processed within cytoplasmic Yb-bodies. Results Here we show that the nucleo-cytoplasmic traffic of piRNA precursors encoded by the flamenco locus is subjected to a spatio-temporal regulation. Precursor RNAs first gather in a single nuclear focus, Dot COM, close to the nuclear periphery, and transit through the membrane before being delivered to the cytoplasmic Yb-bodies. Early in oogenesis, flamenco transcripts are rapidly transferred to the cytoplasm making their initial nuclear gathering in Dot COM too transient to be visualized. As oogenesis proceeds, the cytoplasmic delivery steadily decreases concomitantly with the decrease in the protein levels of Armi and Yb, two components of the Yb-bodies. Both events lead to a reduction of Yb-body assembly in late stages of oogenesis, which likely results in a drop in piRNA production. Conclusion Our findings show a spatio-temporal regulation of the piRNA biogenesis in the follicle cells of Drosophila ovaries, that involves coordinated control of both piRNA precursors and components of the piRNA processing machinery. This newly unveiled regulation establishes another level of complexity in the production of piRNAs and suggests a stage-dependent involvement of the piRNA biogenesis in the mechanism of transposable elements silencing along oogenesis. Electronic supplementary material The online version of this article (10.1186/s13100-019-0170-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cynthia Dennis
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
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Duc C, Yoth M, Jensen S, Mouniée N, Bergman CM, Vaury C, Brasset E. Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion. Genome Biol 2019; 20:127. [PMID: 31227013 PMCID: PMC6587276 DOI: 10.1186/s13059-019-1736-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs called PIWI-interacting RNAs (piRNAs) produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline gains protection from a new transposon invasion. RESULTS To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line. CONCLUSIONS Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of "auto-immunization" of a germline endangered by mobilization of a surrounding somatic TE.
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Affiliation(s)
- Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
- Present address: UFIP UMR-CNRS 6286, Epigénétique: prolifération et différenciation, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, 44322 Nantes, France
| | - Marianne Yoth
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Silke Jensen
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Nolwenn Mouniée
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Casey M. Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, 120 E. Green St, Athens, GA 30602 USA
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
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Genenncher B, Durdevic Z, Hanna K, Zinkl D, Mobin MB, Senturk N, Da Silva B, Legrand C, Carré C, Lyko F, Schaefer M. Mutations in Cytosine-5 tRNA Methyltransferases Impact Mobile Element Expression and Genome Stability at Specific DNA Repeats. Cell Rep 2019; 22:1861-1874. [PMID: 29444437 DOI: 10.1016/j.celrep.2018.01.061] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/18/2017] [Accepted: 01/19/2018] [Indexed: 12/22/2022] Open
Abstract
The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5) RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects. In contrast, NSun2 function affected mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in both RCMT mutants indicated that tRNA-dependent processes affected mobile element expression and DNA repeat stability. Importantly, further experiments indicated that complex formation with RNA could also contribute to the impact of RCMT function on gene expression control. These results thus uncover a link between tRNA modification enzymes, the expression of repeat DNA, and genomic integrity.
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Affiliation(s)
- Bianca Genenncher
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Zeljko Durdevic
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Daniela Zinkl
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Mehrpouya Balaghy Mobin
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Nevcin Senturk
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Bruno Da Silva
- Drosophila Genetics and Epigenetics Lab, Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), 9, Quai St Bernard, Boîte courrier 24, 75252 Paris Cedex 05, France
| | - Carine Legrand
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Clément Carré
- Drosophila Genetics and Epigenetics Lab, Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), 9, Quai St Bernard, Boîte courrier 24, 75252 Paris Cedex 05, France
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Matthias Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria.
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A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells. G3-GENES GENOMES GENETICS 2019; 9:403-412. [PMID: 30530643 PMCID: PMC6385967 DOI: 10.1534/g3.118.200872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The small interfering RNA (siRNA) pathway is the main and best studied invertebrate antiviral response. Other poorly characterized protein based antiviral mechanisms also contribute to the control of viral replication in insects. In addition, it remains unclear whether tissue specific factors contribute to RNA and protein-based antiviral immunity mechanisms. In vivo screens to identify such factors are challenging and time consuming. In addition, the scored phenotype is usually limited to survival and/or viral load. Transgenic viral replicons are valuable tools to overcome these limitations and screen for novel antiviral factors. Here we describe transgenic Drosophila melanogaster lines encoding a Flock House Virus-derived replicon (FHV∆B2eGFP), expressing GFP as a reporter of viral replication. This replicon is efficiently controlled by the siRNA pathway in most somatic tissues, with GFP fluorescence providing a reliable marker for the activity of antiviral RNAi. Interestingly, in follicular somatic cells (FSC) of ovaries, this replicon is still partially repressed in an siRNA independent manner. We did not detect replicon derived Piwi-interacting RNAs in FSCs and identified 31 differentially expressed genes between restrictive and permissive FSCs. Altogether, our results uncovered a yet unidentified RNAi-independent mechanism controlling FHV replication in FSCs of ovaries and validate the FHV∆B2eGFP replicon as a tool to screen for novel tissue specific antiviral mechanisms.
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37
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Fontdevila A. Hybrid Genome Evolution by Transposition: An Update. J Hered 2019; 110:124-136. [PMID: 30107415 DOI: 10.1093/jhered/esy040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/06/2018] [Indexed: 02/02/2023] Open
Abstract
Contrary to the view that hybrids are lineages devoid of evolutionary value, a number of case studies that have been lately reported show how hybrids are at the origin of many species. Some well-documented cases demonstrate that bursts of transposition often follow hybridization, generating new genetic variability. Studies in hybrid transposition strongly suggest that epigenetic changes and divergence in piRNA pathways drive deregulation in TE landscapes. Here, I have focused on mechanisms acting in Drosophila hybrids between two cactophilic species. The results reported here show that while hybrid instability by transposition is a genome-wide event, deregulation by TE overexpression in hybrid ovaries is not a general rule. When piRNA pools of ovaries are studied, results show that TEs with parental differences higher than 2-fold in their piRNA amounts are not more commonly deregulated in hybrids than TEs with similar levels, partially discrediting the generality of the maternal cytotype hypothesis. Some promising results on the piRNA pathway global failure hypothesis, which states that accumulated divergence of piRNA effector proteins is responsible for hybrid TE deregulation, have also been obtained. Altogether, these results suggest that TE deregulation might be driven by several interacting mechanisms. A natural scenario is proposed in which genome instability by transposition leads to hybrid genome reorganization. Small hybrid populations, subjected to natural selection helped by genetic drift, evolve new adaptations adapted to novel environments. The final step is either introgression or even a new hybrid species.
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Affiliation(s)
- Antonio Fontdevila
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
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Czech B, Munafò M, Ciabrelli F, Eastwood EL, Fabry MH, Kneuss E, Hannon GJ. piRNA-Guided Genome Defense: From Biogenesis to Silencing. Annu Rev Genet 2018; 52:131-157. [PMID: 30476449 PMCID: PMC10784713 DOI: 10.1146/annurev-genet-120417-031441] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
PIWI-interacting RNAs (piRNAs) and their associated PIWI clade Argonaute proteins constitute the core of the piRNA pathway. In gonadal cells, this conserved pathway is crucial for genome defense, and its main function is to silence transposable elements. This is achieved through posttranscriptional and transcriptional gene silencing. Precursors that give rise to piRNAs require specialized transcription and transport machineries because piRNA biogenesis is a cytoplasmic process. The ping-pong cycle, a posttranscriptional silencing mechanism, combines the cleavage-dependent silencing of transposon RNAs with piRNA production. PIWI proteins also function in the nucleus, where they scan for nascent target transcripts with sequence complementarity, instructing transcriptional silencing and deposition of repressive chromatin marks at transposon loci. Although studies have revealed numerous factors that participate in each branch of the piRNA pathway, the precise molecular roles of these factors often remain unclear. In this review, we summarize our current understanding of the mechanisms involved in piRNA biogenesis and function.
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Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Filippo Ciabrelli
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Martin H Fabry
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
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Geisler C. A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production. BMC Biotechnol 2018; 18:8. [PMID: 29415704 PMCID: PMC5803895 DOI: 10.1186/s12896-017-0412-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/28/2017] [Indexed: 01/01/2023] Open
Abstract
Background Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although extremely sensitive for known viruses, this approach can easily miss viruses that are too dissimilar to viruses in the database. Moreover, it is computationally intensive and requires reference cell genome databases. To avoid these drawbacks, we set out to develop an alternative approach. We reasoned that searching genome and transcriptome assemblies for adventitious viral contaminants using TBLASTN with a compact viral protein database covering extant viral diversity as the query could be fast and sensitive without a requirement for high performance computing hardware. Results We tested our approach on Spodoptera frugiperda Sf-RVN, a recently isolated insect cell line, to determine if it was contaminated with one or more adventitious viruses. We used Illumina reads to assemble the Sf-RVN genome and transcriptome and searched them for adventitious viral contaminants using TBLASTN with our viral protein database. We found no evidence of viral contamination, which was substantiated by the fact that our searches otherwise identified diverse sequences encoding virus-like proteins. These sequences included Maverick, R1 LINE, and errantivirus transposons, all of which are common in insect genomes. We also identified previously described as well as novel endogenous viral elements similar to ORFs encoded by diverse insect viruses. Conclusions Our results demonstrate TBLASTN searching massively parallel sequencing (MPS) assemblies with a compact, manually curated viral protein database is more sensitive for adventitious virus detection than BLASTN, as we identified various sequences that encoded virus-like proteins, but had no similarity to viral sequences at the nucleotide level. Moreover, searches were fast without requiring high performance computing hardware. Our study also documents the enhanced biosafety profile of Sf-RVN as compared to other Sf cell lines, and supports the notion that Sf-RVN is highly suitable for the production of safe biologicals. Electronic supplementary material The online version of this article (doi: 10.1186/s12896-017-0412-z) contains supplementary material, which is available to authorized users.
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Yamashiro H, Siomi MC. PIWI-Interacting RNA in Drosophila: Biogenesis, Transposon Regulation, and Beyond. Chem Rev 2017; 118:4404-4421. [PMID: 29281264 DOI: 10.1021/acs.chemrev.7b00393] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind PIWI proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA-RNA base pairing. However, the uniqueness of this piRNA pathway has emerged through intensive genetic, biochemical, bioinformatic, and structural investigations. Here, we review the studies that elucidated the piRNA pathway, mainly in Drosophila, by describing both historical and recent progress. Studies in other species that have made important contributions to the field are also described.
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Affiliation(s)
- Haruna Yamashiro
- Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo 113-0032 , Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo 113-0032 , Japan
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piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature 2017; 552:268-272. [PMID: 29211718 PMCID: PMC5933846 DOI: 10.1038/nature25018] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated1. The piwi-interacting small RNAs (piRNAs) pathway is critically important for transposable element regulation, by inducing transcriptional silencing or post-transcriptional decay of mRNAs2. Here, we show that piRNAs and piRNA biogenesis components regulate pre-mRNA splicing of P transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in germ cells. Unexpectedly, we show that the piRNA pathway components do not act to reduce P-element transposon transcript levels during P-M hybrid dysgenesis, a syndrome that affects germline development in Drosophila3,4. Instead, splicing regulation is mechanistically achieved in concert with piRNA-mediated changes to repressive chromatin states, and relies on the function of the Piwi-piRNA complex proteins Asterix/Gtsf15–7 and Panoramix/Silencio8,9, as well as Heterochromatin Protein 1a (Su(var)205/HP1a). Furthermore, we show that this machinery, together with the piRNA Flamenco cluster10, not only controls the accumulation of Gypsy retrotransposon transcripts11 but also regulates splicing of Gypsy mRNAs in cultured ovarian somatic cells, a process required for the production of infectious particles that can lead to heritable transposition events12,13. Our findings identify splicing regulation as a new role and essential function for the Piwi pathway in protecting the genome against transposon mobility, and provide a model system for studying the role of chromatin structure in modulating alternative splicing during development.
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Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:164-176. [PMID: 28602845 PMCID: PMC5487533 DOI: 10.1016/j.gpb.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/02/2017] [Accepted: 01/12/2017] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established “transposition-selection” population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.
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Ryazansky S, Radion E, Mironova A, Akulenko N, Abramov Y, Morgunova V, Kordyukova MY, Olovnikov I, Kalmykova A. Natural variation of piRNA expression affects immunity to transposable elements. PLoS Genet 2017; 13:e1006731. [PMID: 28448516 PMCID: PMC5407775 DOI: 10.1371/journal.pgen.1006731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/31/2017] [Indexed: 11/25/2022] Open
Abstract
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon HeT-A, which we have observed in one particular transposon-resistant R strain. Transposon activity in the germline is suppressed by the PIWI-interacting RNA (piRNA) pathway. The resistance of natural Drosophila strains to transposon invasion varies considerably, but the nature of this variability is unknown. We discovered that natural variation in the efficiency of primary piRNA production in the germline causes dramatic differences in the susceptibility to expansion of a newly invaded transposon. A high level of piRNA production in the germline is achieved by increased expression of piRNA precursors. In one of the most transposon-resistant strains, increased content of primary piRNA is observed in both the germline and ovarian somatic cells. We suggest that polymorphisms in piRNA pathway factors are responsible for increased piRNA production. piRNA pathway proteins have been shown to be evolving rapidly under selective pressure. Our data are the first to describe a phenotype that might be caused by this kind of polymorphism. We also demonstrate a likely explanation as to why an overly active piRNA pathway can cause more harm than good in Drosophila: Highly efficient piRNA processing leads to elimination of domesticated telomeric retrotransposons essential for telomere elongation, an effect which has been observed in a natural strain that is extremely resistant to transposon invasion.
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Affiliation(s)
- Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta Radion
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Mironova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yuri Abramov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Y. Kordyukova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Venner S, Miele V, Terzian C, Biémont C, Daubin V, Feschotte C, Pontier D. Ecological networks to unravel the routes to horizontal transposon transfers. PLoS Biol 2017; 15:e2001536. [PMID: 28199335 PMCID: PMC5331948 DOI: 10.1371/journal.pbio.2001536] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.
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Affiliation(s)
- Samuel Venner
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Vincent Miele
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Christophe Terzian
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- UMR754 INRA, Université Claude Bernard Lyon 1, Lyon, France
- Ecole Pratique des Hautes Etudes, Paris, France
| | - Christian Biémont
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Vincent Daubin
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, Utah, United States of America
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive UMR5558-CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
- LabEx ECOFECT (Eco-Evolutionary Dynamics of Infectious Diseases), Université Claude Bernard Lyon 1, Villeurbanne, Lyon, France
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Dehghani M, Lasko P. Multiple Functions of the DEAD-Box Helicase Vasa in Drosophila Oogenesis. Results Probl Cell Differ 2017; 63:127-147. [PMID: 28779316 DOI: 10.1007/978-3-319-60855-6_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The DEAD-box helicase Vasa (Vas) has been most extensively studied in the fruit fly, Drosophila melanogaster, and numerous roles for it in germline development have been discovered. Here, we summarize the present state of knowledge about processes during oogenesis that involve Vas, as well as functions of Vas as a maternal determinant of embryonic spatial patterning and germ cell specification. We review literature that implicates Vas in Piwi-interacting RNA (piRNA) biogenesis in germline cells and in regulating mitosis in germline stem cells (GSCs). We describe the functions of Vas in translational activation of two mRNAs, gurken (grk) and mei-P26, which encode proteins that are important regulators of developmental processes, as Grk specifies both the dorsal-ventral and the anterior-posterior axis of the embryo and Mei-P26 promotes GSC differentiation. The role of Vas in assembly of polar granules, ribonucleoprotein particles that accumulate in the posterior pole plasm of the oocyte and are essential for germ cell specification and posterior embryonic patterning, is also described.
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Affiliation(s)
- Mehrnoush Dehghani
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec, Canada, H3G 0B1
| | - Paul Lasko
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, Québec, Canada, H3G 0B1.
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Pierce SK, Mahadevan P, Massey SE, Middlebrooks ML. A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica. THE BIOLOGICAL BULLETIN 2016; 231:236-244. [PMID: 28048954 DOI: 10.1086/691071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus. However, nucleotide BLAST analysis of the whole genome resulted in hits to only a few portions of the genome, indicating that the Elysia chlorotica retrovirus is novel, has not been previously sequenced, and does not have great genetic similarity to other known viral species. When more invertebrate retroviral genomes are examined, a more precise phylogenetic placement of the Elysia chlorotica retrovirus can be determined.
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Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster. Genetics 2016; 204:631-644. [PMID: 27558137 DOI: 10.1534/genetics.116.187922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 08/18/2016] [Indexed: 11/18/2022] Open
Abstract
Protective mechanisms based on RNA silencing directed against the propagation of transposable elements are highly conserved in eukaryotes. The control of transposable elements is mediated by small noncoding RNAs, which derive from transposon-rich heterochromatic regions that function as small RNA-generating loci. These clusters are transcribed and the precursor transcripts are processed to generate Piwi-interacting RNAs (piRNAs) and endogenous small interfering RNAs (endo-siRNAs), which silence transposable elements in gonads and somatic tissues. The flamenco locus is a Drosophila melanogaster small RNA cluster that controls gypsy and other transposable elements, and has played an important role in understanding how small noncoding RNAs repress transposable elements. In this study, we describe a cosuppression mechanism triggered by new euchromatic gypsy insertions in genetic backgrounds carrying flamenco alleles defective in gypsy suppression. We found that the silencing of gypsy is accompanied by the silencing of other transposons regulated by flamenco, and of specific flamenco sequences from which small RNAs against gypsy originate. This cosuppression mechanism seems to depend on a post-transcriptional regulation that involves both endo-siRNA and piRNA pathways and is associated with the occurrence of developmental defects. In conclusion, we propose that new gypsy euchromatic insertions trigger a post-transcriptional silencing of gypsy sense and antisense sequences, which modifies the flamenco activity. This cosuppression mechanism interferes with some developmental processes, presumably by influencing the expression of specific genes.
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Czech B, Hannon GJ. One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing. Trends Biochem Sci 2016; 41:324-337. [PMID: 26810602 PMCID: PMC4819955 DOI: 10.1016/j.tibs.2015.12.008] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 01/06/2023]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense mechanism that protects the genetic information of animal germ cells from the deleterious effects of molecular parasites, such as transposons. Discovered nearly a decade ago, this small RNA silencing system comprises PIWI-clade Argonaute proteins and their associated RNA-binding partners, the piRNAs. In this review, we highlight recent work that has advanced our understanding of how piRNAs preserve genome integrity across generations. We discuss the mechanism of piRNA biogenesis, give an overview of common themes as well as differences in piRNA-mediated silencing between species, and end by highlighting known and emerging functions of piRNAs.
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Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
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Upadhyay M, Martino Cortez Y, Wong-Deyrup S, Tavares L, Schowalter S, Flora P, Hill C, Nasrallah MA, Chittur S, Rangan P. Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila. PLoS Genet 2016; 12:e1005918. [PMID: 27019121 PMCID: PMC4809502 DOI: 10.1371/journal.pgen.1005918] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/15/2016] [Indexed: 11/18/2022] Open
Abstract
Germline stem cell (GSC) self-renewal and differentiation are required for the sustained production of gametes. GSC differentiation in Drosophila oogenesis requires expression of the histone methyltransferase dSETDB1 by the somatic niche, however its function in this process is unknown. Here, we show that dSETDB1 is required for the expression of a Wnt ligand, Drosophila Wingless type mouse mammary virus integration site number 4 (dWnt4) in the somatic niche. dWnt4 signaling acts on the somatic niche cells to facilitate their encapsulation of the GSC daughter, which serves as a differentiation cue. dSETDB1 is known to repress transposable elements (TEs) to maintain genome integrity. Unexpectedly, we found that independent upregulation of TEs also downregulated dWnt4, leading to GSC differentiation defects. This suggests that dWnt4 expression is sensitive to the presence of TEs. Together our results reveal a chromatin-transposon-Wnt signaling axis that regulates stem cell fate.
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Affiliation(s)
- Maitreyi Upadhyay
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
| | - Yesenia Martino Cortez
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
- NYU Langone Medical Center, New York, New York, United States of America
| | - SiuWah Wong-Deyrup
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
| | - Leticia Tavares
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
| | - Sean Schowalter
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Pooja Flora
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
| | - Corinne Hill
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
- Department of Environmental Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts, United States of America
| | - Mohamad Ali Nasrallah
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
| | - Sridar Chittur
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
- CFG Core Facility, University at Albany SUNY, Rensselaer, New York, United States of America
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York, United States of America
- * E-mail:
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50
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A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements. Stem Cells Int 2015; 2016:7595791. [PMID: 26681955 PMCID: PMC4670677 DOI: 10.1155/2016/7595791] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/11/2015] [Indexed: 11/17/2022] Open
Abstract
Transposons are mobile genetic elements that threaten the survival of species by destabilizing the germline genomes. Limiting the spread of these selfish elements is imperative. Germ cells employ specialized small regulatory RNA pathways to restrain transposon activity. PIWI proteins and Piwi-interacting RNAs (piRNAs) silence transposons at the transcriptional and posttranscriptional level with loss-of-function mutant animals universally exhibiting sterility often associated with germ cell defects. This short review aims to illustrate basic strategies of piRNA-guided defense against transposons. Mechanisms of piRNA silencing are most readily studied in Drosophila melanogaster, which serves as a model to delineate molecular concepts and as a reference for mammalian piRNA systems. PiRNA pathways utilize two major strategies to handle the challenges of transposon control: (1) the hard-wired molecular memory of prior transpositions enables recognition of mobile genetic elements and discriminates transposons from host genes; (2) a feed-forward adaptation mechanism shapes piRNA populations to selectively combat the immediate threat of transposon transcripts. In flies, maternally contributed PIWI-piRNA complexes bolster both of these lines of defense and ensure transgenerational immunity. While recent studies have provided a conceptual framework of what could be viewed as an ancient immune system, we are just beginning to appreciate its many molecular innovations.
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