1
|
Jansen G, Gebert D, Kumar TR, Simmons E, Murphy S, Teixeira FK. Tolerance thresholds underlie responses to DNA damage during germline development. Genes Dev 2024; 38:631-654. [PMID: 39054057 PMCID: PMC11368186 DOI: 10.1101/gad.351701.124] [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: 04/11/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
Selfish DNA modules like transposable elements (TEs) are particularly active in the germline, the lineage that passes genetic information across generations. New TE insertions can disrupt genes and impair the functionality and viability of germ cells. However, we found that in P-M hybrid dysgenesis in Drosophila, a sterility syndrome triggered by the P-element DNA transposon, germ cells harbor unexpectedly few new TE insertions despite accumulating DNA double-strand breaks (DSBs) and inducing cell cycle arrest. Using an engineered CRISPR-Cas9 system, we show that generating DSBs at silenced P-elements or other noncoding sequences is sufficient to induce germ cell loss independently of gene disruption. Indeed, we demonstrate that both developing and adult mitotic germ cells are sensitive to DSBs in a dosage-dependent manner. Following the mitotic-to-meiotic transition, however, germ cells become more tolerant to DSBs, completing oogenesis regardless of the accumulated genome damage. Our findings establish DNA damage tolerance thresholds as crucial safeguards of genome integrity during germline development.
Collapse
Affiliation(s)
- Gloria Jansen
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, United Kingdom
| | - Daniel Gebert
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, United Kingdom
| | | | - Emily Simmons
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sarah Murphy
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Felipe Karam Teixeira
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom;
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, United Kingdom
| |
Collapse
|
2
|
Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. Mob DNA 2023; 14:8. [PMID: 37452430 PMCID: PMC10347736 DOI: 10.1186/s13100-023-00296-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. RESULTS We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide consistent estimates of [Formula: see text]50 non-reference TE insertions per strain and that Ty2 has the highest number of non-reference TE insertions in a species-wide panel of [Formula: see text]1000 yeast genomes. Finally, we show that best-in-class predictors for yeast applied to resequencing data have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences revealed previously for experimentally-induced Ty1 insertions to spontaneous insertions for other copia-superfamily retrotransposons in yeast. CONCLUSION McClintock ( https://github.com/bergmanlab/mcclintock/ ) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors in other species.
Collapse
Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
| | | | - Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
- Department of Genetics, University of Georgia, Athens, GA USA
| |
Collapse
|
3
|
Bologa AM, Stoica I, Constantin ND, Ecovoiu AA. The Landscape of the DNA Transposons in the Genome of the Horezu_LaPeri Strain of Drosophila melanogaster. INSECTS 2023; 14:494. [PMID: 37367310 DOI: 10.3390/insects14060494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023]
Abstract
Natural transposons (NTs) represent mobile DNA sequences found in both prokaryotic and eukaryotic genomes. Drosophila melanogaster (the fruit fly) is a eukaryotic model organism with NTs standing for about 20% of its genome and has contributed significantly to the understanding of various aspects of transposon biology. Our study describes an accurate approach designed to map class II transposons (DNA transposons) in the genome of the Horezu_LaPeri fruit fly strain, consecutive to Oxford Nanopore Technology sequencing. A whole genome bioinformatics analysis was conducted using Genome ARTIST_v2, LoRTE and RepeatMasker tools to identify DNA transposons insertions. Then, a gene ontology enrichment analysis was performed in order to evaluate the potential adaptive role of some DNA transposons insertions. Herein, we describe DNA transposon insertions specific for the Horezu_LaPeri genome and a predictive functional analysis of some insertional alleles. The PCR validation of P-element insertions specific for this fruit fly strain, along with a putative consensus sequence for the KP element, is also reported. Overall, the genome of the Horezu_LaPeri strain contains several insertions of DNA transposons associated with genes known to be involved in adaptive processes. For some of these genes, insertional alleles obtained via mobilization of the artificial transposons were previously reported. This is a very alluring aspect, as it suggests that insertional mutagenesis experiments conducting adaptive predictions for laboratory strains may be confirmed by mirroring insertions which are expected to be found at least in some natural fruit fly strains.
Collapse
Affiliation(s)
- Alexandru Marian Bologa
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
| | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
| | | | - Alexandru Al Ecovoiu
- Department of Genetics, Faculty of Biology, University of Bucharest, 060101 Bucharest, Romania
| |
Collapse
|
4
|
Wang L, Zhang S, Hadjipanteli S, Saiz L, Nguyen L, Silva E, Kelleher E. P-element invasion fuels molecular adaptation in laboratory populations of Drosophila melanogaster. Evolution 2023; 77:980-994. [PMID: 36749648 PMCID: PMC10078945 DOI: 10.1093/evolut/qpad017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/02/2023] [Accepted: 02/06/2023] [Indexed: 02/08/2023]
Abstract
Transposable elements (TEs) are mobile genetic parasites that frequently invade new host genomes through horizontal transfer. Invading TEs often exhibit a burst of transposition, followed by reduced transposition rates as repression evolves in the host. We recreated the horizontal transfer of P-element DNA transposons into a Drosophila melanogaster host and followed the expansion of TE copies and evolution of host repression in replicate laboratory populations reared at different temperatures. We observed that while populations maintained at high temperatures rapidly go extinct after TE invasion, those maintained at lower temperatures persist, allowing for TE spread and the evolution of host repression. We also surprisingly discovered that invaded populations experienced recurrent insertion of P-elements into a specific long non-coding RNA, lncRNA:CR43651, and that these insertion alleles are segregating at unusually high frequency in experimental populations, indicative of positive selection. We propose that, in addition to driving the evolution of repression, transpositional bursts of invading TEs can drive molecular adaptation.
Collapse
Affiliation(s)
- Luyang Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Shuo Zhang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Savana Hadjipanteli
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Lorissa Saiz
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Lisa Nguyen
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Efren Silva
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Erin Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| |
Collapse
|
5
|
Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528343. [PMID: 36824955 PMCID: PMC9948991 DOI: 10.1101/2023.02.13.528343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
BACKGROUND Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. RESULTS We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide a consistent and biologically meaningful view of non-reference TE insertions in a species-wide panel of ∼1000 yeast genomes, as evaluated by coverage-based abundance estimates and expected patterns of tRNA promoter targeting. Finally, we show that best-in-class predictors for yeast have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences first revealed experimentally for Ty1 to natural insertions and related copia-superfamily retrotransposons in yeast. CONCLUSION McClintock (https://github.com/bergmanlab/mcclintock/) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors for other species.
Collapse
Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA
| | | | - Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA
- Department of Genetics, University of Georgia, Athens, GA
| |
Collapse
|
6
|
Zakharenko LP, Petrovskii DV, Bykov RA. The P-Element Has Not Significant Effect on the Drosophila simulans Viability. Mol Biol 2023. [DOI: 10.1134/s0026893323020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
7
|
Kofler R, Nolte V, Schlötterer C. The transposition rate has little influence on the plateauing level of the P-element. Mol Biol Evol 2022; 39:6613335. [PMID: 35731857 PMCID: PMC9254008 DOI: 10.1093/molbev/msac141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The popular trap model assumes that the invasions of transposable elements (TEs) in mammals and invertebrates are stopped by piRNAs that emerge after insertion of the TE into a piRNA cluster. It remains, however, still unclear which factors influence the dynamics of TE invasions. The activity of the TE (i.e., transposition rate) is one frequently discussed key factor. Here we take advantage of the temperature-dependent activity of the P-element, a widely studied eukaryotic TE, to test how TE activity affects the dynamics of a TE invasion. We monitored P-element invasion dynamics in experimental Drosophila simulans populations at hot and cold culture conditions. Despite marked differences in transposition rates, the P-element reached very similar copy numbers at both temperatures. The reduction of the insertion rate upon approaching the copy number plateau was accompanied by similar amounts of piRNAs against the P-element at both temperatures. Nevertheless, we also observed fewer P-element insertions in piRNA clusters than expected, which is not compatible with a simple trap model. The ping-pong cycle, which degrades TE transcripts, becomes typically active after the copy number plateaued. We generated a model, with few parameters, that largely captures the observed invasion dynamics. We conclude that the transposition rate has at the most only a minor influence on TE abundance, but other factors, such as paramutations or selection against TE insertions are shaping the TE composition.
Collapse
Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| |
Collapse
|
8
|
Serrato-Capuchina A, D’Agostino ERR, Peede D, Roy B, Isbell K, Wang J, Matute DR. P-elements strengthen reproductive isolation within the Drosophila simulans species complex. Evolution 2021; 75:2425-2440. [PMID: 34463356 PMCID: PMC8772388 DOI: 10.1111/evo.14319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. We also find that another TE, I-element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.
Collapse
Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emmanuel R. R. D’Agostino
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Kristin Isbell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Daniel R. Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| |
Collapse
|
9
|
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] [MESH Headings] [Grants] [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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Srivastav SP, Rahman R, Ma Q, Pierre J, Bandyopadhyay S, Lau NC. Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development. eLife 2019; 8:49948. [PMID: 31845649 PMCID: PMC6917496 DOI: 10.7554/elife.49948] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/16/2019] [Indexed: 12/20/2022] Open
Abstract
Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome in Drosophila called gonadal dysgenesis (GD). Harwich (Har) strains with P-elements cause severe GD in F1 daughters when Har fathers mate with mothers lacking P-element-piRNAs (i.e. ISO1 strain). To address the mystery of why Har induces severe GD, we bred hybrid Drosophila with Har genomic fragments into the ISO1 background to create HISR-D or HISR-N lines that still cause Dysgenesis or are Non-dysgenic, respectively. In these lines, we discovered a highly truncated P-element variant we named ‘Har-P’ as the most frequent de novo insertion. Although HISR-D lines still contain full-length P-elements, HISR-N lines lost functional P-transposase but retained Har-P’s that when crossed back to P-transposase restores GD induction. Finally, we uncovered P-element-piRNA-directed repression on Har-P’s transmitted paternally to suppress somatic transposition. The Drosophila short Har-P’s and full-length P-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals. DNA provides the instructions needed for life, a role that relies on it being a very stable and organized molecule. However, some sections of DNA are able to move from one place in the genome to another. When these “mobile genetic elements” move they may disrupt other genes and cause disease. For example, a mobile section of DNA known as the P-element causes a condition called gonadal dysgenesis in female fruit flies, leading to infertility. Only certain strains of fruit flies carry P-elements and the severity of gonadal dysgenesis in their daughters varies. For example, when male fruit flies of a strain known as Harwich (or Har for short) is crossed with female fruit flies that do not contain P-elements, all of their daughters develop severe gonadal dysgenesis and are infertile. However, if the cross is done the other way around, and female Har flies mate with males that do not contain P-elements, the daughters are fertile because the Har mothers provide their daughters with protective molecules that silence the P-elements. But it was a mystery as to why the P-elements from the Har fathers always caused such severe gonadal dysgenesis in all the daughters. Here, Srivastav et al. bred fruit flies to create offspring that had different pieces of Har DNA in a genetic background that was normally free from P-elements; they then analyzed the ‘hybrid’ offspring to identify which pieces of the Har genome caused gonadal dysgenesis in the daughter flies. These experiments showed that Har flies possess a very short variant of the P-element (named “Har-P”) that is more mobile than other variants. However, the Har-P variants still depended on an enzyme known as P-transposase encoded by the full-length P-elements to move around the genome. Further experiments showed that other strains of fruit flies that cause severe gonadal dysgenesis also had very short P-element variants that were almost identical to Har-P. These findings may explain why Har and some other strains of fruit flies drive severe gonadal dysgenesis. In the future, it may be possible to transfer P-transposase and Har-P into mosquitoes, ticks and other biting insects to make them infertile and help reduce the spread of certain diseases in humans.
Collapse
Affiliation(s)
- Satyam P Srivastav
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Reazur Rahman
- Department of Biology, Brandeis University, Waltham, United States
| | - Qicheng Ma
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Jasmine Pierre
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Saptaparni Bandyopadhyay
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States.,Department of Biology, Brandeis University, Waltham, United States.,Genome Science Institute, Boston University School of Medicine, Boston, United States
| |
Collapse
|
12
|
Weilguny L, Kofler R. DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition. Mol Ecol Resour 2019; 19:1346-1354. [PMID: 31056858 PMCID: PMC6791034 DOI: 10.1111/1755-0998.13030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 11/28/2022]
Abstract
Transposable elements (TEs) are selfish DNA sequences that multiply within host genomes. They are present in most species investigated so far at varying degrees of abundance and sequence diversity. The TE composition may not only vary between but also within species and could have important biological implications. Variation in prevalence among populations may for example indicate a recent TE invasion, whereas sequence variation could indicate the presence of hyperactive or inactive forms. Gaining unbiased estimates of TE composition is thus vital for understanding the evolutionary dynamics of transposons. To this end, we developed DeviaTE, a tool to analyse and visualize TE abundance using Illumina or Sanger sequencing reads. Our tool requires sequencing reads of one or more samples (tissue, individual or population) and consensus sequences of TEs. It generates a table and a visual representation of TE composition. This allows for an intuitive assessment of coverage, sequence divergence, segregating SNPs and indels, as well as the presence of internal and terminal deletions. By contrasting the coverage between TEs and single copy genes, DeviaTE derives unbiased estimates of TE abundance. We show that naive approaches, which do not consider regions spanned by internal deletions, may substantially underestimate TE abundance. Using published data we demonstrate that DeviaTE can be used to study the TE composition within samples, identify clinal variation in TEs, compare TE diversity among species, and monitor TE invasions. Finally we present careful validations with publicly available and simulated data. DeviaTE is implemented in Python and distributed under the GPLv3 (https://github.com/W-L/deviaTE).
Collapse
Affiliation(s)
- Lukas Weilguny
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| |
Collapse
|
13
|
Merenciano M, Iacometti C, González J. A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster. Mob DNA 2019; 10:10. [PMID: 30911338 PMCID: PMC6415491 DOI: 10.1186/s13100-019-0152-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
Transposable elements (TEs) are not randomly distributed in the genome. A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. In this work, we have further analyzed the promoter region of CG18446. We screened 218 strains collected in 15 natural populations, and we found that the CG18446 promoter region contains 20 independent roo insertions. Based on phylogenetic analysis, we suggest that the presence of multiple roo insertions in this region is likely to be the result of several bursts of transposition. Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. We found that, similar to hsp gene promoters, chromatin accessibility could be one of the factors explaining the recurrent insertions of roo elements in CG18446 promoter region.
Collapse
Affiliation(s)
- Miriam Merenciano
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain
| | - Camillo Iacometti
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain.,2Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Josefa González
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain
| |
Collapse
|
14
|
Kelleher ES, Jaweria J, Akoma U, Ortega L, Tang W. QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline. PLoS Biol 2018; 16:e2006040. [PMID: 30376574 PMCID: PMC6207299 DOI: 10.1371/journal.pbio.2006040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are obligate genetic parasites that propagate in host genomes by replicating in germline nuclei, thereby ensuring transmission to offspring. This selfish replication not only produces deleterious mutations—in extreme cases, TE mobilization induces genotoxic stress that prohibits the production of viable gametes. Host genomes could reduce these fitness effects in two ways: resistance and tolerance. Resistance to TE propagation is enacted by germline-specific small-RNA-mediated silencing pathways, such as the Piwi-interacting RNA (piRNA) pathway, and is studied extensively. However, it remains entirely unknown whether host genomes may also evolve tolerance by desensitizing gametogenesis to the harmful effects of TEs. In part, the absence of research on tolerance reflects a lack of opportunity, as small-RNA-mediated silencing evolves rapidly after a new TE invades, thereby masking existing variation in tolerance. We have exploited the recent historical invasion of the Drosophila melanogaster genome by P-element DNA transposons in order to study tolerance of TE activity. In the absence of piRNA-mediated silencing, the genotoxic stress imposed by P-elements disrupts oogenesis and, in extreme cases, leads to atrophied ovaries that completely lack germline cells. By performing quantitative trait locus (QTL) mapping on a panel of recombinant inbred lines (RILs) that lack piRNA-mediated silencing of P-elements, we uncovered multiple QTL that are associated with differences in tolerance of oogenesis to P-element transposition. We localized the most significant QTL to a small 230-kb euchromatic region, with the logarithm of the odds (LOD) peak occurring in the bruno locus, which codes for a critical and well-studied developmental regulator of oogenesis. Genetic, cytological, and expression analyses suggest that bruno dosage modulates germline stem cell (GSC) loss in the presence of P-element activity. Our observations reveal segregating variation in TE tolerance for the first time, and implicate gametogenic regulators as a source of tolerant variants in natural populations. Transposable elements (TEs), or “jumping genes,” are mobile fragments of selfish DNA that leave deleterious mutations and DNA damage in their wake as they spread through host genomes. Their harmful effects are known to select for resistance by the host, in which the propagation of TEs is regulated and reduced. Here, we study for the first time whether host cells might also exhibit tolerance to TEs, by reducing their harmful effects without directly controlling their movement. By taking advantage of a panel of wild-type Drosophila melanogaster that lack resistance to P-element DNA transposons, we identified a small region of the genome that influences tolerance of P-element activity. We further demonstrate that a gene within that region, bruno, strongly influences the negative effects of P-element mobilization on the fly. When bruno dosage is reduced, the fertility of females carrying mobile P-elements is enhanced. The bruno locus encodes a protein with no known role in TE regulation but multiple well-characterized functions in oogenesis. We propose that bruno function reduces tolerance of the developing oocyte to DNA damage that is caused by P-elements.
Collapse
Affiliation(s)
- Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- * E-mail:
| | - Jaweria Jaweria
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Uchechukwu Akoma
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lily Ortega
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Wenpei Tang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| |
Collapse
|