1
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Huang Y, Lee YCG. Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics. Proc Biol Sci 2024; 291:20232775. [PMID: 38593848 PMCID: PMC11003778 DOI: 10.1098/rspb.2023.2775] [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: 12/08/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024] Open
Abstract
Transposable elements (TEs) are selfish genetic elements whose antagonistic interactions with hosts represent a common genetic conflict in eukaryotes. To resolve this conflict, hosts have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, this mechanism is imperfect and fails to fully halt TE replication. Furthermore, TE epigenetic silencing can inadvertently spread repressive marks to adjacent functional sequences, a phenomenon considered a 'curse' of this conflict resolution. Here, we used forward simulations to explore how TE epigenetic silencing and its harmful side effects shape the evolutionary dynamics of TEs and their hosts. Our findings reveal that epigenetic silencing allows TEs and their hosts to stably coexist under a wide range of conditions, because the underlying molecular mechanisms give rise to copy-number dependency of the strength of TE silencing. Interestingly, contrary to intuitive expectations that TE epigenetic silencing should evolve to be as strong as possible, we found a selective benefit for modifier alleles that weaken TE silencing under biologically feasible conditions. These results reveal that the dual nature of TE epigenetic silencing, with both positive and negative effects, complicates its evolutionary trajectory and makes it challenging to determine whether TE epigenetic silencing is a 'blessing' or a 'curse'.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
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2
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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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3
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Fablet M, Salces-Ortiz J, Jacquet A, Menezes BF, Dechaud C, Veber P, Rebollo R, Vieira C. A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements' Influence on Gene Expression Is Species-Specific. Genome Biol Evol 2023; 15:evad160. [PMID: 37652057 PMCID: PMC10492446 DOI: 10.1093/gbe/evad160] [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: 02/21/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They can be controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of several Drosophila melanogaster and Drosophila simulans wild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K9me3 and H3K4me3). Our results reveal a stronger epigenetic effect of TEs on ortholog genes in D. simulans compared with D. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes in D. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark in D. melanogaster. Overall, this work contributes to the understanding of species-specific influence of TEs within genomes. It provides a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.
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Affiliation(s)
- Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Judit Salces-Ortiz
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Angelo Jacquet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Bianca F Menezes
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Philippe Veber
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Villeurbanne, France
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4
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Miller DE, Dorador AP, Van Vaerenberghe K, Li A, Grantham EK, Cerbin S, Cummings C, Barragan M, Egidy RR, Scott AR, Hall KE, Perera A, Gilliland WD, Hawley RS, Blumenstiel JP. Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion. PLoS Genet 2023; 19:e1010598. [PMID: 36809339 PMCID: PMC9983838 DOI: 10.1371/journal.pgen.1010598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/03/2023] [Accepted: 01/04/2023] [Indexed: 02/23/2023] Open
Abstract
Transposable elements (TE) are selfish genetic elements that can cause harmful mutations. In Drosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Several factors likely limit the accumulation of exponentially amplifying TEs within genomes. First, synergistic interactions between TEs that amplify their harm with increasing copy number are proposed to limit TE copy number. However, the nature of this synergy is poorly understood. Second, because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes in Drosophila melanogaster, a truncated Doc retrotransposon within a neighboring gene was found to trigger the germline silencing of ald, the Drosophila Mps1 homolog, a gene essential for proper chromosome segregation in meiosis. A subsequent screen for suppressors of this silencing identified a new insertion of a Hobo DNA transposon in the same neighboring gene. Here we describe how the original Doc insertion triggers flanking piRNA biogenesis and local gene silencing. We show that this local gene silencing occurs in cis and is dependent on deadlock, a component of the Rhino-Deadlock-Cutoff (RDC) complex, to trigger dual-strand piRNA biogenesis at TE insertions. We further show how the additional Hobo insertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the original Doc insertion. These results support a model of TE-mediated gene silencing by piRNA biogenesis in cis that depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions, illuminates the complex nature of their interactions and supports a model in which off-target gene silencing shapes the evolution of the RDC complex.
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Affiliation(s)
- Danny E. Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Ana P. Dorador
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Kelley Van Vaerenberghe
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Angela Li
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Emily K. Grantham
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Stefan Cerbin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Celeste Cummings
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Marilyn Barragan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Rhonda R. Egidy
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Allison R. Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kate E. Hall
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William D. Gilliland
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - R. Scott Hawley
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Justin P. Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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5
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Watson OT, Buchmann G, Young P, Lo K, Remnant EJ, Yagound B, Shambrook M, Hill AF, Oldroyd BP, Ashe A. Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera. BMC Genomics 2022; 23:257. [PMID: 35379185 PMCID: PMC8978429 DOI: 10.1186/s12864-022-08478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Results Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in the semen of other animals. Intriguingly we also find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. Conclusions We conclude that small RNAs may play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of-origin effects on gene expression and reproductive physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08478-9.
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Affiliation(s)
- Owen T Watson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gabriele Buchmann
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Paul Young
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute NSW 2010, Darlinghurst, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Emily J Remnant
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mitch Shambrook
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Andrew F Hill
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia.,Institute for Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Benjamin P Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia. .,Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany.
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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6
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Roy M, Viginier B, Mayeux CA, Ratinier M, Fablet M. Infections by Transovarially Transmitted DMelSV in Drosophila Have No Impact on Ovarian Transposable Element Transcripts but Increase Their Amounts in the Soma. Genome Biol Evol 2021; 13:evab207. [PMID: 34498066 PMCID: PMC8459167 DOI: 10.1093/gbe/evab207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2021] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are genomic parasites, which activity is tightly controlled in germline cells. Using Sindbis virus, it was recently demonstrated that viral infections affect TE transcript amounts in somatic tissues. However, the strongest evolutionary impacts are expected in gonads, because that is where the genomes of the next generations lie. Here, we investigated this aspect using the Drosophila melanogaster Sigma virus. It is particularly relevant in the genome/TE interaction given its tropism to ovaries, which is the organ displaying the more sophisticated TE control pathways. Our results in Drosophila simulans flies allowed us to confirm the existence of a strong homeostasis of the TE transcriptome in ovaries upon infection, which, however, rely on TE-derived small RNA modulations. In addition, we performed a meta-analysis of RNA-seq data and propose that the immune pathway that is triggered upon viral infection determines the direction of TE transcript modulation in somatic tissues.
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Affiliation(s)
- Marlène Roy
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
- EPHE, PSL Research University, INRA, Université de Lyon, Université Claude Bernard Lyon1, UMR754, IVPC, Lyon, France
| | - Barbara Viginier
- EPHE, PSL Research University, INRA, Université de Lyon, Université Claude Bernard Lyon1, UMR754, IVPC, Lyon, France
| | - Camille A Mayeux
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
| | - Maxime Ratinier
- EPHE, PSL Research University, INRA, Université de Lyon, Université Claude Bernard Lyon1, UMR754, IVPC, Lyon, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
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7
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Saint-Leandre B, Capy P, Hua-Van A, Filée J. piRNA and Transposon Dynamics in Drosophila: A Female Story. Genome Biol Evol 2021; 12:931-947. [PMID: 32396626 PMCID: PMC7337185 DOI: 10.1093/gbe/evaa094] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline. However, it is not known whether piRNA functions are also important in the male germline or whether and how piRNAs are affected by the global genomic context. To address these questions, we compared genome sequences, transcriptomes, and small RNA libraries extracted from entire testes and ovaries of two sister species: D. melanogaster and Drosophila simulans. We found that most TE-derived piRNAs were produced in ovaries and that piRNA pathway genes were strongly overexpressed in ovaries compared with testes, indicating that the silencing of TEs by the piRNA pathway mainly took place in the female germline. To study the relationship between host piRNAs and TE landscape, we analyzed TE genomic features and how they correlate with piRNA production in the two species. In D. melanogaster, we found that TE-derived piRNAs target recently active TEs. In contrast, although Drosophila simulans TEs do not display any features of recent activity, the host still intensively produced silencing piRNAs targeting old TE relics. Together, our results show that the piRNA silencing response mainly takes place in Drosophila ovaries and indicate that the host piRNA response is implemented following a burst of TE activity and could persist long after the extinction of active TE families.
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Affiliation(s)
- Bastien Saint-Leandre
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurelie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jonathan Filée
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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8
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Fabry MH, Falconio FA, Joud F, Lythgoe EK, Czech B, Hannon GJ. Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis. eLife 2021; 10:e68573. [PMID: 34236313 PMCID: PMC8352587 DOI: 10.7554/elife.68573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal lineage, and this has demonstrated importance in the specification of piRNA source loci and in silencing of I- and P-elements in the germ cells of daughters. Maternally inherited Piwi protein enters somatic nuclei in early embryos prior to zygotic genome activation and persists therein for roughly half of the time required to complete embryonic development. To investigate the role of the piRNA pathway in the embryonic soma, we created a conditionally unstable Piwi protein. This enabled maternally deposited Piwi to be cleared from newly laid embryos within 30 min and well ahead of the activation of zygotic transcription. Examination of RNA and protein profiles over time, and correlation with patterns of H3K9me3 deposition, suggests a role for maternally deposited Piwi in attenuating zygotic transposon expression in somatic cells of the developing embryo. In particular, robust deposition of piRNAs targeting roo, an element whose expression is mainly restricted to embryonic development, results in the deposition of transient heterochromatic marks at active roo insertions. We hypothesize that roo, an extremely successful mobile element, may have adopted a lifestyle of expression in the embryonic soma to evade silencing in germ cells.
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Affiliation(s)
- Martin H Fabry
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Federica A Falconio
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Fadwa Joud
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Emily K Lythgoe
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Benjamin Czech
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Gregory J Hannon
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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9
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Gonzalez LE, Tang X, Lin H. Maternal Piwi Regulates Primordial Germ Cell Development to Ensure the Fertility of Female Progeny in Drosophila. Genetics 2021; 219:6303617. [PMID: 34142134 DOI: 10.1093/genetics/iyab091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 12/18/2022] Open
Abstract
In many animals, germline development is initiated by proteins and RNAs that are expressed maternally. PIWI proteins and their associated small noncoding PIWI-interacting RNAs (piRNAs), which guide PIWI to target RNAs by base-pairing, are among the maternal components deposited into the germline of the Drosophila early embryo. Piwi has been extensively studied in the adult ovary and testis, where it is required for transposon suppression, germline stem cell self-renewal, and fertility. Consequently, loss of Piwi in the adult ovary using piwi-null alleles or knockdown from early oogenesis results in complete sterility, limiting investigation into possible embryonic functions of maternal Piwi. In this study, we show that the maternal Piwi protein persists in the embryonic germline through gonad coalescence, suggesting that maternal Piwi can regulate germline development beyond early embryogenesis. Using a maternal knockdown strategy, we find that maternal Piwi is required for the fertility and normal gonad morphology of female, but not male, progeny. Following maternal piwi knockdown, transposons were mildly derepressed in the early embryo but were fully repressed in the ovaries of adult progeny. Furthermore, the maternal piRNA pool was diminished, reducing the capacity of the PIWI/piRNA complex to target zygotic genes during embryogenesis. Examination of embryonic germ cell proliferation and ovarian gene expression showed that the germline of female progeny was partially masculinized by maternal piwi knockdown. Our study reveals a novel role for maternal Piwi in the germline development of female progeny and suggests that the PIWI/piRNA pathway is involved in germline sex determination in Drosophila.
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Affiliation(s)
- Lauren E Gonzalez
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.,Department of Genetics, Yale School of Medicine, New Haven, CT 06519, USA
| | - Xiongzhuo Tang
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.,Department of Cell Biology, Yale School of Medicine, New Haven, CT 06519, USA
| | - Haifan Lin
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.,Department of Cell Biology, Yale School of Medicine, New Haven, CT 06519, USA
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10
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Schwarz F, Wierzbicki F, Senti KA, Kofler R. Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century. Mol Biol Evol 2021; 38:1482-1497. [PMID: 33247725 PMCID: PMC8042734 DOI: 10.1093/molbev/msaa308] [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] [Indexed: 12/15/2022] Open
Abstract
It was long thought that solely three different transposable elements (TEs)-the I-element, the P-element, and hobo-invaded natural Drosophila melanogaster populations within the last century. By sequencing the "living fossils" of Drosophila research, that is, D. melanogaster strains sampled from natural populations at different time points, we show that a fourth TE, Tirant, invaded D. melanogaster populations during the past century. Tirant likely spread in D. melanogaster populations around 1938, followed by the I-element, hobo, and, lastly, the P-element. In addition to the recent insertions of the canonical Tirant, D. melanogaster strains harbor degraded Tirant sequences in the heterochromatin which are likely due to an ancient invasion, likely predating the split of D. melanogaster and D. simulans. These degraded insertions produce distinct piRNAs that were unable to prevent the novel Tirant invasion. In contrast to the I-element, P-element, and hobo, we did not find that Tirant induces any hybrid dysgenesis symptoms. This absence of apparent phenotypic effects may explain the late discovery of the Tirant invasion. Recent Tirant insertions were found in all investigated natural populations. Populations from Tasmania carry distinct Tirant sequences, likely due to a founder effect. By investigating the TE composition of natural populations and strains sampled at different time points, insertion site polymorphisms, piRNAs, and phenotypic effects, we provide a comprehensive study of a natural TE invasion.
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Affiliation(s)
- Florian Schwarz
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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11
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12
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Hongkuan Z, Karsoon T, Shengkang L, Hongyu M, Huaiping Z. The functional roles of the non-coding RNAs in molluscs. Gene 2020; 768:145300. [PMID: 33207256 DOI: 10.1016/j.gene.2020.145300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/10/2023]
Abstract
This review focus on the current knowledge of non-coding RNAs (ncRNAs) in molluscs. In this review, we provide an overview of long ncRNAs (lncRNA), microRNAs (miRNA) and piwi-interacting RNAs (piRNA), followed by evidence for the regulation of ncRNAs in variety of biological process in molluscs, including development, biomineralization and innate immune response. This review advances our understanding on the roles of ncRNAs in molluscs and suggest the future direction to fully understand the epigenetic regulatory network of molluscs.
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Affiliation(s)
- Zhang Hongkuan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Tan Karsoon
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Li Shengkang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Ma Hongyu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China
| | - Zheng Huaiping
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou 515063, China; Mariculture Research Center for Subtropical Shellfish & Algae of Guangdong Province, Shantou 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou 515063, China.
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13
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Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020; 11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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14
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Lewis A, Berkyurek AC, Greiner A, Sawh AN, Vashisht A, Merrett S, Flamand MN, Wohlschlegel J, Sarov M, Miska EA, Duchaine TF. A Family of Argonaute-Interacting Proteins Gates Nuclear RNAi. Mol Cell 2020; 78:862-875.e8. [PMID: 32348780 PMCID: PMC7613089 DOI: 10.1016/j.molcel.2020.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 02/19/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022]
Abstract
Nuclear RNA interference (RNAi) pathways work together with histone modifications to regulate gene expression and enact an adaptive response to transposable RNA elements. In the germline, nuclear RNAi can lead to trans-generational epigenetic inheritance (TEI) of gene silencing. We identified and characterized a family of nuclear Argonaute-interacting proteins (ENRIs) that control the strength and target specificity of nuclear RNAi in C. elegans, ensuring faithful inheritance of epigenetic memories. ENRI-1/2 prevent misloading of the nuclear Argonaute NRDE-3 with small RNAs that normally effect maternal piRNAs, which prevents precocious nuclear translocation of NRDE-3 in the early embryo. Additionally, they are negative regulators of nuclear RNAi triggered from exogenous sources. Loss of ENRI-3, an unstable protein expressed mostly in the male germline, misdirects the RNAi response to transposable elements and impairs TEI. The ENRIs determine the potency and specificity of nuclear RNAi responses by gating small RNAs into specific nuclear Argonautes.
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Affiliation(s)
- Alexandra Lewis
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | | | - Andre Greiner
- Molecular Cell Biology and Genetics, Max Planck Institute, 01307 Dresden, Germany
| | - Ahilya N Sawh
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Stephanie Merrett
- Molecular Cell Biology and Genetics, Max Planck Institute, 01307 Dresden, Germany
| | - Mathieu N Flamand
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Mihail Sarov
- Molecular Cell Biology and Genetics, Max Planck Institute, 01307 Dresden, Germany
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Thomas F Duchaine
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada.
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15
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Kelleher ES, Barbash DA, Blumenstiel JP. Taming the Turmoil Within: New Insights on the Containment of Transposable Elements. Trends Genet 2020; 36:474-489. [PMID: 32473745 DOI: 10.1016/j.tig.2020.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are mobile genetic parasites that can exponentially increase their genomic abundance through self-propagation. Classic theoretical papers highlighted the importance of two potentially escalating forces that oppose TE spread: regulated transposition and purifying selection. Here, we review new insights into mechanisms of TE regulation and purifying selection, which reveal the remarkable foresight of these theoretical models. We further highlight emergent connections between transcriptional control enacted by small RNAs and the contribution of TE insertions to structural mutation and host-gene regulation. Finally, we call for increased comparative analysis of TE dynamics and fitness effects, as well as host control mechanisms, to reveal how interconnected forces shape the differential prevalence and distribution of TEs across the tree of life.
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16
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Abstract
Transposable elements (TEs) are genomic parasites that are found in all genomes, some of which display sequence similarity to certain viruses. In insects, TEs are controlled by the Piwi-interacting small interfering RNA (piRNA) pathway in gonads, while the small interfering RNA (siRNA) pathway is dedicated to TE somatic control and defense against viruses. So far, these two small interfering RNA pathways are considered to involve distinct molecular effectors and are described as independent. Using Sindbis virus (SINV) in Drosophila, here we show that viral infections affect TE transcript amounts via modulations of the piRNA and siRNA repertoires, with the clearest effects in somatic tissues. These results suggest that viral acute or chronic infections may impact TE activity and, thus, the tempo of genetic diversification. In addition, these results deserve further evolutionary considerations regarding potential benefits to the host, the virus, or the TEs.
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17
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Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains. G3-GENES GENOMES GENETICS 2019; 9:855-865. [PMID: 30658967 PMCID: PMC6404621 DOI: 10.1534/g3.118.200789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
All genomes contain repeated sequences that are known as transposable elements (TEs). Among these are endogenous retroviruses (ERVs), which are sequences similar to retroviruses and are transmitted across generations from parent to progeny. These sequences are controlled in genomes through epigenetic mechanisms. At the center of the epigenetic control of TEs are small interfering RNAs of the piRNA class, which trigger heterochromatinization of TE sequences. The tirant ERV of Drosophila simulans displays intra-specific variability in copy numbers, insertion sites, and transcription levels, providing us with a well-suited model to study the dynamic relationship between a TE family and the host genome through epigenetic mechanisms. We show that tirant transcript amounts and piRNA amounts are positively correlated in ovaries in normal conditions, unlike what was previously described following divergent crosses. In addition, we describe tirant insertion polymorphism in the genomes of three D. simulans wild-type strains, which reveals a limited number of insertions that may be associated with gene transcript level changes through heterochromatin spreading and have phenotypic impacts. Taken together, our results participate in the understanding of the equilibrium between the host genome and its TEs.
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18
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Almeida MV, de Jesus Domingues AM, Ketting RF. Maternal and zygotic gene regulatory effects of endogenous RNAi pathways. PLoS Genet 2019; 15:e1007784. [PMID: 30759082 PMCID: PMC6391025 DOI: 10.1371/journal.pgen.1007784] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/26/2019] [Accepted: 01/23/2019] [Indexed: 11/30/2022] Open
Abstract
Endogenous small RNAs (sRNAs) and Argonaute proteins are ubiquitous regulators of gene expression in germline and somatic tissues. sRNA-Argonaute complexes are often expressed in gametes and are consequently inherited by the next generation upon fertilization. In Caenorhabditis elegans, 26G-RNAs are primary endogenous sRNAs that trigger the expression of downstream secondary sRNAs. Two subpopulations of 26G-RNAs exist, each of which displaying strongly compartmentalized expression: one is expressed in the spermatogenic gonad and associates with the Argonautes ALG-3/4; plus another expressed in oocytes and in embryos, which associates with the Argonaute ERGO-1. The determinants and dynamics of gene silencing elicited by 26G-RNAs are largely unknown. Here, we provide diverse new insights into these endogenous sRNA pathways of C. elegans. Using genetics and deep sequencing, we dissect a maternal effect of the ERGO-1 branch of the 26G-RNA pathway. We find that maternal primary sRNAs can trigger the production of zygotic secondary sRNAs that are able to silence targets, even in the absence of zygotic primary triggers. Thus, the interaction of maternal and zygotic sRNA populations, assures target gene silencing throughout animal development. Furthermore, we explore other facets of 26G-RNA biology related to the ALG-3/4 branch. We find that sRNA abundance, sRNA pattern of origin and the 3’ UTR length of target transcripts are predictors of the regulatory outcome by the Argonautes ALG-3/4. Lastly, we provide evidence suggesting that ALG-3 and ALG-4 regulate their own mRNAs in a negative feedback loop. Altogether, we provide several new regulatory insights on the dynamics, target regulation and self-regulation of the endogenous RNAi pathways of C. elegans. Small RNAs (sRNAs) and their partner Argonaute proteins regulate the expression of target RNAs. When sperm and egg meet upon fertilization, a diverse set of proteins and RNA, including sRNA-Argonaute complexes, is passed on to the developing progeny. Thus, these two players are important to initiate specific gene expression programs in the next generation. The nematode Caenorhabditis elegans expresses several classes of sRNAs. 26G-RNAs are a particular class of sRNAs that are divided into two subpopulations: one expressed in the spermatogenic gonad and another expressed in oocytes and in embryos. In this work, we describe the dynamics whereby oogenic 26G-RNAs setup gene silencing in the next generation. In addition, we show several ways that spermatogenic 26G-RNAs and their partner Argonautes, ALG-3 and ALG-4, use to regulate their targets. Finally, we show that ALG-3 and ALG-4 are fine-tuning their own expression, a rare role of Argonaute proteins. Overall, we provide new insights into how sRNAs and Argonautes are regulating gene expression.
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Affiliation(s)
- Miguel Vasconcelos Almeida
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, Mainz, Germany
| | | | - René F. Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, Mainz, Germany
- * E-mail:
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Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Res 2018; 45:e17. [PMID: 28204592 PMCID: PMC5389681 DOI: 10.1093/nar/gkw953] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Hélène Lopez-Maestre
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France
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20
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Wakisaka KT, Ichiyanagi K, Ohno S, Itoh M. Association of zygotic piRNAs derived from paternal P elements with hybrid dysgenesis in Drosophila melanogaster. Mob DNA 2018; 9:7. [PMID: 29441132 PMCID: PMC5800288 DOI: 10.1186/s13100-018-0110-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 01/27/2023] Open
Abstract
Background P-element transposition in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster. Maternally deposited piRNAs suppress P-element transposition in the progeny, linking them to P-M phenotypes; however, the role of zygotic piRNAs derived from paternal P elements is poorly understood. Results To elucidate the molecular basis of P-element suppression by zygotic factors, we investigated the genomic constitution and P-element piRNA production derived from fathers. As a result, we characterized males of naturally derived Q, M’ and P strains, which show different capacities for the P-element mobilizations introduced after hybridizations with M-strain females. The amounts of piRNAs produced in ovaries of F1 hybrids varied among the strains and were influenced by the characteristics of the piRNA clusters that harbored the P elements. Importantly, while both the Q- and M’-strain fathers restrict the P-element mobilization in ovaries of their daughters, the Q-strain fathers supported the production of the highest piRNA expression in the ovaries of their daughters, and the M’ strain carries KP elements in transcriptionally active regions directing the highest expression of KP elements in their daughters. Interestingly, the zygotic P-element piRNAs, but not the KP element mRNA, contributed to the variations in P transposition immunity in the granddaughters. Conclusions The piRNA-cluster-embedded P elements and the transcriptionally active KP elements from the paternal genome are both important suppressors of P element activities that are co-inherited by the progeny. Expression levels of the P-element piRNA and KP-element mRNA vary among F1 progeny due to the constitution of the paternal genome, and are involved in phenotypic variation in the subsequent generation. Electronic supplementary material The online version of this article (10.1186/s13100-018-0110-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Tsuji Wakisaka
- 1Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan
| | - Kenji Ichiyanagi
- 2Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Seiko Ohno
- 3Center for Epidemiologic Research in Asia, Shiga Univesity of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Masanobu Itoh
- 1Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan.,4Center for Advanced Insect Research Promotion (CAIRP), Kyoto Institute of Technology, Kyoto, 606-8585 Japan
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21
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Abstract
Piwi-interacting RNAs (piRNAs) are the non-coding RNAs with 24-32 nucleotides (nt). They exhibit stark differences in length, expression pattern, abundance, and genomic organization when compared to micro-RNAs (miRNAs). There are hundreds of thousands unique piRNA sequences in each species. Numerous piRNAs have been identified and deposited in public databases. Since the piRNAs were originally discovered and well-studied in the germline, a few other studies have reported the presence of piRNAs in somatic cells including neurons. This paper reviewed the common features, biogenesis, functions, and distributions of piRNAs and summarized their specific functions in the brain. This review may provide new insights and research direction for brain disorders.
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Affiliation(s)
- Lingjun Zuo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Zhiren Wang
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Yunlong Tan
- Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine and Department of Psychology, University of Nevada, Las Vegas, NV, USA
| | - Xingguang Luo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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22
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Qiu W, Guo X, Lin X, Yang Q, Zhang W, Zhang Y, Zuo L, Zhu Y, Li CSR, Ma C, Luo X. Transcriptome-wide piRNA profiling in human brains of Alzheimer's disease. Neurobiol Aging 2017; 57:170-177. [PMID: 28654860 DOI: 10.1016/j.neurobiolaging.2017.05.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/21/2017] [Accepted: 05/26/2017] [Indexed: 01/03/2023]
Abstract
Discovered in the brains of multiple animal species, piRNAs may contribute to the pathogenesis of neuropsychiatric illnesses. The present study aimed to identify brain piRNAs across transcriptome that are associated with Alzheimer's disease (AD). Prefrontal cortical tissues of 6 AD cases and 6 controls were examined for piRNA expression levels using an Arraystar HG19 piRNA array (containing 23,677 piRNAs) and genotyped for 17 genome-wide significant and replicated risk SNPs. We examined whether piRNAs are expressed differently between AD cases and controls and explored the potential regulatory effects of risk SNPs on piRNA expression levels. We identified a total of 9453 piRNAs in human brains, with 103 nominally (p < 0.05) differentially (>1.5 fold) expressed in AD cases versus controls and most of the 103 piRNAs nominally correlated with genome-wide significant risk SNPs. We conclude that piRNAs are abundant in human brains and may represent risk biomarkers of AD.
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Affiliation(s)
- Wenying Qiu
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaoyun Guo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Shanghai Mental Health Center, Shanghai, China
| | - Xiandong Lin
- Department of Pathology, Fujian Provincial Cancer Hospital, the Teaching Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Qian Yang
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wanying Zhang
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yong Zhang
- Tianjin Mental Health Center, Tianjin, China
| | - Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Yong Zhu
- Department of Environmental Health Sciences, Yale University School of Public Health, New Haven, CT, USA
| | - Chiang-Shan R Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China.
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23
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Identification of misexpressed genetic elements in hybrids between Drosophila-related species. Sci Rep 2017; 7:40618. [PMID: 28091568 PMCID: PMC5238404 DOI: 10.1038/srep40618] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022] Open
Abstract
Crosses between close species can lead to genomic disorders, often considered to be the cause of hybrid incompatibility, one of the initial steps in the speciation process. How these incompatibilities are established and what are their causes remain unclear. To understand the initiation of hybrid incompatibility, we performed reciprocal crosses between two species of Drosophila (D. mojavensis and D. arizonae) that diverged less than 1 Mya. We performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses. Using an innovative procedure of co-assembling transcriptomes, we show that parental lines differ in the expression of their genes and transposable elements. Reciprocal hybrids presented specific gene categories and few transposable element families misexpressed relative to the parental lines. Because TEs are mainly silenced by piwi-interacting RNAs (piRNAs), we hypothesize that in hybrids the deregulation of specific TE families is due to the absence of such small RNAs. Small RNA sequencing confirmed our hypothesis and we therefore propose that TEs can indeed be major players of genome differentiation and be implicated in the first steps of genomic incompatibilities through small RNA regulation.
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Replicated Risk Nicotinic Cholinergic Receptor Genes for Nicotine Dependence. Genes (Basel) 2016; 7:genes7110095. [PMID: 27827986 PMCID: PMC5126781 DOI: 10.3390/genes7110095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/20/2016] [Accepted: 11/02/2016] [Indexed: 01/31/2023] Open
Abstract
It has been hypothesized that the nicotinic acetylcholine receptors (nAChRs) play important roles in nicotine dependence (ND) and influence the number of cigarettes smoked per day (CPD) in smokers. We compiled the associations between nicotinic cholinergic receptor genes (CHRNs) and ND/CPD that were replicated across different studies, reviewed the expression of these risk genes in human/mouse brains, and verified their expression using independent samples of both human and mouse brains. The potential functions of the replicated risk variants were examined using cis-eQTL analysis or predicted using a series of bioinformatics analyses. We found replicated and significant associations for ND/CPD at 19 SNPs in six genes in three genomic regions (CHRNB3-A6, CHRNA5-A3-B4 and CHRNA4). These six risk genes are expressed in at least 18 distinct areas of the human/mouse brain, with verification in our independent human and mouse brain samples. The risk variants might influence the transcription, expression and splicing of the risk genes, alter RNA secondary or protein structure. We conclude that the replicated associations between CHRNB3-A6, CHRNA5-A3-B4,CHRNA4 and ND/CPD are very robust. More research is needed to examine how these genetic variants contribute to the risk for ND/CPD.
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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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26
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Romero-Soriano V, Garcia Guerreiro MP. Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids. PLoS One 2016; 11:e0147903. [PMID: 26812285 PMCID: PMC4728067 DOI: 10.1371/journal.pone.0147903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/11/2016] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii-D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny.
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Affiliation(s)
- Valèria Romero-Soriano
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Maria Pilar Garcia Guerreiro
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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Hermant C, Boivin A, Teysset L, Delmarre V, Asif-Laidin A, van den Beek M, Antoniewski C, Ronsseray S. Paramutation in Drosophila Requires Both Nuclear and Cytoplasmic Actors of the piRNA Pathway and Induces Cis-spreading of piRNA Production. Genetics 2015; 201:1381-96. [PMID: 26482790 PMCID: PMC4676525 DOI: 10.1534/genetics.115.180307] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/05/2015] [Indexed: 01/24/2023] Open
Abstract
Transposable element activity is repressed in the germline in animals by PIWI-interacting RNAs (piRNAs), a class of small RNAs produced by genomic loci mostly composed of TE sequences. The mechanism of induction of piRNA production by these loci is still enigmatic. We have shown that, in Drosophila melanogaster, a cluster of tandemly repeated P-lacZ-white transgenes can be activated for piRNA production by maternal inheritance of a cytoplasm containing homologous piRNAs. This activated state is stably transmitted over generations and allows trans-silencing of a homologous transgenic target in the female germline. Such an epigenetic conversion displays the functional characteristics of a paramutation, i.e., a heritable epigenetic modification of one allele by the other. We report here that piRNA production and trans-silencing capacities of the paramutated cluster depend on the function of the rhino, cutoff, and zucchini genes involved in primary piRNA biogenesis in the germline, as well as on that of the aubergine gene implicated in the ping-pong piRNA amplification step. The 21-nt RNAs, which are produced by the paramutated cluster, in addition to 23- to 28-nt piRNAs are not necessary for paramutation to occur. Production of these 21-nt RNAs requires Dicer-2 but also all the piRNA genes tested. Moreover, cytoplasmic transmission of piRNAs homologous to only a subregion of the transgenic locus can generate a strong paramutated locus that produces piRNAs along the whole length of the transgenes. Finally, we observed that maternally inherited transgenic small RNAs can also impact transgene expression in the soma. In conclusion, paramutation involves both nuclear (Rhino, Cutoff) and cytoplasmic (Aubergine, Zucchini) actors of the piRNA pathway. In addition, since it is observed between nonfully homologous loci located on different chromosomes, paramutation may play a crucial role in epigenome shaping in Drosophila natural populations.
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Affiliation(s)
- Catherine Hermant
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Antoine Boivin
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Laure Teysset
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Valérie Delmarre
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Amna Asif-Laidin
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
| | - Marius van den Beek
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Drosophila Genetics and Epigenetics," F-75005, Paris, France CNRS, FR3631, Institut de Biologie Paris-Seine, ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
| | - Christophe Antoniewski
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Drosophila Genetics and Epigenetics," F-75005, Paris, France CNRS, FR3631, Institut de Biologie Paris-Seine, ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
| | - Stéphane Ronsseray
- Sorbonne Universités, UPMC University of Paris 06, Institut de Biologie Paris-Seine, UMR7622, Laboratoire Biologie du Développement, F-75005, Paris, France CNRS, UMR7622, "Epigenetic Repression and Mobile DNA," F-75005, Paris, France
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Lim RSM, Kai T. A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners. Semin Cell Dev Biol 2015; 47-48:17-31. [PMID: 26582251 DOI: 10.1016/j.semcdb.2015.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.
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Affiliation(s)
- Robyn S M Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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Zhong F, Zhou N, Wu K, Guo Y, Tan W, Zhang H, Zhang X, Geng G, Pan T, Luo H, Zhang Y, Xu Z, Liu J, Liu B, Gao W, Liu C, Ren L, Li J, Zhou J, Zhang H. A SnoRNA-derived piRNA interacts with human interleukin-4 pre-mRNA and induces its decay in nuclear exosomes. Nucleic Acids Res 2015; 43:10474-91. [PMID: 26405199 PMCID: PMC4666397 DOI: 10.1093/nar/gkv954] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/10/2015] [Indexed: 02/06/2023] Open
Abstract
PIWI interacting RNAs (piRNAs) are highly expressed in germline cells and are involved in maintaining genome integrity by silencing transposons. These are also involved in DNA/histone methylation and gene expression regulation in somatic cells of invertebrates. The functions of piRNAs in somatic cells of vertebrates, however, remain elusive. We found that snoRNA-derived and C (C′)/D′ (D)-box conserved piRNAs are abundant in human CD4 primary T-lymphocytes. piRNA (piR30840) significantly downregulated interleukin-4 (IL-4) via sequence complementarity binding to pre-mRNA intron, which subsequently inhibited the development of Th2 T-lymphocytes. Piwil4 and Ago4 are associated with this piRNA, and this complex further interacts with Trf4-Air2-Mtr4 Polyadenylation (TRAMP) complex, which leads to the decay of targeted pre-mRNA through nuclear exosomes. Taken together, we demonstrate a novel piRNA mechanism in regulating gene expression in highly differentiated somatic cells and a possible novel target for allergy therapeutics.
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Affiliation(s)
- Fudi Zhong
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Nan Zhou
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Kang Wu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yubiao Guo
- Respiratory Division & Medicine Intensive Care Unit, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Weiping Tan
- Department of Pediatrics, the Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Hong Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xue Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Guannan Geng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Ting Pan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhibin Xu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Bingfeng Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenchao Gao
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Liangliang Ren
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jun Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jie Zhou
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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30
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Gabriel JM, Hollick JB. Paramutation in maize and related behaviors in metazoans. Semin Cell Dev Biol 2015; 44:11-21. [PMID: 26318741 DOI: 10.1016/j.semcdb.2015.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/18/2015] [Indexed: 12/31/2022]
Abstract
Paramutation refers to both the process and results of trans-homolog interactions causing heritable changes in both gene regulation and silencing abilities. Originally described in plants, paramutation-like behaviors have now been reported in model metazoans. Here we detail our current understanding of the paramutation mechanism as defined in Zea mays and compare this paradigm to these metazoan examples. Experimental results implicate functional roles of small RNAs in all these model organisms that highlight a diversity of mechanisms by which these molecules specify meiotically heritable regulatory information in the eukarya.
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Affiliation(s)
- Janelle M Gabriel
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Jay B Hollick
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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31
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García-López J, Alonso L, Cárdenas DB, Artaza-Alvarez H, Hourcade JDD, Martínez S, Brieño-Enríquez MA, Del Mazo J. Diversity and functional convergence of small noncoding RNAs in male germ cell differentiation and fertilization. RNA (NEW YORK, N.Y.) 2015; 21:946-962. [PMID: 25805854 PMCID: PMC4408801 DOI: 10.1261/rna.048215.114] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
The small noncoding RNAs (sncRNAs) are considered as post-transcriptional key regulators of male germ cell development. In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs, or rRNAs processing may also play important regulatory roles in spermatogenesis. By next-generation sequencing (NGS), we characterized the sncRNA populations detected at three milestone stages in male germ differentiation: primordial germ cells (PGCs), pubertal spermatogonia cells, and mature spermatozoa. To assess their potential transmission through the spermatozoa during fertilization, the sncRNAs of mouse oocytes and zygotes were also analyzed. Both, microRNAs and snoRNA-derived small RNAs are abundantly expressed in PGCs but transiently replaced by piRNAs in spermatozoa and endo-siRNAs in oocytes and zygotes. Exhaustive analysis of miRNA sequence variants also shows an increment of noncanonical microRNA forms along male germ cell differentiation. RNAs-derived from tRNAs and rRNAs interacting with PIWI proteins are not generated by the ping-pong pathway and could be a source of primary piRNAs. Moreover, our results strongly suggest that the small RNAs-derived from tRNAs and rRNAs are interacting with PIWI proteins, and specifically with MILI. Finally, computational analysis revealed their potential involvement in post-transcriptional regulation of mRNA transcripts suggesting functional convergence among different small RNA classes in germ cells and zygotes.
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Affiliation(s)
- Jesús García-López
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Lola Alonso
- Department of Bioinformatics Service, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - David B Cárdenas
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Haydeé Artaza-Alvarez
- Department of Bioinformatics Service, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Juan de Dios Hourcade
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Sergio Martínez
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Miguel A Brieño-Enríquez
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Jesús Del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
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Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae. Mol Genet Genomics 2015; 290:1471-83. [PMID: 25711309 DOI: 10.1007/s00438-015-1012-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/15/2015] [Indexed: 01/08/2023]
Abstract
Hybridization between different genomes is a source of genomic instability, sometimes associated with transposable element (TE) mobilization. Previous work showed that hybridization between the species Drosophila buzzatii and Drosophila koepferae induced mobilization of different (TEs), the Osvaldo retrotransposon being the most unstable. However, we ignore the mechanisms involved in this transposition release in interspecific hybrids. In order to disentangle the mechanisms involved in this process, we performed Osvaldo expression studies in somatic and germinal tissues from hybrids and parental species. There was a trend towards increased Osvaldo expression in the somatic tissues of hybrid females and males, which was always significant in males compared to the parental species D. buzzatii but, not in females compared to maternal species D. koepferae. There were massive changes of Osvaldo expression in the testes, which varied depending on the hybrid generation and family. Moreover, Osvaldo hybridization signals, restricted to the apical and primary spermatocyte regions in parents, occupied broader region in the hybrids. In ovaries, there were no significant differences in Osvaldo expression rates between hybrids and the maternal species D. koepferae. The transcript location was restricted to ovarian nurse cells in both parents and hybrids, undetectable in some hybrids. This research highlights first, the existence of putative complex deregulation mechanisms different between sexes and cell types and second, disruption of Osvaldo activity particularly evident in testes from sterile hybrid males. Deeper studies of the total transcriptome in hybrids and parental species are necessary to gain a better knowledge of the TE deregulation pathways in hybrids.
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33
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Host control of insect endogenous retroviruses: small RNA silencing and immune response. Viruses 2014; 6:4447-64. [PMID: 25412365 PMCID: PMC4246233 DOI: 10.3390/v6114447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/04/2014] [Accepted: 11/11/2014] [Indexed: 12/02/2022] Open
Abstract
Endogenous retroviruses are relics of ancient infections from retroviruses that managed to integrate into the genome of germline cells and remained vertically transmitted from parent to progeny. Subsequent to the endogenization process, these sequences can move and multiply in the host genome, which can have deleterious consequences and disturb genomic stability. Natural selection favored the establishment of silencing pathways that protect host genomes from the activity of endogenous retroviruses. RNA silencing mechanisms are involved, which utilize piRNAs. The response to exogenous viral infections uses siRNAs, a class of small RNAs that are generated via a distinct biogenesis pathway from piRNAs. However, interplay between both pathways has been identified, and interactions with anti-bacterial and anti-fungal immune responses are also suspected. This review focuses on Diptera (Arthropods) and intends to compile pieces of evidence showing that the RNA silencing pathway of endogenous retrovirus regulation is not independent from immunity and the response to infections. This review will consider the mechanisms that allow the lasting coexistence of viral sequences and host genomes from an evolutionary perspective.
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34
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Chambeyron S, Seitz H. Insect small non-coding RNA involved in epigenetic regulations. CURRENT OPINION IN INSECT SCIENCE 2014; 1:1-9. [PMID: 32846724 DOI: 10.1016/j.cois.2014.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/01/2014] [Accepted: 05/01/2014] [Indexed: 06/11/2023]
Abstract
Small regulatory RNAs can not only guide post-transcriptional repression of target genes, but some of them can also direct heterochromatin formation of specific genomic loci. Here we review the published literature on small RNA-guided epigenetic regulation in insects. The recent development of novel analytical technologies (deep sequencing and RNAi screens) has led to the identification of some of the factors involved in these processes, as well as their molecular mechanism and subcellular localization. Other findings uncovered an additional mode of epigenetic control, where maternally inherited small RNAs can affect phenotypes in a stable, transgenerational manner. The evolutive history of small RNA effector proteins in insects suggests that these two modes of regulation are variably conserved among species.
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Affiliation(s)
- Séverine Chambeyron
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), UPR 1142, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Hervé Seitz
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), UPR 1142, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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Carnelossi EAG, Lerat E, Henri H, Martinez S, Carareto CMA, Vieira C. Specific activation of an I-like element in Drosophila interspecific hybrids. Genome Biol Evol 2014; 6:1806-17. [PMID: 24966182 PMCID: PMC4122939 DOI: 10.1093/gbe/evu141] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2014] [Indexed: 12/29/2022] Open
Abstract
The non-long terminal repeat (LTR) retrotransposon I, which belongs to the I superfamily of non-LTR retrotransposons, is well known in Drosophila because it transposes at a high frequency in the female germline cells in I-R hybrid dysgenic crosses of Drosophila melanogaster. Here, we report the occurrence and the upregulation of an I-like element in the hybrids of two sister species belonging to the repleta group of the genus Drosophila, D. mojavensis, and D. arizonae. These two species display variable degrees of pre- and postzygotic isolation, depending on the geographic origin of the strains. We took advantage of these features to explore the transposable element (TE) dynamics in interspecific crosses. We fully characterized the copies of this TE family in the D. mojavensis genome and identified at least one complete copy. We showed that this element is transcriptionally active in the ovaries and testes of both species and in their hybrids. Moreover, we showed that this element is upregulated in hybrid males, which could be associated with the male-sterile phenotype.
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Affiliation(s)
- Elias A G Carnelossi
- UNESP-Universidade Estadual Paulista, Laboratório de Evolução Molecular, Departamento de Biologia, São José do Rio Preto, São Paulo, BrazilUniversité de Lyon, Université Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne
| | - Emmanuelle Lerat
- Université de Lyon, Université Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne
| | - Hélène Henri
- Université de Lyon, Université Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne
| | - Sonia Martinez
- Université de Lyon, Université Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne
| | - Claudia M A Carareto
- UNESP-Universidade Estadual Paulista, Laboratório de Evolução Molecular, Departamento de Biologia, São José do Rio Preto, São Paulo, Brazil
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, VilleurbanneInstitut Universitaire de France, Paris, France
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36
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Abstract
Cell identities can be stable over a long time due to a “cellular memory” of expression profiles achieved through epigenetic mechanisms. In this review, Stuwe et al. describe recent studies demonstrating that short noncoding RNAs can also provide molecular signals that define epigenetic states of cells, leading to transgenerational epigenetic inheritance. Cells in multicellular organisms have distinct identities characterized by their profiles of expressed genes. Cell identities can be stable over a long time and through multiple cellular divisions but are also responsive to extracellular signals. Since the DNA sequence is identical in all cells, a “cellular memory” of expression profiles is achieved by what are defined as epigenetic mechanisms. Two major molecular principles—networks of transcription factors and maintenance of cis-chromatin modifications—have been implicated in maintaining cellular memory. Here we describe recent studies demonstrating that short noncoding RNAs can also provide molecular signals that define epigenetic states of cells. Small RNAs can act independently or cooperate with chromatin modifications to achieve long-lasting effects necessary for cellular memory and transgenerational inheritance.
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Affiliation(s)
- Evelyn Stuwe
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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37
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Enhanced evolution by stochastically variable modification of epigenetic marks in the early embryo. Proc Natl Acad Sci U S A 2014; 111:6353-8. [PMID: 24733912 DOI: 10.1073/pnas.1402585111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Evolution by gene duplication is generally accepted as one of the crucial driving forces for the gain of new complexity and functions, but the formation of pseudogenes remains a problem for this mechanism. Here we expand on earlier ideas that epigenetic modifications can drive neo- and subfunctionalization in evolution by gene duplication. We explore the effects of stochastic epigenetic modifications on the evolution (and thus development) of complex organisms in a constant environment. Modeling is done both using a modified genetic drift analytical treatment and computer simulations, which were found to agree. A transposon silencing model is also explored. Some key assumptions made include (i) stochastic, incomplete removal (or addition) of repressive epigenetic marks takes place during a window(s) of opportunity in the zygote and early embryo; (ii) there is no statistical variation of the marks after the window closes; and (iii) the genes affected are sensitive to dosage. Our genetic drift treatment takes into account that after gene duplication the prevailing case upon which selection operates is a duplicate/singlet heterozygote; to the best of our knowledge, this has not been considered in previous treatments. We conclude from our modeling that stochastic epigenetic modifications, with rates consistent with experimental observation, can both increase the rate of gene fixation and decrease pseudogenization, thus dramatically improving the efficacy of evolution by gene duplication. We also find that a transposon silencing model is advantageous for fixation of recessive genes in diploid organisms, especially with large effective population sizes.
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38
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Vela D, Fontdevila A, Vieira C, García Guerreiro MP. A genome-wide survey of genetic instability by transposition in Drosophila hybrids. PLoS One 2014; 9:e88992. [PMID: 24586475 PMCID: PMC3930673 DOI: 10.1371/journal.pone.0088992] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/14/2014] [Indexed: 12/16/2022] Open
Abstract
Hybridization between species is a genomic instability factor involved in increasing mutation rate and new chromosomal rearrangements. Evidence of a relationship between interspecific hybridization and transposable element mobilization has been reported in different organisms, but most studies are usually performed with particular TEs and do not discuss the real effect of hybridization on the whole genome. We have therefore studied whole genome instability of Drosophila interspecific hybrids, looking for the presence of new AFLP markers in hybrids. A high percentage (27–90%) of the instability markers detected corresponds to TEs belonging to classes I and II. Moreover, three transposable elements (Osvaldo, Helena and Galileo) representative of different families, showed an overall increase of transposition rate in hybrids compared to parental species. This research confirms the hypothesis that hybridization induces genomic instability by transposition bursts and suggests that genomic stress by transposition could contribute to a relaxation of mechanisms controlling TEs in the Drosophila genome.
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Affiliation(s)
- Doris Vela
- Grup de Biología Evolutiva, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Antonio Fontdevila
- Grup de Biología Evolutiva, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon1, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - María Pilar García Guerreiro
- Grup de Biología Evolutiva, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- * E-mail:
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39
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Ross RJ, Weiner MM, Lin H. PIWI proteins and PIWI-interacting RNAs in the soma. Nature 2014; 505:353-359. [PMID: 24429634 PMCID: PMC4265809 DOI: 10.1038/nature12987] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/20/2013] [Indexed: 12/17/2022]
Abstract
The discovery of millions of PIWI-interacting RNAs revealed a fascinating and unanticipated dimension of biology. The PIWI-piRNA pathway has been commonly perceived as germline-specific, even though the somatic function of PIWI proteins was documented when they were first discovered. Recent studies have begun to re-explore this pathway in somatic cells in diverse organisms, particularly lower eukaryotes. These studies have illustrated the multifaceted somatic functions of the pathway not only in transposon silencing but also in genome rearrangement and epigenetic programming, with biological roles in stem-cell function, whole-body regeneration, memory and possibly cancer.
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Affiliation(s)
- Robert J Ross
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06509, USA
| | - Molly M Weiner
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06509, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06509, USA
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40
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Gu T, Elgin SCR. Maternal depletion of Piwi, a component of the RNAi system, impacts heterochromatin formation in Drosophila. PLoS Genet 2013; 9:e1003780. [PMID: 24068954 PMCID: PMC3777992 DOI: 10.1371/journal.pgen.1003780] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/25/2013] [Indexed: 02/05/2023] Open
Abstract
A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains, and how that chromatin state is faithfully transmitted. Stable heterochromatin is necessary to silence transposable elements (TEs) and maintain genome integrity. Both the RNAi system and heterochromatin components HP1 (Swi6) and H3K9me2/3 are required for initial establishment of heterochromatin structures in S. pombe. Here we utilize both loss of function alleles and the newly developed Drosophila melanogaster transgenic shRNA lines to deplete proteins of interest at specific development stages to dissect their roles in heterochromatin assembly in early zygotes and in maintenance of the silencing chromatin state during development. Using reporters subject to Position Effect Variegation (PEV), we find that depletion of key proteins in the early embryo can lead to loss of silencing assayed at adult stages. The piRNA component Piwi is required in the early embryo for reporter silencing in non-gonadal somatic cells, but knock-down during larval stages has no impact. This implies that Piwi is involved in targeting HP1a when heterochromatin is established at the late blastoderm stage and possibly also during embryogenesis, but that the silent chromatin state created is transmitted through cell division independent of the piRNA system. In contrast, heterochromatin structural protein HP1a is required for both initial heterochromatin assembly and the following mitotic inheritance. HP1a profiles in piwi mutant animals confirm that Piwi depletion leads to decreased HP1a levels in pericentric heterochromatin, particularly in TEs. The results suggest that the major role of the piRNA system in assembly of heterochromatin in non-gonadal somatic cells occurs in the early embryo during heterochromatin formation, and further demonstrate that failure of heterochromatin formation in the early embryo impacts the phenotype of the adult.
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Affiliation(s)
- Tingting Gu
- Department of Biology, Washington University, Saint Louis, Missouri, United States of America
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