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Sarkies P. The curious case of the disappearing piRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1849. [PMID: 38629193 DOI: 10.1002/wrna.1849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024]
Abstract
Small non-coding RNAs are key regulators of gene expression across eukaryotes. Piwi-interacting small RNAs (piRNAs) are a specific type of small non-coding RNAs, conserved across animals, which are best known as regulators of genome stability through their ability to target transposable elements for silencing. Despite the near ubiquitous presence of piRNAs in animal lineages, there are some examples where the piRNA pathway has been lost completely, most dramatically in nematodes where loss has occurred in at least four independent lineages. In this perspective I will provide an evaluation of the presence of piRNAs across animals, explaining how it is known that piRNAs are missing from certain organisms. I will then consider possible explanations for why the piRNA pathway might have been lost and evaluate the evidence in favor of each possible mechanism. While it is still impossible to provide definitive answers, these theories will prompt further investigations into why such a highly conserved pathway can nevertheless become dispensable in certain lineages. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, UK
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2
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Scarpa A, Kofler R. The impact of paramutations on the invasion dynamics of transposable elements. Genetics 2023; 225:iyad181. [PMID: 37819004 PMCID: PMC10697812 DOI: 10.1093/genetics/iyad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
According to the prevailing view, the trap model, the activity of invading transposable elements (TEs) is greatly reduced when a TE copy jumps into a piRNA cluster, which triggers the emergence of piRNAs that silence the TE. One crucial component in the host defence are paramutations. Mediated by maternally deposited piRNAs, paramutations convert TE insertions into piRNA producing loci, thereby transforming selfish TEs into agents of the host defence. Despite this significant effect, the impact of paramutations on the dynamics of TE invasions remains unknown. To address this issue, we performed extensive forward simulations of TE invasions with piRNA clusters and paramutations. We found that paramutations significantly affect TE dynamics, by accelerating the silencing of TE invasions, reducing the number of insertions accumulating during the invasions and mitigating the fitness cost of TEs. We also demonstrate that piRNA production induced by paramutations, an epigenetically inherited trait, may be positively selected. Finally, we show that paramutations may account for three important open problems with the trap model. Firstly, paramutated TE insertions may compensate for the insufficient number of insertions in piRNA clusters observed in previous studies. Secondly, paramutations may explain the discrepancy between the observed and the expected abundance of different TE families in Drosophila melanogaster. Thirdly, piRNA clusters may be crucial to trigger the host defence, but paramutations render the clusters dispensable once the defence has been established. This could account for the lack of TE activation when three major piRNA clusters were deleted in a previous study.
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Affiliation(s)
- Almorò Scarpa
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien 1210, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien 1210, Austria
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3
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Lawlor MA, Ellison CE. Evolutionary dynamics between transposable elements and their host genomes: mechanisms of suppression and escape. Curr Opin Genet Dev 2023; 82:102092. [PMID: 37517354 PMCID: PMC10530431 DOI: 10.1016/j.gde.2023.102092] [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: 02/28/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 08/01/2023]
Abstract
Transposable elements (TEs) are ubiquitous among eukaryotic species. Their evolutionary persistence is likely due to a combination of tolerogenic, evasive/antagonistic, and cooperative interactions with their host genomes. Here, we focus on metazoan species and review recent advances related to the harmful effects of TE insertions, including how epigenetic effects and TE-derived RNAs can damage host cells. We discuss new findings related to host pathways that silence TEs, such as the piRNA pathway and the APOBEC3 and Kruppel-associated box zinc finger gene families. Finally, we summarize novel strategies used by TEs to evade host silencing, including the Y chromosome as a permissive niche for TE mobilization and TE counterdefense strategies to block host silencing factors.
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4
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Tomar SS, Hua-Van A, Le Rouzic A. A population genetics theory for piRNA-regulated transposable elements. Theor Popul Biol 2023; 150:1-13. [PMID: 36863578 DOI: 10.1016/j.tpb.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
Transposable elements (TEs) are self-reproducing selfish DNA sequences that can invade the genome of virtually all living species. Population genetics models have shown that TE copy numbers generally reach a limit, either because the transposition rate decreases with the number of copies (transposition regulation) or because TE copies are deleterious, and thus purged by natural selection. Yet, recent empirical discoveries suggest that TE regulation may mostly rely on piRNAs, which require a specific mutational event (the insertion of a TE copy in a piRNA cluster) to be activated - the so-called TE regulation "trap model". We derived new population genetics models accounting for this trap mechanism, and showed that the resulting equilibria differ substantially from previous expectations based on a transposition-selection equilibrium. We proposed three sub-models, depending on whether or not genomic TE copies and piRNA cluster TE copies are selectively neutral or deleterious, and we provide analytical expressions for maximum and equilibrium copy numbers, as well as cluster frequencies for all of them. In the full neutral model, the equilibrium is achieved when transposition is completely silenced, and this equilibrium does not depend on the transposition rate. When genomic TE copies are deleterious but not cluster TE copies, no long-term equilibrium is possible, and active TEs are eventually eliminated after an active incomplete invasion stage. When all TE copies are deleterious, a transposition-selection equilibrium exists, but the invasion dynamics is not monotonic, and the copy number peaks before decreasing. Mathematical predictions were in good agreement with numerical simulations, except when genetic drift and/or linkage disequilibrium dominates. Overall, the trap-model dynamics appeared to be substantially more stochastic and less repeatable than traditional regulation models.
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Affiliation(s)
- Siddharth S Tomar
- Université Paris-Saclay, CNRS, IRD, UMR EGCE, 12 Route 128, Gif-sur-Yvette, 91190, France.
| | - Aurélie Hua-Van
- Université Paris-Saclay, CNRS, IRD, UMR EGCE, 12 Route 128, Gif-sur-Yvette, 91190, France.
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR EGCE, 12 Route 128, Gif-sur-Yvette, 91190, France.
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5
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Wierzbicki F, Kofler R, Signor S. Evolutionary dynamics of piRNA clusters in Drosophila. Mol Ecol 2023; 32:1306-1322. [PMID: 34878692 DOI: 10.1111/mec.16311] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022]
Abstract
Small RNAs produced from transposable element (TE)-rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defence against selfish DNA. In animals, it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat-rich regions are difficult to assemble and compare. Here, we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species, we show that piRNA clusters are evolving rapidly. While 70%-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.
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Affiliation(s)
- Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
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6
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Li T, Wang H, Ma K, Wu Y, Qi X, Liu Z, Li Q, Zhang Y, Ma Y. Identification and functional characterization of developmental-stage-dependent piRNAs in Tibetan sheep testes. J Anim Sci 2023; 101:skad189. [PMID: 37282774 PMCID: PMC10321380 DOI: 10.1093/jas/skad189] [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: 03/13/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023] Open
Abstract
The core function of the testes is to produce sperms, which is the prerequisite for maintaining male fertility. PIWI-interacting RNAs (piRNAs) are a class of non-coding small RNAs that are mainly enriched in the reproductive organ and play a key role in germ cell development and spermatogenesis. However, the expression and function of piRNAs in the testes of Tibetan sheep, a domestic animal endemic to the Tibetan Plateau, remain unknown. In this study, we evaluated the sequence structure, expression profile, and potential function of piRNAs in testicular tissues from Tibetan sheep at different developmental stages (3 months, 1 year, and 3 years of age, respectively) by small RNA sequencing. Of the identified piRNAs, the sequence lengths of 24-26 nt and 29 nt dominate. Most piRNA sequences begin with uracil and have a distinct ping-pong structure which mainly distributes in exons, repeat regions, introns, and other unannotated regions of the genome. The piRNAs in the repeat region are primarily derived from the retrotransposons: long terminal repeats, long interspersed nuclear elements, and short interspersed elements. These piRNAs constitute 2,568 piRNA clusters, which mainly distribute on chromosomes 1, 2, 3, 5, 11, 13, 14, and 24, and of these clusters, a total of 529 piRNA clusters were differentially expressed in at least two age groups. Most of the piRNAs were expressed in a low abundance in the testes of developing Tibetan sheep. A total of 41,552 and 2,529 differential piRNAs were identified in testes from 3 months vs. 1 year, and 1 year vs. 3 years, respectively, presenting significantly increased abundance for most piRNAs in 1 year and 3 years compared with 3 months. The functional evaluation of the target genes showed that the differential piRNAs are mainly involved in regulating gene expression, transcription, protein modification, and cell development during spermatogenesis and testicular development. In conclusion, this study focused on the sequence structure and expression characteristics of piRNAs in the testis of Tibetan sheep and provided new insights into the functional mechanism of piRNAs in testicular development and spermatogenesis of sheep.
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Affiliation(s)
- Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Keyan Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yi Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xingcai Qi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zilong Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yong Zhang
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
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Liu X, Majid M, Yuan H, Chang H, Zhao L, Nie Y, He L, Liu X, He X, Huang Y. Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism. BMC Biol 2022; 20:243. [PMID: 36307800 PMCID: PMC9615261 DOI: 10.1186/s12915-022-01441-w] [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: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis♀1C = 6.60 pg, Angaracris rhodopa♀1C = 16.36 pg) to ascertain the influence of piRNAs.
Results
We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria, and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level.
Conclusions
Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.
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Torri A, Jaeger J, Pradeu T, Saleh MC. The origin of RNA interference: Adaptive or neutral evolution? PLoS Biol 2022; 20:e3001715. [PMID: 35767561 PMCID: PMC9275709 DOI: 10.1371/journal.pbio.3001715] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/12/2022] [Indexed: 11/30/2022] Open
Abstract
The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability. Where does RNA interference come from? This Essay describes a new step-by-step evolutionary model of how RNA interference might have originated in early eukaryotes through neutral events from the molecular machinery present in prokaryotes.
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Affiliation(s)
- Alessandro Torri
- Virus & RNA interference Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
- * E-mail: (AT); (M-CS)
| | | | - Thomas Pradeu
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Institut d’histoire et de philosophie des sciences et des techniques, CNRS UMR 8590, Pantheon-Sorbonne University, Paris, France
| | - Maria-Carla Saleh
- Virus & RNA interference Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
- * E-mail: (AT); (M-CS)
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9
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Vandewege MW, Patt RN, Merriman DK, Ray DA, Hoffmann FG. The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. RNA (NEW YORK, N.Y.) 2022; 28:609-621. [PMID: 35064043 PMCID: PMC8925971 DOI: 10.1261/rna.078862.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are genomic parasites that can propagate throughout host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and germline mobilization is a challenge to genome integrity. There are defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides the opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. To do so, we compared the PIWI/piRNA dynamics in squirrels to observations from the rabbit and mouse. Despite a lack of young insertions in squirrels, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three Piwi genes were not expressed, prior to P8 in squirrel testis, and there was little TE expression change with the onset of Piwi expression. We also demonstrated there was not a major expression change in the young squirrel LINE families in the transition from juvenile to adult testis in contrast to young mouse and rabbit LINE families. These observations lead us to conclude that PIWI suppression, was weaker for squirrel LINEs and SINEs and did not strongly reduce their transcription. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.
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Affiliation(s)
- Michael W Vandewege
- Department of Biology, Eastern New Mexico University, Portales, New Mexico 88130, USA
| | - Roy N Patt
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas 78245-0549, USA
| | - Dana K Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin 54901, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, USA
- Institute of Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Pettie N, Llopart A, Comeron JM. Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba. PLoS Genet 2022; 18:e1010087. [PMID: 35320272 PMCID: PMC8979470 DOI: 10.1371/journal.pgen.1010087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 04/04/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
The number and location of crossovers across genomes are highly regulated during meiosis, yet the key components controlling them are fast evolving, hindering our understanding of the mechanistic causes and evolutionary consequences of changes in crossover rates. Drosophila melanogaster has been a model species to study meiosis for more than a century, with an available high-resolution crossover map that is, nonetheless, missing for closely related species, thus preventing evolutionary context. Here, we applied a novel and highly efficient approach to generate whole-genome high-resolution crossover maps in D. yakuba to tackle multiple questions that benefit from being addressed collectively within an appropriate phylogenetic framework, in our case the D. melanogaster species subgroup. The genotyping of more than 1,600 individual meiotic events allowed us to identify several key distinct properties relative to D. melanogaster. We show that D. yakuba, in addition to higher crossover rates than D. melanogaster, has a stronger centromere effect and crossover assurance than any Drosophila species analyzed to date. We also report the presence of an active crossover-associated meiotic drive mechanism for the X chromosome that results in the preferential inclusion in oocytes of chromatids with crossovers. Our evolutionary and genomic analyses suggest that the genome-wide landscape of crossover rates in D. yakuba has been fairly stable and captures a significant signal of the ancestral crossover landscape for the whole D. melanogaster subgroup, even informative for the D. melanogaster lineage. Contemporary crossover rates in D. melanogaster, on the other hand, do not recapitulate ancestral crossovers landscapes. As a result, the temporal stability of crossover landscapes observed in D. yakuba makes this species an ideal system for applying population genetic models of selection and linkage, given that these models assume temporal constancy in linkage effects. Our studies emphasize the importance of generating multiple high-resolution crossover rate maps within a coherent phylogenetic context to broaden our understanding of crossover control during meiosis and to improve studies on the evolutionary consequences of variable crossover rates across genomes and time.
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Affiliation(s)
- Nikale Pettie
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Ana Llopart
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Josep M. Comeron
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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11
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Casale AM, Liguori F, Ansaloni F, Cappucci U, Finaurini S, Spirito G, Persichetti F, Sanges R, Gustincich S, Piacentini L. Transposable element activation promotes neurodegeneration in a Drosophila model of Huntington's disease. iScience 2022; 25:103702. [PMID: 35036881 PMCID: PMC8752904 DOI: 10.1016/j.isci.2021.103702] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/22/2021] [Accepted: 12/23/2021] [Indexed: 12/17/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant disorder with progressive motor dysfunction and cognitive decline. The disease is caused by a CAG repeat expansion in the IT15 gene, which elongates a polyglutamine stretch of the HD protein, Huntingtin. No therapeutic treatments are available, and new pharmacological targets are needed. Retrotransposons are transposable elements (TEs) that represent 40% and 30% of the human and Drosophila genomes and replicate through an RNA intermediate. Mounting evidence suggests that mammalian TEs are active during neurogenesis and may be involved in diseases of the nervous system. Here we show that TE expression and mobilization are increased in a Drosophila melanogaster HD model. By inhibiting TE mobilization with Reverse Transcriptase inhibitors, polyQ-dependent eye neurodegeneration and genome instability in larval brains are rescued and fly lifespan is increased. These results suggest that TE activation may be involved in polyQ-induced neurotoxicity and a potential pharmacological target. Transposable elements: new pathogenic players in Huntington's disease polyQ-Htt expression leads to widespread heterochromatin relaxation Reverse transcriptase inhibitors rescue HD-induced neurodegeneration
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Affiliation(s)
- Assunta Maria Casale
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Liguori
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Federico Ansaloni
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Ugo Cappucci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Sara Finaurini
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Giovanni Spirito
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | | | - Remo Sanges
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Lucia Piacentini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
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12
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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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13
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Schneider L, Guo YK, Birch D, Sarkies P. Network-based visualisation reveals new insights into transposable element diversity. Mol Syst Biol 2021; 17:e9600. [PMID: 34169647 PMCID: PMC8226279 DOI: 10.15252/msb.20209600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 01/12/2023] Open
Abstract
Transposable elements (TEs) are widespread across eukaryotic genomes, yet their content varies widely between different species. Factors shaping the diversity of TEs are poorly understood. Understanding the evolution of TEs is difficult because their sequences diversify rapidly and TEs are often transferred through non‐conventional means such as horizontal gene transfer. We developed a method to track TE evolution using network analysis to visualise TE sequence and TE content across different genomes. We illustrate our method by first using a monopartite network to study the sequence evolution of Tc1/mariner elements across focal species. We identify a connection between two subfamilies associated with convergent acquisition of a domain from a protein‐coding gene. Second, we use a bipartite network to study how TE content across species is shaped by epigenetic silencing mechanisms. We show that the presence of Piwi‐interacting RNAs is associated with differences in network topology after controlling for phylogenetic effects. Together, our method demonstrates how a network‐based approach can identify hitherto unknown properties of TE evolution across species.
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Affiliation(s)
- Lisa Schneider
- MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Imperial College, London, UK.,Data Sciences Institute, Imperial College, London, UK
| | - Yi-Ke Guo
- Data Sciences Institute, Imperial College, London, UK
| | - David Birch
- Data Sciences Institute, Imperial College, London, UK
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Imperial College, London, UK
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14
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Weilguny L, Vlachos C, Selvaraju D, Kofler R. Reconstructing the Invasion Route of the P-Element in Drosophila melanogaster Using Extant Population Samples. Genome Biol Evol 2020; 12:2139-2152. [PMID: 33210145 PMCID: PMC7750958 DOI: 10.1093/gbe/evaa190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2020] [Indexed: 12/19/2022] Open
Abstract
The P-element, one of the best understood eukaryotic transposable elements, spread in natural Drosophila melanogaster populations in the last century. It invaded American populations first and later spread to the Old World. Inferring this invasion route was made possible by a unique resource available in D. melanogaster: Many strains sampled from different locations over the course of the last century. Here, we test the hypothesis that the invasion route of the P-element may be reconstructed from extant population samples using internal deletions (IDs) as markers. These IDs arise at a high rate when DNA transposons, such as the P-element, are active. We suggest that inferring invasion routes is possible as: 1) the fraction of IDs increases in successively invaded populations, which also explains the striking differences in the ID content between American and European populations, and 2) successively invaded populations end up with similar sets of IDs. This approach allowed us to reconstruct the invasion route of the P-element with reasonable accuracy. Our approach also sheds light on the unknown timing of the invasion in African populations: We suggest that African populations were invaded after American but before European populations. Simulations of TE invasions in spatially distributed populations confirm that IDs may allow us to infer invasion routes. Our approach might be applicable to other DNA transposons in different host species.
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Affiliation(s)
- Lukas Weilguny
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Christos Vlachos
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.,Vienna Graduate School of Population Genetics, Wien, Austria
| | - Divya Selvaraju
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.,Vienna Graduate School of Population Genetics, Wien, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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15
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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: 46] [Impact Index Per Article: 11.5] [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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16
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Wang L, Barbash DA, Kelleher ES. Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity. PLoS Genet 2020; 16:e1008861. [PMID: 32525870 PMCID: PMC7310878 DOI: 10.1371/journal.pgen.1008861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 06/23/2020] [Accepted: 05/14/2020] [Indexed: 02/05/2023] Open
Abstract
In metazoan germlines, the piRNA pathway acts as a genomic immune system, employing small RNA-mediated silencing to defend host DNA from the harmful effects of transposable elements (TEs). Expression of genomic TEs is proposed to initiate self regulation by increasing the production of repressive piRNAs, thereby “adapting” piRNA-mediated control to the most active TE families. Surprisingly, however, piRNA pathway proteins, which execute piRNA biogenesis and enforce silencing of targeted sequences, evolve rapidly and adaptively in animals. If TE silencing is ensured through piRNA biogenesis, what necessitates changes in piRNA pathway proteins? Here we used interspecific complementation to test for functional differences between Drosophila melanogaster and D. simulans alleles of three adaptively evolving piRNA pathway proteins: Armitage, Aubergine and Spindle-E. In contrast to piRNA-mediated transcriptional regulators examined in previous studies, these three proteins have cytoplasmic functions in piRNA maturation and post-transcriptional silencing. Across all three proteins we observed interspecific divergence in the regulation of only a handful of TE families, which were more robustly silenced by the heterospecific piRNA pathway protein. This unexpected result suggests that unlike transcriptional regulators, positive selection has not acted on cytoplasmic piRNA effector proteins to enhance their function in TE repression. Rather, TEs may evolve to “escape” silencing by host proteins. We further discovered that D. simulans alleles of aub and armi exhibit enhanced off-target effects on host transcripts in a D. melanogaster background, as well as modest reductions in the efficiency of piRNA biogenesis, suggesting that promiscuous binding of D. simulans Aub and Armi proteins to host transcripts reduces their participation in piRNA production. Avoidance of genomic auto-immunity may therefore be a critical target of selection. Our observations suggest that piRNA effector proteins are subject to an evolutionary trade-off between defending the host genome from the harmful effect of TEs while also minimizing collateral damage to host genes. Transposable elements are mobile fragments of selfish DNA that burden host genomes with deleterious mutations and incite genome instability. Host cells employ a specialized small-RNA mediated silencing pathway, the piRNA pathway, to act as a genomic immune system suppressing the mobilization of TEs. Changes in genomic TE content are met with rapid changes in the piRNA pool, thereby maintaining host control over transposition. However, piRNA pathway proteins—which enact piRNA biogenesis and silence target TEs—also evolve adaptively. To isolate forces that underlie this adaptive evolution, we examined functional divergence between two Drosophila species for three adaptively evolving piRNA pathway proteins. To our surprise, we found very few differences in TE regulation, suggesting that evolution has not generally acted to enhance control of TE parasites. Rather, we discovered interspecific differences in the regulation of host mRNAs for two proteins, which suggested that proteins evolve to avoid off-target silencing of host transcripts. We propose that the avoidance of such “genomic autoimmunity” is an important and underappreciated force driving the adaptive evolution of piRNA proteins.
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Affiliation(s)
- Luyang Wang
- Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Daniel A. Barbash
- Dept. Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America
| | - Erin S. Kelleher
- Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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17
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Serrato-Capuchina A, Wang J, Earley E, Peede D, Isbell K, Matute DR. Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster. Genome Biol Evol 2020; 12:808-826. [PMID: 32339225 PMCID: PMC7313671 DOI: 10.1093/gbe/evaa084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short- and long-read sequencing to infer the number of PEs in the genomes of dozens of isofemale lines from two Drosophila species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M × ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species, which suggests that there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species specific.
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Affiliation(s)
| | - Jeremy Wang
- Genetics Department, University of North Carolina, Chapel Hill
| | - Eric Earley
- Genomics in Public Health and Medicine RTI International, Research Triangle Park, North Carolina
| | - David Peede
- Biology Department, University of North Carolina, Chapel Hill
| | - Kristin Isbell
- Biology Department, University of North Carolina, Chapel Hill
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill
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18
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Kukushkina IV, Makhnovskii PA, Nefedova LN, Milyaeva PA, Kuzmin IV, Lavrenov AR, Kim AI. Analysis of Transcriptome of Drosophila melanogaster Strains with Disrupted Control of gypsy Retrotransposon Transposition. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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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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20
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Kofler R. piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions. Genome Biol Evol 2020; 12:736-749. [PMID: 32219390 PMCID: PMC7259680 DOI: 10.1093/gbe/evaa064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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21
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Zhang S, Pointer B, Kelleher ES. Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations. Genome Res 2020; 30:566-575. [PMID: 32238416 PMCID: PMC7197473 DOI: 10.1101/gr.251546.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 03/24/2020] [Indexed: 11/24/2022]
Abstract
The regulation of transposable element (TE) activity by small RNAs is a ubiquitous feature of germlines. However, despite the obvious benefits to the host in terms of ensuring the production of viable gametes and maintaining the integrity of the genomes they carry, it remains controversial whether TE regulation evolves adaptively. We examined the emergence and evolutionary dynamics of repressor alleles after P-elements invaded the Drosophila melanogaster genome in the mid-twentieth century. In many animals including Drosophila, repressor alleles are produced by transpositional insertions into piRNA clusters, genomic regions encoding the Piwi-interacting RNAs (piRNAs) that regulate TEs. We discovered that ∼94% of recently collected isofemale lines in the Drosophila melanogaster Genetic Reference Panel (DGRP) contain at least one P-element insertion in a piRNA cluster, indicating that repressor alleles are produced by de novo insertion at an exceptional rate. Furthermore, in our sample of approximately 200 genomes, we uncovered no fewer than 80 unique P-element insertion alleles in at least 15 different piRNA clusters. Finally, we observe no footprint of positive selection on P-element insertions in piRNA clusters, suggesting that the rapid evolution of piRNA-mediated repression in D. melanogaster was driven primarily by mutation. Our results reveal for the first time how the unique genetic architecture of piRNA production, in which numerous piRNA clusters can encode regulatory small RNAs upon transpositional insertion, facilitates the nonadaptive rapid evolution of repression.
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Affiliation(s)
- Shuo Zhang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Beverly Pointer
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Erin S Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
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22
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Abstract
In mammals and invertebrates, the proliferation of an invading transposable element (TE) is thought to be stopped by an insertion into a piRNA cluster. Here, we explore the dynamics of TE invasions under this trap model using computer simulations. We found that piRNA clusters confer a substantial benefit, effectively preventing extinction of host populations from a proliferation of deleterious TEs. TE invasions consist of three distinct phases: first, the TE amplifies within the population, next TE proliferation is stopped by segregating cluster insertions, and finally the TE is inactivated by fixation of a cluster insertion. Suppression by segregating cluster insertions is unstable and bursts of TE activity may yet occur. The transposition rate and the population size mostly influence the length of the phases but not the amount of TEs accumulating during an invasion. Solely, the size of piRNA clusters was identified as a major factor influencing TE abundance. We found that a single nonrecombining cluster is more efficient in stopping invasions than clusters distributed over several chromosomes. Recombination among cluster sites makes it necessary that each diploid carries, on the average, four cluster insertions to stop an invasion. Surprisingly, negative selection in a model with piRNA clusters can lead to a novel equilibrium state, where TE copy numbers remain stable despite only some individuals in a population carrying a cluster insertion. In Drosophila melanogaster, the trap model accounts for the abundance of TEs produced in the germline but fails to predict the abundance of TEs produced in the soma.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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23
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Luo S, Zhang H, Duan Y, Yao X, Clark AG, Lu J. The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster. BMC Evol Biol 2020; 20:14. [PMID: 31992188 PMCID: PMC6988346 DOI: 10.1186/s12862-020-1580-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 01/13/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The piwi-interacting RNAs (piRNAs) are small non-coding RNAs that specifically repress transposable elements (TEs) in the germline of Drosophila. Despite our expanding understanding of TE:piRNA interaction, whether there is an evolutionary arms race between TEs and piRNAs was unclear. RESULTS Here, we studied the population genomics of TEs and piRNAs in the worldwide strains of D. melanogaster. By conducting a correlation analysis between TE contents and the abundance of piRNAs from ovaries of representative strains of D. melanogaster, we find positive correlations between TEs and piRNAs in six TE families. Our simulations further highlight that TE activities and the strength of purifying selection against TEs are important factors shaping the interactions between TEs and piRNAs. Our studies also suggest that the de novo generation of piRNAs is an important mechanism to repress the newly invaded TEs. CONCLUSIONS Our results revealed the existence of an evolutionary arms race between the copy numbers of TEs and the abundance of antisense piRNAs at the population level. Although the interactions between TEs and piRNAs are complex and many factors should be considered to impact their interaction dynamics, our results suggest the emergence, repression specificity and strength of piRNAs on TEs should be considered in studying the landscapes of TE insertions in Drosophila. These results deepen our understanding of the interactions between piRNAs and TEs, and also provide novel insights into the nature of genomic conflicts of other forms.
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Affiliation(s)
- Shiqi Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- College of Plant Protection, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China
| | - Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Xinmin Yao
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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24
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Jain G, Stuendl A, Rao P, Berulava T, Pena Centeno T, Kaurani L, Burkhardt S, Delalle I, Kornhuber J, Hüll M, Maier W, Peters O, Esselmann H, Schulte C, Deuschle C, Synofzik M, Wiltfang J, Mollenhauer B, Maetzler W, Schneider A, Fischer A. A combined miRNA-piRNA signature to detect Alzheimer's disease. Transl Psychiatry 2019; 9:250. [PMID: 31591382 PMCID: PMC6779890 DOI: 10.1038/s41398-019-0579-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/05/2019] [Accepted: 08/18/2019] [Indexed: 01/03/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder causing huge emotional and economic burden to our societies. An effective therapy has not been implicated yet, which is in part also due to the fact that pathological changes occur years before clinical symptoms manifest. Thus, there is a great need for the development of a translatable biomarker. Recent evidence highlights microRNAs as candidate biomarkers. In this study, we use next-generation sequencing to study the small noncoding RNAome (sncRNAome) in exosomes derived from human cerebrospinal fluid (CSF). We show that the sncRNAome from CSF-derived exosomes is dominated not only by microRNAs (miRNAs) but also by PIWI-interacting RNAs (piRNAs). We define a combined signature consisting of three miRNAs and three piRNAs that are suitable to detect AD with an AUC of 0.83 in a replication cohort and furthermore predict the conversion of mild-cognitive impaired (MCI) patients to AD dementia with an AUC of 0.86 for the piRNA signature. When combining the smallRNA signature with pTau and Aβ 42/40 ratio the AUC reaches 0.98. Our study reports a novel exosomal small noncoding RNA signature to detect AD pathology and provides the first evidence that in addition to miRNAs, piRNAs should also be considered as a candidate biomarker for AD.
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Affiliation(s)
- Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany
| | - Anne Stuendl
- 0000 0004 0438 0426grid.424247.3Translational Dementia Research, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Pooja Rao
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany
| | - Tea Berulava
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany
| | - Tonatiuh Pena Centeno
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany ,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Goettingen, Germany
| | - Lalit Kaurani
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany
| | - Ivana Delalle
- 0000 0004 0367 5222grid.475010.7Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Johannes Kornhuber
- 0000 0001 2107 3311grid.5330.5Department of Psychiatry and Psychotherapy, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Michael Hüll
- 0000 0000 9428 7911grid.7708.8Center for Geriatric Medicine and Gerontology, University Medical Center Freiburg, 79106 Freiburg, Germany ,0000 0000 9428 7911grid.7708.8Department of Psychiatry and Psychotherapy, University Medical Centre Freiburg, 79106 Freiburg, Germany
| | - Wolfgang Maier
- 0000 0001 2240 3300grid.10388.32Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, 53127 Bonn, Germany
| | - Oliver Peters
- 0000 0001 2248 7639grid.7468.dDepartment of Psychiatry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 12200 Berlin, Germany ,0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), 12203 Berlin, Germany ,0000 0001 1014 0849grid.419491.0Memory Clinic and Dementia Prevention Center, Experimental and Clinical Research Center (ECRC), 13125 Berlin, Germany
| | - Hermann Esselmann
- 0000 0001 0482 5331grid.411984.1Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany
| | - Claudia Schulte
- 0000 0001 2190 1447grid.10392.39Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany ,0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Christian Deuschle
- 0000 0001 2190 1447grid.10392.39Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany ,0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Mathis Synofzik
- 0000 0001 2190 1447grid.10392.39Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany ,0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Jens Wiltfang
- 0000 0001 0482 5331grid.411984.1Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany ,0000000123236065grid.7311.4iBiMED, Medical Sciences Department, University of Aveiro, Aveiro, Portugal ,German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Göttingen, Germany
| | - Brit Mollenhauer
- 0000 0001 0482 5331grid.411984.1Department of Neurology, University Medical Center Göttingen (UMG), 37075 Göttingen, Germany ,grid.440220.0Paracelsus-Elena-Klinik, 34128 Kassel, Germany
| | - Walter Maetzler
- 0000 0001 2190 1447grid.10392.39Center of Neurology, Department of Neurodegeneration and Hertie-Institute for Clinical Brain Research, University of Tuebingen, 72076 Tuebingen, Germany ,0000 0004 0438 0426grid.424247.3German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany ,0000 0004 0646 2097grid.412468.dDepartment of Neurology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Anja Schneider
- Translational Dementia Research, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany. .,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, 53127, Bonn, Germany.
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075, Göttingen, Germany. .,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), 37075, Göttingen, Germany.
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25
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Ray DA, Grimshaw JR, Halsey MK, Korstian JM, Osmanski AB, Sullivan KAM, Wolf KA, Reddy H, Foley N, Stevens RD, Knisbacher BA, Levy O, Counterman B, Edelman NB, Mallet J. Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths. Genome Biol Evol 2019; 11:2162-2177. [PMID: 31214686 PMCID: PMC6685494 DOI: 10.1093/gbe/evz125] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.
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Affiliation(s)
- David A Ray
- Department of Biological Science, Texas Tech University
| | | | | | | | | | | | | | - Harsith Reddy
- Department of Biological Science, Texas Tech University
| | - Nicole Foley
- Department of Biological Science, Texas Tech University
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX
| | | | - Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Orr Levy
- Department of Physics, Bar-Ilan University, Ramat Gan, Israel
| | | | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University
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26
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Pattinson CL, Gill JM, Lippa SM, Brickell TA, French LM, Lange RT. Concurrent Mild Traumatic Brain Injury and Posttraumatic Stress Disorder Is Associated With Elevated Tau Concentrations in Peripheral Blood Plasma. J Trauma Stress 2019; 32:546-554. [PMID: 31291489 PMCID: PMC6690750 DOI: 10.1002/jts.22418] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 01/22/2019] [Accepted: 02/03/2019] [Indexed: 12/19/2022]
Abstract
Concurrent mild traumatic brain injury (mTBI) and posttraumatic stress disorder (PTSD) are common in U.S. military service members and veterans. Tau and amyloid-beta-42 (Aβ42) are proteins that have been linked to cognitive impairment, neurological hallmarks of Alzheimer's disease, and may also relate to recovery from mTBI. However, the role of these proteins in the maintenance or resolution of chronic symptoms has not yet been determined. Participants in the current study were 102 service members and veterans who had sustained an mTBI (n = 84) or injured controls (IC) without TBI (n = 18). They were categorized into three groups based on the presence or absence of mTBI and PTSD: IC/PTSD-Absent (n = 18), mTBI/PTSD-Absent (n = 63), and mTBI/PTSD-Present (n = 21). Concentrations of tau and Aβ42 in peripheral blood plasma were measured using SimoaTM , an ultrasensitive technology, and compared across groups. Tau concentrations were highest in the mTBI/PTSD-Present group, F(2, 99) = 4.33, p = .016, compared to the other two groups. Linear multiple regression was conducted to determine the independent effects of PTSD and mTBI on tau concentrations, controlling for gender and sleep medication. PTSD was a significant and independent predictor of tau concentrations, β = .25, p = .009, ηp 2 = .26. Aβ42 concentrations did not differ between the groups. The results indicated that PTSD was associated with an elevation of tau in peripheral blood and suggest that there may be increased biological effects of PTSD in this young cohort of service members and veterans following mTBI.
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Affiliation(s)
- Cassandra L. Pattinson
- National Institutes of Health, National Institute of Nursing Research, Bethesda, Maryland, USA
| | - Jessica M. Gill
- National Institutes of Health, National Institute of Nursing Research, Bethesda, Maryland, USA
| | - Sara M. Lippa
- Defense and Veterans Brain Injury Center, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Tracey A. Brickell
- Defense and Veterans Brain Injury Center, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Louis M. French
- Defense and Veterans Brain Injury Center, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Rael T. Lange
- Defense and Veterans Brain Injury Center, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, Maryland, USA,University of British Columbia, Vancouver, British Columbia, Canada
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27
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Enforcement is central to the evolution of cooperation. Nat Ecol Evol 2019; 3:1018-1029. [PMID: 31239554 DOI: 10.1038/s41559-019-0907-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/26/2019] [Indexed: 01/21/2023]
Abstract
Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.
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28
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Duc C, Yoth M, Jensen S, Mouniée N, Bergman CM, Vaury C, Brasset E. Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion. Genome Biol 2019; 20:127. [PMID: 31227013 PMCID: PMC6587276 DOI: 10.1186/s13059-019-1736-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs called PIWI-interacting RNAs (piRNAs) produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline gains protection from a new transposon invasion. RESULTS To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line. CONCLUSIONS Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of "auto-immunization" of a germline endangered by mobilization of a surrounding somatic TE.
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Affiliation(s)
- Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
- Present address: UFIP UMR-CNRS 6286, Epigénétique: prolifération et différenciation, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, 44322 Nantes, France
| | - Marianne Yoth
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Silke Jensen
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Nolwenn Mouniée
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Casey M. Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, 120 E. Green St, Athens, GA 30602 USA
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
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29
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Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes (Basel) 2019; 10:genes10050338. [PMID: 31064091 PMCID: PMC6562904 DOI: 10.3390/genes10050338] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
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Affiliation(s)
- Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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Abstract
Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA, genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no or a negative effect on organismal fitness. [1-6] Genomes have traditionally been viewed as cohesive units, with genes acting together to improve the fitness of the organism. However, when genes have some control over their own transmission, the rules can change, and so just like all social groups, genomes are vulnerable to selfish behaviour by their parts. Early observations of selfish genetic elements were made almost a century ago, but the topic did not get widespread attention until several decades later. Inspired by the gene-centred views of evolution popularized by George Williams[7] and Richard Dawkins,[8] two papers were published back-to-back in Nature in 1980-by Leslie Orgel and Francis Crick[9] and Ford Doolittle and Carmen Sapienza[10] respectively-introducing the concept of selfish genetic elements (at the time called "selfish DNA") to the wider scientific community. Both papers emphasized that genes can spread in a population regardless of their effect on organismal fitness as long as they have a transmission advantage. Selfish genetic elements have now been described in most groups of organisms, and they demonstrate a remarkable diversity in the ways by which they promote their own transmission.[11] Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes, ranging from genome size and architecture to speciation.[12].
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Affiliation(s)
- J. Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- * E-mail: (JAÅ); (AGC)
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- * E-mail: (JAÅ); (AGC)
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Kelleher ES, Azevedo RBR, Zheng Y. The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element. Genome Biol Evol 2018; 10:3038-3057. [PMID: 30252073 PMCID: PMC6404463 DOI: 10.1093/gbe/evy218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are genomic parasites that impose fitness costs on their
hosts by producing deleterious mutations and disrupting gametogenesis. Host genomes avoid
these costs by regulating TE activity, particularly in germline cells where new insertions
are heritable and TEs are exceptionally active. However, the capacity of different
TE-associated fitness costs to select for repression in the host, and the role of
selection in the evolution of TE regulation more generally remain controversial. In this
study, we use forward, individual-based simulations to examine the evolution of
small-RNA-mediated TE regulation, a conserved mechanism for TE repression that is employed
by both prokaryotes and eukaryotes. To design and parameterize a biologically realistic
model, we drew on an extensive survey of empirical studies of the transposition and
regulation of P-element DNA transposons in Drosophila
melanogaster. We observed that even under conservative assumptions, where
small-RNA-mediated regulation reduces transposition only, repression evolves rapidly and
adaptively after the genome is invaded by a new TE in simulated populations. We further
show that the spread of repressor alleles through simulated populations is greatly
enhanced by two additional TE-imposed fitness costs: dysgenic sterility and ectopic
recombination. Finally, we demonstrate that the adaptive mutation rate to repression is a
critical parameter that influences both the evolutionary trajectory of host repression and
the associated proliferation of TEs after invasion in simulated populations. Our findings
suggest that adaptive evolution of TE regulation may be stronger and more prevalent than
previously appreciated, and provide a framework for interpreting empirical data.
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Affiliation(s)
- Erin S Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston
| | | | - Yichen Zheng
- Department of Biology and Biochemistry, University of Houston, Houston.,Biodiversitt und Klima Forschungszentrum, Senckenberg Gesellschaft fr Naturforschung, Frankfurt am Main, Germany.,Institute of Genetics, University of Cologne, 50674 Cologne, NRW, Germany
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32
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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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33
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Song MJ, Schaack S. Evolutionary Conflict between Mobile DNA and Host Genomes. Am Nat 2018; 192:263-273. [DOI: 10.1086/698482] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Gainetdinov I, Skvortsova Y, Kondratieva S, Funikov S, Azhikina T. Two modes of targeting transposable elements by piRNA pathway in human testis. RNA (NEW YORK, N.Y.) 2017; 23:1614-1625. [PMID: 28842508 PMCID: PMC5648030 DOI: 10.1261/rna.060939.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 08/23/2017] [Indexed: 06/07/2023]
Abstract
PIWI proteins and their partner small RNAs, termed piRNAs, are known to control transposable elements (TEs) in the germline. Here, we provide evidence that in humans this control is exerted in two different modes. On the one hand, production of piRNAs specifically targeting evolutionarily youngest TEs (L1HS, L1PA2-L1PA6, LTR12C, SVA) is present both at prenatal and postnatal stages of spermatogenesis and is performed without involvement of piRNA clusters. On the other hand, at postnatal stages, piRNAs deriving from pachytene clusters target "older" TEs and thus complement cluster-independent piRNA production to achieve relevant targeting of virtually all TEs expressed in postnatal testis. We also find that converging transcription of antisense-oriented genes contributes to the origin of genic postnatal prepachytene clusters. Finally, while a fraction of pachytene piRNAs was previously shown to arise from long intergenic noncoding RNAs (lincRNAs, i.e., pachytene piRNA cluster primary transcripts), we ascertain that these are a specific set of lincRNAs that both possess distinguishing epigenetic features and are expressed exclusively in testis.
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Affiliation(s)
- Ildar Gainetdinov
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Yulia Skvortsova
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sofia Kondratieva
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sergey Funikov
- Department of Structural, Functional and Evolutionary Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Tatyana Azhikina
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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35
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Saint-Leandre B, Clavereau I, Hua-Van A, Capy P. Transcriptional polymorphism ofpiRNA regulatory genes underlies themarineractivity inDrosophila simulanstestes. Mol Ecol 2017; 26:3715-3731. [DOI: 10.1111/mec.14145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/28/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Bastien Saint-Leandre
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Isabelle Clavereau
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Aurelie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS; Univ. Paris-Sud, IRD; Université Paris-Saclay; Gif-sur-Yvette Cedex France
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36
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Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:164-176. [PMID: 28602845 PMCID: PMC5487533 DOI: 10.1016/j.gpb.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/02/2017] [Accepted: 01/12/2017] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established “transposition-selection” population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) were demonstrated to be master repressors of TE activities in Drosophila. The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The interaction between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysgenesis for the I-R and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.
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37
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Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing. Genetics 2017; 203:1513-31. [PMID: 27516614 DOI: 10.1534/genetics.115.184119] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/25/2016] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are both important drivers of genome evolution and genetic parasites with potentially dramatic consequences for host fitness. The recent explosion of research on regulatory RNAs reveals that small RNA-mediated silencing is a conserved genetic mechanism through which hosts repress TE activity. The invasion of the Drosophila melanogaster genome by P elements, which happened on a historical timescale, represents an incomparable opportunity to understand how small RNA-mediated silencing of TEs evolves. Repression of P-element transposition emerged almost concurrently with its invasion. Recent studies suggest that this repression is implemented in part, and perhaps predominantly, by the Piwi-interacting RNA (piRNA) pathway, a small RNA-mediated silencing pathway that regulates TE activity in many metazoan germlines. In this review, I consider the P-element invasion from both a molecular and evolutionary genetic perspective, reconciling classic studies of P-element regulation with the new mechanistic framework provided by the piRNA pathway. I further explore the utility of the P-element invasion as an exemplar of the evolution of piRNA-mediated silencing. In light of the highly-conserved role for piRNAs in regulating TEs, discoveries from this system have taxonomically broad implications for the evolution of repression.
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38
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Adrion JR, Song MJ, Schrider DR, Hahn MW, Schaack S. Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster. Genome Biol Evol 2017; 9:1329-1340. [PMID: 28338986 PMCID: PMC5447328 DOI: 10.1093/gbe/evx050] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 02/06/2023] Open
Abstract
Knowing the rate at which transposable elements (TEs) insert and delete is critical for understanding their role in genome evolution. We estimated spontaneous rates of insertion and deletion for all known, active TE superfamilies present in a set of Drosophila melanogaster mutation-accumulation (MA) lines using whole genome sequence data. Our results demonstrate that TE insertions far outpace TE deletions in D. melanogaster. We found a significant effect of background genotype on TE activity, with higher rates of insertions in one MA line. We also found significant rate heterogeneity between the chromosomes, with both insertion and deletion rates elevated on the X relative to the autosomes. Further, we identified significant associations between TE activity and chromatin state, and tested for associations between TE activity and other features of the local genomic environment such as TE content, exon content, GC content, and recombination rate. Our results provide the most detailed assessment of TE mobility in any organism to date, and provide a useful benchmark for both addressing theoretical predictions of TE dynamics and for exploring large-scale patterns of TE movement in D. melanogaster and other species.
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Affiliation(s)
| | - Michael J. Song
- Department of Integrative Biology, University of California, Berkeley, CA
| | - Daniel R. Schrider
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN
- School of Informatics and Computing, Indiana University, Bloomington, IN
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Sun YH, Xie LH, Zhuo X, Chen Q, Ghoneim D, Zhang B, Jagne J, Yang C, Li XZ. Domestic chickens activate a piRNA defense against avian leukosis virus. eLife 2017; 6. [PMID: 28384097 PMCID: PMC5383398 DOI: 10.7554/elife.24695] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 12/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious. DOI:http://dx.doi.org/10.7554/eLife.24695.001 Viruses called retroviruses can infect animal cells and merge their genetic information with those of the animal causing damage to the animal’s genetic blueprints. Once retroviruses are integrated into a cell they can sometimes get passed down through the generations over the centuries. Almost half of the human genetic code, for example, is made from ancient retroviruses and other foreign sequences. Over time many of these ancient viruses lost the ability to infect other cells and became trapped within cells but they can still jump out and damage the animal’s genetic code under certain circumstances. These trapped foreign sequences are called transposable elements. Animal cells produce molecules called piRNAs to shut down transposable elements. Most piRNAs are produced from genetic information that originally came from integrated retroviruses and that has been hijacked to defend the cell, a similar strategy as Crisper system in bacteria. Domestic chickens produce piRNAs against a virus called avian leukosis virus (or ALV for short) – which commonly infects domestic fowl. The virus also infected the wild ancestors of chickens, known as red jungle fowl, but these birds do not produce piRNAs. This provides an ideal setting to study the evolution of piRNAs in an animal that is not too distantly related to humans (chickens and humans both have backbones, and are therefore both warm-blooded vertebrates). Sun et al. examined cells from the testicles of domestic chickens and red jungle fowl as an example of the role of piRNAs in protecting genetic information in vertebrates. The investigation revealed that piRNAs against all previously trapped viruses in the chicken’s genetic code are produced in chickens to stop them from causing more damage. Sun et al. also observed the creation of piRNAs in chickens in response to ALV that had not yet become trapped in the chicken’s genetic code. Importantly, the piRNAs could control these retroviruses while they were still infectious. The experiments also revealed that piRNAs against ALV are produced from a single copy of ALV that is found in both domestic and wild chickens. The results showed that cells can produce new piRNAs using these pre-existing viral copies within their own genetics. This illustrates that production of piRNA from existing genetic material can be activated in response to certain cues. Further work will seek to discover how existing genetic information becomes a source of piRNAs. In the United States, 8 billion domestic chickens are consumed each year, and a better understanding of how these birds defend themselves against viral infections could increase the productivity of the poultry industry around the world. Moreover, because other viruses trapped in the chicken’s genetic code are related to similar viruses in humans, future discoveries made in this area could help to guide research that will benefit human health as well. DOI:http://dx.doi.org/10.7554/eLife.24695.002
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Affiliation(s)
- Yu Huining Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Li Huitong Xie
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Xiaoyu Zhuo
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States
| | - Qiang Chen
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Dalia Ghoneim
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, United States
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Canada
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
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Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus. J Mol Evol 2016; 83:126-136. [PMID: 27743003 DOI: 10.1007/s00239-016-9759-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/06/2016] [Indexed: 01/26/2023]
Abstract
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules. In most known animals, TE activity in the germline is primarily regulated by the Piwi-interacting RNA (piRNA) pathway. In this study, we test the hypothesis that salamanders' unusually high TE loads reflect the loss of the ancestral piRNA-mediated TE-silencing machinery. We characterized the small RNA pool in the female and male adult gonads, testing for the presence of small RNA molecules that bear the characteristics of TE-targeting piRNAs. We also analyzed the amino acid sequences of piRNA pathway proteins from salamanders and other vertebrates, testing whether the overall patterns of sequence divergence are consistent with conserved pathway function across the vertebrate clade. Our results do not support the hypothesis of piRNA pathway loss; instead, they suggest that the piRNA pathway is expressed in salamanders. Given these results, we propose hypotheses to explain how the extraordinary TE loads in salamander genomes could have accumulated, despite the expression of TE-silencing machinery.
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Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS Genet 2015; 11:e1005652. [PMID: 26588211 PMCID: PMC4654475 DOI: 10.1371/journal.pgen.1005652] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/15/2015] [Indexed: 12/18/2022] Open
Abstract
The Piwi pathway is deeply conserved amongst animals because one of its essential functions is to repress transposons. However, many Piwi-interacting RNAs (piRNAs) do not base-pair to transposons and remain mysterious in their targeting function. The sheer number of piRNA cluster (piC) loci in animal genomes and infrequent piRNA sequence conservation also present challenges in determining which piC loci are most important for development. To address this question, we determined the piRNA expression patterns of piC loci across a wide phylogenetic spectrum of animals, and reveal that most genic and intergenic piC loci evolve rapidly in their capacity to generate piRNAs, regardless of known transposon silencing function. Surprisingly, we also uncovered a distinct set of piC loci with piRNA expression conserved deeply in Eutherian mammals. We name these loci Eutherian-Conserved piRNA cluster (ECpiC) loci. Supporting the hypothesis that conservation of piRNA expression across ~100 million years of Eutherian evolution implies function, we determined that one ECpiC locus generates abundant piRNAs antisense to the STOX1 transcript, a gene clinically associated with preeclampsia. Furthermore, we confirmed reduced piRNAs in existing mouse mutations at ECpiC-Asb1 and -Cbl, which also display spermatogenic defects. The Asb1 mutant testes with strongly reduced Asb1 piRNAs also exhibit up-regulated gene expression profiles. These data indicate ECpiC loci may be specially adapted to support Eutherian reproduction. Animal genomes from flies to humans contain many hundreds of non-coding elements called Piwi-interacting RNAs (piRNAs) cluster loci (piC loci). Some of these elements generate piRNAs that direct the silencing of transposable elements, which are pervasive genetic parasites. However, we lack an understanding of the targeting function for the remaining bulk of piRNAs because their loci are not complementarity to transposable elements. In addition, the field does not know if all piC loci are quickly evolving, or if some piC loci might be deeply conserved in piRNA expression, an indication of its potentially functional importance. Our study confirms the highly rapid evolution in piRNA expression capacity for the majority of piC loci in flies and mammals, with many clade- and species-specific piC loci expression patterns. In spite of this, we also discover a cohort of piC loci that are deeply conserved in piRNA expression from the human to the dog, a significantly broad phylogenetic spectrum of eutherian mammals. However, this conservation in piRNA expression ends at non-eutherian mammals like marsupials and monotremes. Existing mutations in two of these Eutherian-Conserved piC (ECpiC) loci impair mouse reproduction and abrogate piRNA production. Therefore, we suggest these ECpiC loci are conserved for piRNA expression due to their important function in eutherian reproduction and stand out as prime candidates for future genetic studies.
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Affiliation(s)
- Gung-wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yuliya A. Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jessica A. Matts
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mei Zeng
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Daniel Gerlach
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Michael Yu
- Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bonnie Berger
- Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mayumi Naramura
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Benjamin T. Kile
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res 2015; 43:10655-72. [PMID: 26578579 PMCID: PMC4678822 DOI: 10.1093/nar/gkv1193] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/24/2015] [Indexed: 01/01/2023] Open
Abstract
To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.
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Affiliation(s)
- Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Gung-wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Abhay Kanodia
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Yuliya A Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Björn Brembs
- Institute of Zoology, Universität Regensburg, Regensburg, Germany
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, UK
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA 02454, USA
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Yang XZ, Chen JY, Liu CJ, Peng J, Wee YR, Han X, Wang C, Zhong X, Shen QS, Liu H, Cao H, Chen XW, Tan BCM, Li CY. Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates. Mol Biol Evol 2015; 32:3143-57. [PMID: 26341297 PMCID: PMC4652623 DOI: 10.1093/molbev/msv183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Although millions of RNA editing events have been reported to modify hereditary information across the primate transcriptome, evidence for their functional significance remains largely elusive, particularly for the vast majority of editing sites in noncoding regions. Here, we report a new mechanism for the functionality of RNA editing—a crosstalk with PIWI-interacting RNA (piRNA) biogenesis. Exploiting rhesus macaque as an emerging model organism closely related to human, in combination with extensive genome and transcriptome sequencing in seven tissues of the same animal, we deciphered accurate RNA editome across both long transcripts and the piRNA species. Superimposing and comparing these two distinct RNA editome profiles revealed 4,170 editing-bearing piRNA variants, or epiRNAs, that primarily derived from edited long transcripts. These epiRNAs represent distinct entities that evidence an intersection between RNA editing regulations and piRNA biogenesis. Population genetics analyses in a macaque population of 31 independent animals further demonstrated that the epiRNA-associated RNA editing is maintained by purifying selection, lending support to the functional significance of this crosstalk in rhesus macaque. Correspondingly, these findings are consistent in human, supporting the conservation of this mechanism during the primate evolution. Overall, our study reports the earliest lines of evidence for a crosstalk between selectively constrained RNA editing regulation and piRNA biogenesis, and further illustrates that such an interaction may contribute substantially to the diversification of the piRNA repertoire in primates.
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Affiliation(s)
- Xin-Zhuang Yang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia-Yu Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chu-Jun Liu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jiguang Peng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yin Rei Wee
- Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Xiaorui Han
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chenqu Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China Peking-Tsinghua Center for Life Sciences, Beijing, China Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoming Zhong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Hsuan Liu
- Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Huiqing Cao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiao-Wei Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China Peking-Tsinghua Center for Life Sciences, Beijing, China Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Chuan-Yun Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
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Zhang L, Liu W, Shao C, Zhang N, Li H, Liu K, Dong Z, Qi Q, Zhao W, Chen S. Cloning, expression and methylation analysis of piwil2 in half-smooth tongue sole (Cynoglossus semilaevis). Mar Genomics 2014; 18 Pt A:45-54. [DOI: 10.1016/j.margen.2014.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 12/25/2022]
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45
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Metcalfe CJ, Casane D. Accommodating the load: The transposable element content of very large genomes. Mob Genet Elements 2014; 3:e24775. [PMID: 24616835 PMCID: PMC3943481 DOI: 10.4161/mge.24775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/20/2013] [Accepted: 04/22/2013] [Indexed: 01/31/2023] Open
Abstract
Very large genomes, that is, those above 20 Gb, are rare but widely distributed throughout the eukaryotes. They are found within the diatoms, dinoflagellates, metazoans and green plants, but so far have not been found in the excavates. There is a known positive correlation between genome size and the proportion of the genome composed of transposable elements (TEs). Very large genomes may therefore be expected to be almost entirely composed of TEs. Of the large genomes examined, in the angiosperms, gymnosperms and the dinoflagellates only a small portion of the genome was identified as TEs, most of these genomes were unidentified and may be novel or diverse TEs. In the salamanders and lungfish, 25 to 47% of the genome were identifiable retrotransposons, that is, TEs that copy themselves before insertion. However, the predominant class of TEs found in the lungfish was not the same as that found in the salamanders. The little data we have at the moment suggests therefore that the diversity and abundance of TEs is variable between taxa with large genomes, similar to patterns found in taxa with smaller genomes. Based on results from the human genome, we suggest that the ‘missing’ portion of the lungfish and salamander genomes are old, highly divergent, and therefore inactive copies of TEs. The data available indicate that, unlike plants with large genomes, neither the lungfish nor the salamanders show an increased risk of extinction. Based on a slow rate of DNA loss in salamanders it has been suggested that the large salamander genome is the result of run-away genome expansion involving genome size increases via TE proliferation associated with reduced recombination rate. We know of no studies on DNA loss or recombination rates in lungfish genomes, however a similar scenario could describe the process of genome expansion in the lungfish. A series of waves of TE transposition and sequence decay would describe the pattern of TE content seen in both the lungfish and the salamanders. The lungfish and salamanders, therefore, may accommodate their large load of TEs because these TEs have accumulated gradually over a long period of time and have been subject to inactivation and decay.
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Affiliation(s)
- Cushla J Metcalfe
- Instituto de Biociências; Universidade de São Paulo; Cidade Universitária; São Paulo, Brazil
| | - Didier Casane
- Laboratoire Evolution Génomes et Spéciation; UPR9034 CNRS; Gif-sur-Yvette, France ; Université Paris Diderot; Sorbonne Paris Cité, France
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Song J, Liu J, Schnakenberg SL, Ha H, Xing J, Chen KC. Variation in piRNA and transposable element content in strains of Drosophila melanogaster. Genome Biol Evol 2014; 6:2786-98. [PMID: 25267446 PMCID: PMC4224344 DOI: 10.1093/gbe/evu217] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are one of the most important features of genome architecture, so their evolution and relationship with host defense mechanisms have been topics of intense study, especially in model systems such as Drosophila melanogaster. Recently, a novel small RNA-based defense mechanism in animals called the Piwi-interacting RNA (piRNA) pathway was discovered to form an adaptive defense mechanism against TEs. To investigate the relationship between piRNA and TE content between strains of a species, we sequenced piRNAs from 16 inbred lines of D. melanogaster from the Drosophila Genetic Reference Panel. Instead of a global correlation of piRNA expression and TE content, we found evidence for a host response through de novo piRNA production from novel TE insertions. Although approximately 20% of novel TE insertions induced de novo piRNA production, the abundance of de novo piRNAs was low and did not markedly affect the global pool of ovarian piRNAs. Our results provide new insights into the evolution of TEs and the piRNA system in an important model organism.
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Affiliation(s)
- Jimin Song
- Department of Genetics, Rutgers University BioMaPS Institute for Quantitative Biology, Rutgers University
| | - Jixia Liu
- Department of Genetics, Rutgers University BioMaPS Institute for Quantitative Biology, Rutgers University Human Genetics Institute of New Jersey, Rutgers University
| | - Sandra L Schnakenberg
- Department of Genetics, Rutgers University BioMaPS Institute for Quantitative Biology, Rutgers University Developmental Biology Program, Sloan-Kettering Institute, New York, NY
| | - Hongseok Ha
- Department of Genetics, Rutgers University Human Genetics Institute of New Jersey, Rutgers University
| | - Jinchuan Xing
- Department of Genetics, Rutgers University Human Genetics Institute of New Jersey, Rutgers University
| | - Kevin C Chen
- Department of Genetics, Rutgers University BioMaPS Institute for Quantitative Biology, Rutgers University
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Yajima M, Gustafson EA, Song JL, Wessel GM. Piwi regulates Vasa accumulation during embryogenesis in the sea urchin. Dev Dyn 2014; 243:451-8. [PMID: 24218044 PMCID: PMC4018429 DOI: 10.1002/dvdy.24096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/29/2013] [Accepted: 11/07/2013] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Piwi proteins are essential for germ line development, stem cell maintenance, and more recently found to function in epigenetic and somatic gene regulation. In the sea urchin Strongylocentrotus purpuratus, two Piwi proteins, Seawi and Piwi-like1, have been identified, yet their functional contributions have not been reported. RESULTS Here we found that Seawi protein was localized uniformly in the early embryo and then became enriched in the primordial germ cells (PGCs) (the small micromere lineage) from blastula stage and thereafter. Morpholino knockdown of Sp-seawi diminished PGC-specific localization of Seawi proteins, and altered expression of other germ line markers such as Vasa and Gustavus, but had no effect on Nanos. Furthermore, Seawi knockdown transiently resulted in Vasa positive cell proliferation in the right coelomic pouch that appear to be derived from the small micromere lineage, yet they quickly disappeared with an indication of apoptosis by larval stage. Severe Seawi knockdown resulted in an increased number of apoptotic cells in the entire gut area. CONCLUSION Piwi proteins appear to regulate PGC proliferation perhaps through control of Vasa accumulation. In this organism, Piwi is likely regulating mRNAs, not just transposons, and is potentially functioning both inside and outside of the germ line during embryogenesis.
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Affiliation(s)
- Mamiko Yajima
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
| | - Eric A. Gustafson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
| | | | - Gary M. Wessel
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
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Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems. Phys Life Rev 2014; 11:113-34. [DOI: 10.1016/j.plrev.2013.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 11/05/2013] [Indexed: 12/26/2022]
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Clark JP, Lau NC. Piwi Proteins and piRNAs step onto the systems biology stage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:159-97. [PMID: 25201106 PMCID: PMC4248790 DOI: 10.1007/978-1-4939-1221-6_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animal germ cells are totipotent because they maintain a highly unique and specialized epigenetic state for its genome. To accomplish this, germ cells express a rich repertoire of specialized RNA-binding protein complexes such as the Piwi proteins and Piwi-interacting RNAs (piRNAs): a germ-cell branch of the RNA interference (RNAi) phenomenon which includes microRNA and endogenous small interfering RNA pathways. Piwi proteins and piRNAs are deeply conserved in animal evolution and play essential roles in fertility and regeneration. Molecular mechanisms for how these ribonucleoproteins act upon the transcriptome and genome are only now coming to light with the application of systems-wide approaches in both invertebrates and vertebrates. Systems biology studies on invertebrates have revealed that transcriptional and heritable silencing is a main mechanism driven by Piwi proteins and piRNA complexes. In vertebrates, Piwi-targeting mechanisms and piRNA biogenesis have progressed, while the discovery that the nuclease activity of Piwi protein is essential for vertebrate germ cell development but not completely required in invertebrates highlights the many complexities of this pathway in different animals. This review recounts how recent systems-wide approaches have rapidly accelerated our appreciation for the broad reach of the Piwi pathway on germline genome regulation and what questions facing the field await to be unraveled.
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Affiliation(s)
- Josef P. Clark
- Department of Biology and Rosenstiel Biomedical Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Biomedical Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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Fablet M, Akkouche A, Braman V, Vieira C. Variable expression levels detected in the Drosophila effectors of piRNA biogenesis. Gene 2013; 537:149-53. [PMID: 24361206 DOI: 10.1016/j.gene.2013.11.095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/30/2013] [Indexed: 11/18/2022]
Abstract
piRNAs (piwi-interacting RNAs) are a class of small interfering RNAs that play a major role in the regulation of transposable elements (TEs) in Drosophila and are considered of fundamental importance in gonadal development. Genes encoding the effectors of the piRNA machinery are thus often thought to be highly constrained. On the contrary, as actors of genetic immunity, these genes have also been shown to evolve rapidly and display a high level of sequence variability. In order to assess the support for these competing models, we analyzed seven genes of the piRNA pathway using a collection of wild-type strains of Drosophila simulans, which are known to display significant variability in their TE content between strains. We showed that these genes exhibited wide variation in transcript levels, and we discuss some evolutionary considerations regarding the observed variability in TE copy numbers.
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Affiliation(s)
- Marie Fablet
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
| | - Abdou Akkouche
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Virginie Braman
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; Institut Universitaire de France.
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