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Blumenstiel JP. From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements. Semin Cell Dev Biol 2024; 164:1-12. [PMID: 38823219 DOI: 10.1016/j.semcdb.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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2
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Lyčka M, Bubeník M, Závodník M, Peska V, Fajkus P, Demko M, Fajkus J, Fojtová M. TeloBase: a community-curated database of telomere sequences across the tree of life. Nucleic Acids Res 2024; 52:D311-D321. [PMID: 37602392 PMCID: PMC10767889 DOI: 10.1093/nar/gkad672] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023] Open
Abstract
Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, currently available resources, 'Telomerase database' and 'Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by analysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality. To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.
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Affiliation(s)
- Martin Lyčka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Bubeník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Michal Závodník
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Petr Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Martin Demko
- Core Facility Bioinformatics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- Faculty of Informatics, Masaryk University, BrnoCZ-62500, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics, Academy of Sciences of the Czech Republic, BrnoCZ-61200, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, BrnoCZ-62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, BrnoCZ-62500, Czech Republic
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3
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Coelho MA, Ianiri G, David-Palma M, Theelen B, Goyal R, Narayanan A, Lorch JM, Sanyal K, Boekhout T, Heitman J. Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534224. [PMID: 36993584 PMCID: PMC10055393 DOI: 10.1101/2023.03.25.534224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining ( MAT ) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By incorporating newly generated chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere- flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight towards the discovery of a sexual cycle in Malassezia , with possible implications for pathogenicity. Significance Statement Malassezia , the dominant fungal group of the mammalian skin microbiome, is associated with numerous skin disorders. Sexual development and yeast-to-hyphae transitions, governed by genes at two mating-type ( MAT ) loci, are thought to be important for fungal pathogenicity. However, Malassezia sexual reproduction has never been observed. Here, we used chromosome-level assemblies and comparative genomics to uncover unforeseen transitions in MAT loci organization within Malassezia , possibly related with fragility of centromeric-associated regions. Additionally, by expressing different MAT alleles in the same cell, we show that Malassezia can undergo hyphal development and this phenotype is associated with increased expression of key mating genes along with other genes known to be virulence factors, providing a possible connection between hyphal development, sexual reproduction, and pathogenicity.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso 86100, Italy
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
| | - Rohit Goyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Jeffrey M. Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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Hill HJ, Bonser D, Golic KG. Dicentric chromosome breakage in Drosophila melanogaster is influenced by pericentric heterochromatin and occurs in nonconserved hotspots. Genetics 2023; 224:iyad052. [PMID: 37010100 PMCID: PMC10213500 DOI: 10.1093/genetics/iyad052] [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: 10/18/2022] [Revised: 10/18/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Chromosome breakage plays an important role in the evolution of karyotypes and can produce deleterious effects within a single individual, such as aneuploidy or cancer. Forces that influence how and where chromosomes break are not fully understood. In humans, breakage tends to occur in conserved hotspots called common fragile sites (CFS), especially during replication stress. By following the fate of dicentric chromosomes in Drosophila melanogaster, we find that breakage under tension also tends to occur in specific hotspots. Our experimental approach was to induce sister chromatid exchange in a ring chromosome to generate a dicentric chromosome with a double chromatid bridge. In the following cell division, the dicentric bridges may break. We analyzed the breakage patterns of 3 different ring-X chromosomes. These chromosomes differ by the amount and quality of heterochromatin they carry as well as their genealogical history. For all 3 chromosomes, breakage occurs preferentially in several hotspots. Surprisingly, we found that the hotspot locations are not conserved between the 3 chromosomes: each displays a unique array of breakage hotspots. The lack of hotspot conservation, along with a lack of response to aphidicolin, suggests that these breakage sites are not entirely analogous to CFS and may reveal new mechanisms of chromosome fragility. Additionally, the frequency of dicentric breakage and the durability of each chromosome's spindle attachment vary significantly between the 3 chromosomes and are correlated with the origin of the centromere and the amount of pericentric heterochromatin. We suggest that different centromere strengths could account for this.
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Affiliation(s)
- Hunter J Hill
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Danielle Bonser
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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Clatterbuck Soper SF, Meltzer PS. ATRX/DAXX: Guarding the Genome against the Hazards of ALT. Genes (Basel) 2023; 14:genes14040790. [PMID: 37107548 PMCID: PMC10137841 DOI: 10.3390/genes14040790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cells must enact a telomere maintenance mechanism to ensure genomic stability. In a subset of tumors, telomeres are maintained not by telomerase, but through a homologous recombination-based mechanism termed Alternative Lengthening of Telomeres or ALT. The ALT process is linked to mutations in the ATRX/DAXX/H3.3 histone chaperone complex. This complex is responsible for depositing non-replicative histone variant H3.3 at pericentric and telomeric heterochromatin but has also been found to have roles in ameliorating replication in repeat sequences and in promoting DNA repair. In this review, we will discuss ways in which ATRX/DAXX helps to protect the genome, and how loss of this complex allows ALT to take hold.
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6
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Takeuchi C, Yokoshi M, Kondo S, Shibuya A, Saito K, Fukaya T, Siomi H, Iwasaki Y. Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers. Nucleic Acids Res 2022; 50:11580-11599. [PMID: 36373634 PMCID: PMC9723646 DOI: 10.1093/nar/gkac1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.
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Affiliation(s)
- Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Moe Yokoshi
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shu Kondo
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | | | - Yuka W Iwasaki
- To whom correspondence should be addressed. Tel: +81 3 5363 3529; Fax: +81 3 5363 3266;
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7
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Dorador AP, Dalikova M, Cerbin S, Stillman CM, Zych MG, Hawley RS, Miller DE, Ray DA, Funikov SY, Evgen’ev MB, Blumenstiel JP. Paramutation-like Epigenetic Conversion by piRNA at the Telomere of Drosophila virilis. BIOLOGY 2022; 11:biology11101480. [PMID: 36290385 PMCID: PMC9598792 DOI: 10.3390/biology11101480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022]
Abstract
First discovered in maize, paramutation is a phenomenon in which one allele can trigger an epigenetic conversion of an alternate allele. This conversion causes a genetically heterozygous individual to transmit alleles that are functionally the same, in apparent violation of Mendelian segregation. Studies over the past several decades have revealed a strong connection between mechanisms of genome defense against transposable elements by small RNA and the phenomenon of paramutation. For example, a system of paramutation in Drosophila melanogaster has been shown to be mediated by piRNAs, whose primary function is to silence transposable elements in the germline. In this paper, we characterize a second system of piRNA-mediated paramutation-like behavior at the telomere of Drosophila virilis. In Drosophila, telomeres are maintained by arrays of retrotransposons that are regulated by piRNAs. As a result, the telomere and sub-telomeric regions of the chromosome have unique regulatory and chromatin properties. Previous studies have shown that maternally deposited piRNAs derived from a sub-telomeric piRNA cluster can silence the sub-telomeric center divider gene of Drosophila virilis in trans. In this paper, we show that this silencing can also be maintained in the absence of the original silencing allele in a subsequent generation. The precise mechanism of this paramutation-like behavior may be explained by either the production of retrotransposon piRNAs that differ across strains or structural differences in the telomere. Altogether, these results show that the capacity for piRNAs to mediate paramutation in trans may depend on the local chromatin environment and proximity to the uniquely structured telomere regulated by piRNAs. This system promises to provide significant insights into the mechanisms of paramutation.
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Affiliation(s)
- Ana P. Dorador
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Martina Dalikova
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Stefan Cerbin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Chris M. Stillman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Molly G. Zych
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - R. Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Danny E. Miller
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Sergei Y. Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Michael B. Evgen’ev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Justin P. Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
- Correspondence:
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [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: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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Wei KHC, Mai D, Chatla K, Bachtrog D. Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation. Mol Biol Evol 2022; 39:msac080. [PMID: 35485457 PMCID: PMC9075770 DOI: 10.1093/molbev/msac080] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50 = 33.8-38.0 Mb) genome assemblies of seven closely related Drosophila species that belong to the nasuta species group-a poorly studied group of flies that radiated in the last 2 My. We constructed a high-quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare TE insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor bias from reduced fitness impact of TEs inserting near lowly expressed, nonessential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is a nonautonomous DNA element (Drosophila INterspersed Element; DINE) which has gone through multiple bouts of expansions with thousands of full-length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Thus, whereas horizontal transfer followed by the invasion of a naïve genome has been highlighted to explain the long-term survival of TEs, our analysis suggests that evasion of host suppression of resident TEs is a major strategy to persist over evolutionary times. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.
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Affiliation(s)
- Kevin H.-C. Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dat Mai
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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10
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Abstract
Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat-packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.
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Affiliation(s)
- Cara L Brand
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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11
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Murakami T, Paris C, Chirino M, Sasa C, Sakamoto H, Higashi S, Sato K. Unusual chromosome numbers and polyploidy in invasive fire ant populations. Genetica 2021; 149:203-215. [PMID: 34282482 DOI: 10.1007/s10709-021-00128-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/14/2021] [Indexed: 11/25/2022]
Abstract
Fire ants (Solenopsis invicta Buren in J Ga Entomol Soc 7:1-26, 1972), an invasive alien ant species, first spread from South America to the United States in the 1930s, the southern part of the United States by the end of the twentieth century, Oceania, Taiwan, and China in the twenty-first century, and finally to Japan and South Korea in 2017. As these ants have significant negative economic, human health, and environmental impacts, the purpose of this research was to accumulate cytogenetic information regarding fire ants and provide basic data for developing management strategies for their control. Fire ants were collected from invasive populations from Taiwan, Florida (USA), and Buenos Aires (Argentina), and a native population from Puerto Iguazu (Argentina), their point of origination, and analyzed with regard to chromosome number, morphology, and polyploidy, silver-stained nucleolar organizer regions (Ag-NORs), and 18S rDNA and telomere fluorescence in situ hybridization (FISH). The results showed that (1) fire ants from invaded populations differed in chromosome morphology compared to those from native populations; (2) the Florida and Taiwanese fire ant populations evinced greater variability in chromosome numbers and polyploidy variations; (3) the Taiwanese population exhibited significantly increased Ag-NOR signals in interphase cells, with signal number significantly positively correlating with distance from native populations; and (4) substantial diversity of signals was also apparent following 18S rDNA and telomere FISH analyses. Variation in these characteristics were hypothesized to be due to (1) the effect of hybridizations and interbreeding between closely related species or genetically distant populations, and (2) the potential effect of large amounts of insecticides sprayed for pest control.
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Affiliation(s)
- Takahiro Murakami
- Institution of Decision Science for a Sustainable Society, Kyushu University, Motooka 744, Fukuoka, 8190395, Japan.
| | | | | | - Chifune Sasa
- Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hironori Sakamoto
- Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki, 305-0053, Japan
| | - Seigo Higashi
- Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
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12
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Almojil D, Bourgeois Y, Falis M, Hariyani I, Wilcox J, Boissinot S. The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes. Genes (Basel) 2021; 12:genes12060918. [PMID: 34203645 PMCID: PMC8232201 DOI: 10.3390/genes12060918] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.
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Affiliation(s)
- Dareen Almojil
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Yann Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK;
| | - Marcin Falis
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Imtiyaz Hariyani
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Justin Wilcox
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Correspondence:
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13
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McGurk MP, Dion-Côté AM, Barbash DA. Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus. Genetics 2021; 217:iyaa027. [PMID: 33724410 PMCID: PMC8045721 DOI: 10.1093/genetics/iyaa027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Drosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE, and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85 Drosophila melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we instead suggest that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than one-third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes, with niche specialization and telomere instability being previously underappreciated and likely predominant.
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Affiliation(s)
- Michael P McGurk
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Marie Dion-Côté
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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14
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Saint-Leandre B, Christopher C, Levine MT. Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons. eLife 2020; 9:e60987. [PMID: 33350936 PMCID: PMC7755394 DOI: 10.7554/elife.60987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/02/2020] [Indexed: 02/06/2023] Open
Abstract
Essential, conserved cellular processes depend not only on essential, strictly conserved proteins but also on essential proteins that evolve rapidly. To probe this poorly understood paradox, we exploited the rapidly evolving Drosophila telomere-binding protein, cav/HOAP, which protects chromosomes from lethal end-to-end fusions. We replaced the D. melanogaster HOAP with a highly diverged version from its close relative, D. yakuba. The D. yakuba HOAP ('HOAP[yak]') localizes to D. melanogaster telomeres and protects D. melanogaster chromosomes from fusions. However, HOAP[yak] fails to rescue a previously uncharacterized HOAP function: silencing of the specialized telomeric retrotransposons that, instead of telomerase, maintain chromosome length in Drosophila. Whole genome sequencing and cytogenetics of experimentally evolved populations revealed that HOAP[yak] triggers telomeric retrotransposon proliferation, resulting in aberrantly long telomeres. This evolution-generated, separation-of-function allele resolves the paradoxical observation that a fast-evolving essential gene directs an essential, strictly conserved function: telomeric retrotransposon containment, not end-protection, requires evolutionary innovation at HOAP.
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Affiliation(s)
- Bastien Saint-Leandre
- Department of Biology and Epigenetics Institute, University of PennsylvaniaPhiladelphiaUnited States
| | - Courtney Christopher
- Department of Biology and Epigenetics Institute, University of PennsylvaniaPhiladelphiaUnited States
| | - Mia T Levine
- Department of Biology and Epigenetics Institute, University of PennsylvaniaPhiladelphiaUnited States
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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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Hocher A, Taddei A. Subtelomeres as Specialized Chromatin Domains. Bioessays 2020; 42:e1900205. [PMID: 32181520 DOI: 10.1002/bies.201900205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Specificities associated with chromosomal linearity are not restricted to telomeres. Here, recent results obtained on fission and budding yeast are summarized and an attempt is made to define subtelomeres using chromatin features extending beyond the heterochromatin emanating from telomeres. Subtelomeres, the chromosome domains adjacent to telomeres, differ from the rest of the genome by their gene content, rapid evolution, and chromatin features that together contribute to organism adaptation. However, current definitions of subtelomeres are generally based on synteny and are largely gene-centered. Taking into consideration both the peculiar gene content and dynamics as well as the chromatin properties of those domains, it is discussed how chromatin features can contribute to subtelomeric properties and functions, and play a pivotal role in the emergence of subtelomeres.
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Affiliation(s)
- Antoine Hocher
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, F-75005, France.,Sorbonne Université, UPMC University Paris 06, CNRS, UMR3664, Paris, F-75005, France
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17
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Markova DN, Christensen SM, Betrán E. Telomere-Specialized Retroelements in Drosophila: Adaptive Symbionts of the Genome, Neutral, or in Conflict? Bioessays 2019; 42:e1900154. [PMID: 31815300 DOI: 10.1002/bies.201900154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/31/2019] [Indexed: 12/17/2022]
Abstract
Linear chromosomes shorten in every round of replication. In Drosophila, telomere-specialized long interspersed retrotransposable elements (LINEs) belonging to the jockey clade offset this shortening by forming head-to-tail arrays at Drosophila telomere ends. As such, these telomeric LINEs have been considered adaptive symbionts of the genome, protecting it from premature decay, particularly as Drosophila lacks a conventional telomerase holoenzyme. However, as reviewed here, recent work reveals a high degree of variation and turnover in the telomere-specialized LINE lineages across Drosophila. There appears to be no absolute requirement for LINE activity to maintain telomeres in flies, hence the suggestion that the telomere-specialized LINEs may instead be neutral or in conflict with the host, rather than adaptive.
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Affiliation(s)
- Dragomira N Markova
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Shawn M Christensen
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
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18
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Abstract
Conventional approaches to identify a telomere motif in a new genome are laborious and time-intensive. An efficient new methodology based on next-generation sequencing (NGS), de novo sequence repeat finder (SERF) and fluorescence in situ hybridization (FISH) is presented. Unlike existing heuristic approaches, SERF utilizes an exhaustive analysis of raw NGS reads or assembled contigs for rapid de novo detection of conserved tandem repeats representing telomere motifs. SERF was validated using the NGS data from Ipheion uniflorum and Allium cepa with known telomere motifs. The analysis program was then used on NGS data to investigate the telomere motifs in several additional plant species and together with FISH proved to be an efficient approach to identify as yet unknown telomere motifs.
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19
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Saint-Leandre B, Nguyen SC, Levine MT. Diversification and collapse of a telomere elongation mechanism. Genome Res 2019; 29:920-931. [PMID: 31138619 PMCID: PMC6581046 DOI: 10.1101/gr.245001.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/14/2019] [Indexed: 12/18/2022]
Abstract
In most eukaryotes, telomerase counteracts chromosome erosion by adding repetitive sequence to terminal ends. Drosophila melanogaster instead relies on specialized retrotransposons that insert exclusively at telomeres. This exchange of goods between host and mobile element-wherein the mobile element provides an essential genome service and the host provides a hospitable niche for mobile element propagation-has been called a "genomic symbiosis." However, these telomere-specialized, jockey family retrotransposons may actually evolve to "selfishly" overreplicate in the genomes that they ostensibly serve. Under this model, we expect rapid diversification of telomere-specialized retrotransposon lineages and, possibly, the breakdown of this ostensibly symbiotic relationship. Here we report data consistent with both predictions. Searching the raw reads of the 15-Myr-old melanogaster species group, we generated de novo jockey retrotransposon consensus sequences and used phylogenetic tree-building to delineate four distinct telomere-associated lineages. Recurrent gains, losses, and replacements account for this retrotransposon lineage diversity. In Drosophila biarmipes, telomere-specialized elements have disappeared completely. De novo assembly of long reads and cytogenetics confirmed this species-specific collapse of retrotransposon-dependent telomere elongation. Instead, telomere-restricted satellite DNA and DNA transposon fragments occupy its terminal ends. We infer that D. biarmipes relies instead on a recombination-based mechanism conserved from yeast to flies to humans. Telomeric retrotransposon diversification and disappearance suggest that persistently "selfish" machinery shapes telomere elongation across Drosophila rather than completely domesticated, symbiotic mobile elements.
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Affiliation(s)
- Bastien Saint-Leandre
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Son C Nguyen
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mia T Levine
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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20
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Morrish TA, Garcia-Pérez JL. Editorial: Mobile Genetic Elements in Cellular Differentiation, Genome Stability, and Cancer. Front Chem 2017; 5:108. [PMID: 29255704 PMCID: PMC5722799 DOI: 10.3389/fchem.2017.00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/20/2017] [Indexed: 11/23/2022] Open
Affiliation(s)
| | - Jose L Garcia-Pérez
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom.,Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain.,Centre for Genomics and Oncological Research, University of Granada, Granada, Spain
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21
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Chromosome Healing Is Promoted by the Telomere Cap Component Hiphop in Drosophila. Genetics 2017; 207:949-959. [PMID: 28942425 DOI: 10.1534/genetics.117.300317] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/21/2017] [Indexed: 11/18/2022] Open
Abstract
The addition of a new telomere onto a chromosome break, a process termed healing, has been studied extensively in organisms that utilize telomerase to maintain their telomeres. In comparison, relatively little is known about how new telomeres are constructed on broken chromosomes in organisms that do not use telomerase. Chromosome healing was studied in somatic and germline cells of Drosophila melanogaster, a nontelomerase species. We observed, for the first time, that broken chromosomes can be healed in somatic cells. In addition, overexpression of the telomere cap component Hiphop increased the survival of somatic cells with broken chromosomes, while the cap component HP1 did not, and overexpression of the cap protein HOAP decreased their survival. In the male germline, Hiphop overexpression greatly increased the transmission of healed chromosomes. These results indicate that Hiphop can stimulate healing of a chromosome break. We suggest that this reflects a unique function of Hiphop: it is capable of seeding formation of a new telomeric cap on a chromosome end that lacks a telomere.
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22
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Strecker J, Stinus S, Caballero MP, Szilard RK, Chang M, Durocher D. A sharp Pif1-dependent threshold separates DNA double-strand breaks from critically short telomeres. eLife 2017; 6:23783. [PMID: 28826474 PMCID: PMC5595431 DOI: 10.7554/elife.23783] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 07/26/2017] [Indexed: 11/25/2022] Open
Abstract
DNA double-strand breaks (DSBs) and short telomeres are structurally similar, yet they have diametrically opposed fates. Cells must repair DSBs while blocking the action of telomerase on these ends. Short telomeres must avoid recognition by the DNA damage response while promoting telomerase recruitment. In Saccharomyces cerevisiae, the Pif1 helicase, a telomerase inhibitor, lies at the interface of these end-fate decisions. Using Pif1 as a sensor, we uncover a transition point in which 34 bp of telomeric (TG1-3)n repeat sequence renders a DNA end insensitive to Pif1 action, thereby enabling extension by telomerase. A similar transition point exists at natural chromosome ends, where telomeres shorter than ~40 bp are inefficiently extended by telomerase. This phenomenon is not due to known Pif1 modifications and we instead propose that Cdc13 renders TG34+ ends insensitive to Pif1 action. We contend that the observed threshold of Pif1 activity defines a dividing line between DSBs and telomeres.
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Affiliation(s)
- Jonathan Strecker
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sonia Stinus
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mariana Pliego Caballero
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rachel K Szilard
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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23
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Servant G, Deininger PL. Insertion of Retrotransposons at Chromosome Ends: Adaptive Response to Chromosome Maintenance. Front Genet 2016; 6:358. [PMID: 26779254 PMCID: PMC4700185 DOI: 10.3389/fgene.2015.00358] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/10/2015] [Indexed: 01/30/2023] Open
Abstract
The telomerase complex is a specialized reverse transcriptase (RT) that inserts tandem DNA arrays at the linear chromosome ends and contributes to the protection of the genetic information in eukaryotic genomes. Telomerases are phylogenetically related to retrotransposons, encoding also the RT activity required for the amplification of their sequences throughout the genome. Intriguingly the telomerase gene is lost from the Drosophila genome and tandem retrotransposons replace telomeric sequences at the chromosome extremities. This observation suggests the versatility of RT activity in counteracting the chromosome shortening associated with genome replication and that retrotransposons can provide this activity in case of a dysfunctional telomerase. In this review paper, we describe the major classes of retroelements present in eukaryotic genomes in order to point out the differences and similarities with the telomerase complex. In a second part, we discuss the insertion of retroelements at the ends of chromosomes as an adaptive response for dysfunctional telomeres.
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Affiliation(s)
| | - Prescott L. Deininger
- Tulane Cancer Center, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LAUSA
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24
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Morgunova V, Akulenko N, Radion E, Olovnikov I, Abramov Y, Olenina LV, Shpiz S, Kopytova DV, Georgieva SG, Kalmykova A. Telomeric repeat silencing in germ cells is essential for early development in Drosophila. Nucleic Acids Res 2015; 43:8762-73. [PMID: 26240377 PMCID: PMC4605298 DOI: 10.1093/nar/gkv775] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/21/2015] [Indexed: 12/03/2022] Open
Abstract
The germline-specific role of telomeres consists of chromosome end elongation and proper chromosome segregation during early developmental stages. Despite the crucial role of telomeres in germ cells, little is known about telomere biology in the germline. We analyzed telomere homeostasis in the Drosophila female germline and early embryos. A novel germline-specific function of deadenylase complex Ccr4-Not in the telomeric transcript surveillance mechanism is reported. Depletion of Ccr4-Not complex components causes strong derepression of the telomeric retroelement HeT-A in the germ cells, accompanied by elongation of the HeT-A poly(A) tail. Dysfunction of transcription factors Woc and Trf2, as well as RNA-binding protein Ars2, also results in the accumulation of excessively polyadenylated HeT-A transcripts in ovaries. Germline knockdowns of Ccr4-Not components, Woc, Trf2 and Ars2, lead to abnormal mitosis in early embryos, characterized by chromosome missegregation, centrosome dysfunction and spindle multipolarity. Moreover, the observed phenotype is accompanied by the accumulation of HeT-A transcripts around the centrosomes in early embryos, suggesting the putative relationship between overexpression of telomeric transcripts and mitotic defects. Our data demonstrate that Ccr4-Not, Woc, Trf2 and Ars2, components of different regulatory pathways, are required for telomere protection in the germline in order to guarantee normal development.
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Affiliation(s)
- Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elizaveta Radion
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Yuri Abramov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ludmila V Olenina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Sergey Shpiz
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Daria V Kopytova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Sofia G Georgieva
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
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25
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Manicardi GC, Nardelli A, Mandrioli M. Fast chromosomal evolution and karyotype instability: recurrent chromosomal rearrangements in the peach potato aphidMyzus persicae(Hemiptera: Aphididae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12621] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Gian Carlo Manicardi
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 213/d 41125 Modena Italy
| | - Andrea Nardelli
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 213/d 41125 Modena Italy
| | - Mauro Mandrioli
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 213/d 41125 Modena Italy
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26
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Zhang L, Beaucher M, Cheng Y, Rong YS. Coordination of transposon expression with DNA replication in the targeting of telomeric retrotransposons in Drosophila. EMBO J 2014; 33:1148-58. [PMID: 24733842 DOI: 10.1002/embj.201386940] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In Drosophila, a group of retrotransposons is mobilized exclusively to telomeres in a sequence-independent manner. How they target chromosome ends is not understood. Here, we focused on the telomeric element HeT-A and characterized the cell cycle expression and cytological distribution of its protein and RNA products. We determined the timing of telomere replication by creating a single lacO-marked telomere and provide evidence suggesting that transposon expression and recruitment to telomeres is linked to telomere replication. The HeT-A-encoded ORF1p protein is expressed predominantly in S phase, particularly in early S phase. Orf1p binds HeT-A transcripts and forms spherical structures at telomeres undergoing DNA replication. HeT-A sphere formation requires Verrocchio, a putative homolog of the conserved Stn1 telomeric protein. Our results suggest that coupling of telomere elongation and telomere replication is a universal feature, and raise the possibility that transposon recruitment to Drosophila telomeres is mechanistically related to telomerase recruitment in other organisms. Our study also supports a co-adaptive relationship between the Drosophila host and HeT-A mobile elements.
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Affiliation(s)
- Liang Zhang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute (NCI) NIH, Bethesda, MD, USA
| | - Michelle Beaucher
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute (NCI) NIH, Bethesda, MD, USA
| | - Yan Cheng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute (NCI) NIH, Bethesda, MD, USA
| | - Yikang S Rong
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute (NCI) NIH, Bethesda, MD, USA
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27
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Fulcher N, Derboven E, Valuchova S, Riha K. If the cap fits, wear it: an overview of telomeric structures over evolution. Cell Mol Life Sci 2014; 71:847-65. [PMID: 24042202 PMCID: PMC11113737 DOI: 10.1007/s00018-013-1469-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/16/2013] [Accepted: 08/30/2013] [Indexed: 10/26/2022]
Abstract
Genome organization into linear chromosomes likely represents an important evolutionary innovation that has permitted the development of the sexual life cycle; this process has consequently advanced nuclear expansion and increased complexity of eukaryotic genomes. Chromosome linearity, however, poses a major challenge to the internal cellular machinery. The need to efficiently recognize and repair DNA double-strand breaks that occur as a consequence of DNA damage presents a constant threat to native chromosome ends known as telomeres. In this review, we present a comparative survey of various solutions to the end protection problem, maintaining an emphasis on DNA structure. This begins with telomeric structures derived from a subset of prokaryotes, mitochondria, and viruses, and will progress into the typical telomere structure exhibited by higher organisms containing TTAGG-like tandem sequences. We next examine non-canonical telomeres from Drosophila melanogaster, which comprise arrays of retrotransposons. Finally, we discuss telomeric structures in evolution and possible switches between canonical and non-canonical solutions to chromosome end protection.
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Affiliation(s)
- Nick Fulcher
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Elisa Derboven
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Sona Valuchova
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Karel Riha
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
- Central European Institute of Technology, Kamenice 753/5, Brno, Czech Republic
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28
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Garavís M, González C, Villasante A. On the origin of the eukaryotic chromosome: the role of noncanonical DNA structures in telomere evolution. Genome Biol Evol 2013; 5:1142-50. [PMID: 23699225 PMCID: PMC3698924 DOI: 10.1093/gbe/evt079] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The transition of an ancestral circular genome to multiple linear chromosomes was crucial for eukaryogenesis because it allowed rapid adaptive evolution through aneuploidy. Here, we propose that the ends of nascent linear chromosomes should have had a dual function in chromosome end protection (capping) and chromosome segregation to give rise to the “proto-telomeres.” Later on, proper centromeres evolved at subtelomeric regions. We also propose that both noncanonical structures based on guanine–guanine interactions and the end-protection proteins recruited by the emergent telomeric heterochromatin have been required for telomere maintenance through evolution. We further suggest that the origin of Drosophila telomeres may be reminiscent of how the first telomeres arose.
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Affiliation(s)
- Miguel Garavís
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
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29
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Ribeyre C, Shore D. Regulation of telomere addition at DNA double-strand breaks. Chromosoma 2013; 122:159-73. [DOI: 10.1007/s00412-013-0404-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/28/2013] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
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Starnes JH, Thornbury DW, Novikova OS, Rehmeyer CJ, Farman ML. Telomere-targeted retrotransposons in the rice blast fungus Magnaporthe oryzae: agents of telomere instability. Genetics 2012; 191:389-406. [PMID: 22446319 PMCID: PMC3374306 DOI: 10.1534/genetics.111.137950] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 03/11/2012] [Indexed: 02/07/2023] Open
Abstract
The fungus Magnaporthe oryzae is a serious pathogen of rice and other grasses. Telomeric restriction fragments in Magnaporthe isolates that infect perennial ryegrass (prg) are hotspots for genomic rearrangement and undergo frequent, spontaneous alterations during fungal culture. The telomeres of rice-infecting isolates are very stable by comparison. Sequencing of chromosome ends from a number of prg-infecting isolates revealed two related non-LTR retrotransposons (M. oryzae Telomeric Retrotransposons or MoTeRs) inserted in the telomere repeats. This contrasts with rice pathogen telomeres that are uninterrupted by other sequences. Genetic evidence indicates that the MoTeR elements are responsible for the observed instability. MoTeRs represent a new family of telomere-targeted transposons whose members are found exclusively in fungi.
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Affiliation(s)
| | - David W. Thornbury
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | - Olga S. Novikova
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
| | | | - Mark L. Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546
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32
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Abstract
Reverse transcriptases have shaped genomes in many ways. A remarkable example of this shaping is found on telomeres of the genus Drosophila, where retrotransposons have a vital role in chromosome structure. Drosophila lacks telomerase; instead, three telomere-specific retrotransposons maintain chromosome ends. Repeated transpositions to chromosome ends produce long head to tail arrays of these elements. In both form and function, these arrays are analogous to the arrays of repeats added by telomerase to chromosomes in other organisms. Distantly related Drosophila exhibit this variant mechanism of telomere maintenance, which was established before the separation of extant Drosophila species. Nevertheless, the telomere-specific elements still have the hallmarks that characterize non-long terminal repeat (non-LTR) retrotransposons; they have also acquired characteristics associated with their roles at telomeres. These telomeric retrotransposons have shaped the Drosophila genome, but they have also been shaped by the genome. Here, we discuss ways in which these three telomere-specific retrotransposons have been modified for their roles in Drosophila chromosomes.
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33
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Pardue ML, Debaryshe P. Adapting to life at the end of the line: How Drosophila telomeric retrotransposons cope with their job. Mob Genet Elements 2011; 1:128-134. [PMID: 22016861 DOI: 10.4161/mge.1.2.16914] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 06/07/2011] [Indexed: 11/19/2022] Open
Abstract
Drosophila telomeres are remarkable because they are maintained by telomere-specific retrotransposons, rather than the enzyme telomerase that maintains telomeres in almost every other eukaryotic organism. Successive transpositions of the Drosophila retrotransposons onto chromosome ends produce long head-to-tail arrays that are analogous in form and function to the long arrays of short repeats produced by telomerase in other organisms. Nevertheless, Drosophila telomere repeats are retrotransposons, complex entities three orders of magnitude longer than simple telomerase repeats. During the >40-60 My they have been coevolving with their host, these retrotransposons perforce have evolved a complex relationship with Drosophila cells to maintain populations of active elements while carrying out functions analogous to those of telomerase repeats in other organisms. Although they have assumed a vital role in maintaining the Drosophila genome, the three Drosophila telomere-specific elements are non-LTR retrotransposons, closely related to some of the best known non-telomeric elements in the Drosophila genome. Thus, these elements offer an opportunity to study ways in which retrotransposons and their host cells can coevolve cooperatively. The telomere-specific elements display several characteristics that appear important to their roles at the telomere; for example, we have recently reported that they have evolved at least two innovative mechanisms for protecting essential sequence on their 5'ends. Because every element serves as the end of the chromosome immediately after it transposes, its 5'end is subject to chromosomal erosion until it is capped by a new transposition. These two mechanisms make it possible for at least a significant fraction of elements to survive their initial time as the chromosome end without losing sequence necessary to be competent for subsequent transposition. Analysis of sequence from >90 kb of assembled telomere array shows that these mechanisms for small scale sequence protection are part of a unified set which maintains telomere length homeostasis. Here we concentrate on recently elucidated mechanisms that have evolved to provide this small scale 5' protection.
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Affiliation(s)
- Mary-Lou Pardue
- Department of Biology; Massachusetts Institute of Technology; Cambridge, MA USA
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Monti V, Giusti M, Bizzaro D, Manicardi GC, Mandrioli M. Presence of a functional (TTAGG)(n) telomere-telomerase system in aphids. Chromosome Res 2011; 19:625-33. [PMID: 21667174 DOI: 10.1007/s10577-011-9222-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/18/2011] [Accepted: 05/20/2011] [Indexed: 11/28/2022]
Abstract
The structure of the telomeres of four aphid species (Acyrthosiphon pisum, Megoura viciae, Myzus persicae and Rhopalosiphum padi) was evaluated by Southern blotting and fluorescent in situ hybridization, revealing that each chromosomal end consists of a (TTAGG)(n) repeat. The presence of a telomerase coding gene has been verified successively in the A. pisum genome, revealing that aphid telomerase shares sequence identity ranging from 12% to 18% with invertebrate and vertebrate homologues, and possesses the two main domains involved in telomerase activity. Interestingly, telomerase expression has been verified in different somatic tissues suggesting that, in aphids, telomerase activity is not as restricted as in human cells. The study of telomeres in a M. persicae strain with a variable chromosome number showed that aphid telomerase can initiate the de novo synthesis of telomere sequences at internal breakpoints, resulting in the stabilization of chromosomal fragments.
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Affiliation(s)
- Valentina Monti
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
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35
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Grach AA. Alternative telomere-lengthening mechanisms. CYTOL GENET+ 2011. [DOI: 10.3103/s0095452711020046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere. J Virol 2011; 85:4761-71. [PMID: 21389136 DOI: 10.1128/jvi.01604-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events.
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37
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Khurana JS, Xu J, Weng Z, Theurkauf WE. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLoS Genet 2010; 6:e1001246. [PMID: 21179579 PMCID: PMC3003142 DOI: 10.1371/journal.pgen.1001246] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 11/11/2010] [Indexed: 12/30/2022] Open
Abstract
Transposons and other selfish DNA elements can be found in all phyla, and mobilization of these elements can compromise genome integrity. The piRNA (PIWI-interacting RNA) pathway silences transposons in the germline, but it is unclear if this pathway has additional functions during development. Here we show that mutations in the Drosophila piRNA pathway genes, armi, aub, ago3, and rhi, lead to extensive fragmentation of the zygotic genome during the cleavage stage of embryonic divisions. Additionally, aub and armi show defects in telomere resolution during meiosis and the cleavage divisions; and mutations in lig-IV, which disrupt non-homologous end joining, suppress these fusions. By contrast, lig-IV mutations enhance chromosome fragmentation. Chromatin immunoprecipitation studies show that aub and armi mutations disrupt telomere binding of HOAP, which is a component of the telomere protection complex, and reduce expression of a subpopulation of 19- to 22-nt telomere-specific piRNAs. Mutations in rhi and ago3, by contrast, do not block HOAP binding or production of these piRNAs. These findings uncover genetically separable functions for the Drosophila piRNA pathway. The aub, armi, rhi, and ago3 genes silence transposons and maintain chromosome integrity during cleavage-stage embryonic divisions. However, the aub and armi genes have an additional function in assembly of the telomere protection complex.
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Affiliation(s)
- Jaspreet S. Khurana
- Program in Cell and Developmental Dynamics and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jia Xu
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology and Department in Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - William E. Theurkauf
- Program in Cell and Developmental Dynamics and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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38
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Abstract
Telomeres are essential structures at the ends of eukaryotic chromosomes. Work on their structure and function began almost 70 years ago in plants and flies, continued through the Nobel Prize winning work on yeast and ciliates, and goes on today in many model and non-model organisms. The basic molecular mechanisms of telomeres are highly conserved throughout evolution, and our current understanding of how telomeres function is a conglomeration of insights gained from many different species. This review will compare the current knowledge of telomeres in plants with other organisms, with special focus on the functional length of telomeric DNA, the search for TRF homologs, the family of POT1 proteins, and the recent discovery of members of the CST complex.
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Affiliation(s)
- J Matthew Watson
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
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39
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Abstract
Barbara McClintock was the first to suggest that transposons are a source of genome instability and that genotoxic stress assisted in their mobilization. The generation of double-stranded DNA breaks (DSBs) is a severe form of genotoxic stress that threatens the integrity of the genome, activates cell cycle checkpoints, and, in some cases, causes cell death. Applying McClintock's stress hypothesis to humans, are L1 retrotransposons, the most active autonomous mobile elements in the
modern day human genome, mobilized by DSBs? Here, evidence that transposable elements, particularly retrotransposons, are mobilized by genotoxic stress is reviewed. In the setting of DSB formation, L1 mobility may be affected by changes in the substrate for L1 integration, the DNA repair machinery, or the L1 element itself.
The review concludes with a discussion of the potential consequences of L1 mobilization in the setting of genotoxic stress.
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Affiliation(s)
- Evan A. Farkash
- Department of Pathology and Laboratory Medicine,
School of Medicine, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine,
School of Medicine, University of Pennsylvania,
Philadelphia, PA 19104, USA
- 405B Stellar Chance Labs, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA 19104, USA
- *Eline T. Luning Prak:
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40
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Traverse KL, George JA, DeBaryshe PG, Pardue ML. Evolution of species-specific promoter-associated mechanisms for protecting chromosome ends by Drosophila Het-A telomeric transposons. Proc Natl Acad Sci U S A 2010; 107:5064-9. [PMID: 20194755 PMCID: PMC2841908 DOI: 10.1073/pnas.1000612107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The non-LTR retrotransposons forming Drosophila telomeres constitute a robust mechanism for telomere maintenance, one which has persisted since before separation of the extant Drosophila species. These elements in D. melanogaster differ from nontelomeric retrotransposons in ways that give insight into general telomere biology. Here, we analyze telomere-specific retrotransposons from D. virilis, separated from D. melanogaster by 40 to 60 million years, to evaluate the evolutionary divergence of their telomeric traits. The telomeric retrotransposon HeT-A from D. melanogaster has an unusual promoter near its 3' terminus that drives not the element in which it resides, but the adjacent downstream element in a head-to-tail array. An obvious benefit of this promoter is that it adds nonessential sequence to the 5' end of each transcript, which is reverse transcribed and added to the chromosome. Because the 5' end of each newly transposed element forms the end of the chromosome until another element transposes onto it, this nonessential sequence can buffer erosion of sequence essential for HeT-A. Surprisingly, we have now found that HeT-A in D. virilis has a promoter typical of non-LTR retrotransposons. This promoter adds no buffering sequence; nevertheless, the complete 5' end of the element persists in telomere arrays, necessitating a more precise processing of the extreme end of the telomere in D. virilis.
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Affiliation(s)
| | | | - P. G. DeBaryshe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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41
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Ocalewicz K, Dobosz S, Kuzminski H, Goryczko K. Formation of chromosome aberrations in androgenetic rainbow trout Oncorhynchus mykiss. JOURNAL OF FISH BIOLOGY 2009; 75:2373-2379. [PMID: 20738695 DOI: 10.1111/j.1095-8649.2009.02448.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Residues of maternal nuclear DNA in the form of chromosome fragments were observed in the healthy and morphologically normal androgenetic rainbow trout Oncorhynchus mykiss. A hypothetical model for formation of chromosome re-arrangements caused by the incomplete maternal nuclear DNA inactivation in the androgenetic rainbow trout was proposed in the present paper.
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Affiliation(s)
- K Ocalewicz
- Department of Ichthyology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 5, 10-957 Olsztyn, Poland.
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42
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Chen XF, Meng FL, Zhou JQ. Telomere recombination accelerates cellular aging in Saccharomyces cerevisiae. PLoS Genet 2009; 5:e1000535. [PMID: 19557187 PMCID: PMC2694356 DOI: 10.1371/journal.pgen.1000535] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 05/22/2009] [Indexed: 12/19/2022] Open
Abstract
Telomeres are nucleoprotein structures located at the linear ends of eukaryotic chromosomes. Telomere integrity is required for cell proliferation and survival. Although the vast majority of eukaryotic species use telomerase as a primary means for telomere maintenance, a few species can use recombination or retrotransposon-mediated maintenance pathways. Since Saccharomyces cerevisiae can use both telomerase and recombination to replicate telomeres, budding yeast provides a useful system with which to examine the evolutionary advantages of telomerase and recombination in preserving an organism or cell under natural selection. In this study, we examined the life span in telomerase-null, post-senescent type II survivors that have employed homologous recombination to replicate their telomeres. Type II recombination survivors stably maintained chromosomal integrity but exhibited a significantly reduced replicative life span. Normal patterns of cell morphology at the end of a replicative life span and aging-dependent sterility were observed in telomerase-null type II survivors, suggesting the type II survivors aged prematurely in a manner that is phenotypically consistent with that of wild-type senescent cells. The shortened life span of type II survivors was extended by calorie restriction or TOR1 deletion, but not by Fob1p inactivation or Sir2p over-expression. Intriguingly, rDNA recombination was decreased in type II survivors, indicating that the premature aging of type II survivors was not caused by an increase in extra-chromosomal rDNA circle accumulation. Reintroduction of telomerase activity immediately restored the replicative life span of type II survivors despite their heterogeneous telomeres. These results suggest that telomere recombination accelerates cellular aging in telomerase-null type II survivors and that telomerase is likely a superior telomere maintenance pathway in sustaining yeast replicative life span. Telomeres are the specialized structures at the ends of eukaryotic linear chromosomes. The simple guanine-rich DNA repeats at telomeres and their associated proteins are important for chromosome stability. Most eukaryotic species have evolved an enzyme named telomerase to replicate their telomeric DNA. Telomerase usually contains a protein catalytic subunit and a RNA template subunit. A few eukaryotic species can use either telomere recombination or retrotransposon-mediated transposition to accomplish telomere elongation. Interestingly, the baker's yeast Saccharomyces cerevisiae can use both telomerase and recombination to replicate telomeres. In this study, we utilize this unique eukaryotic model system to compare the efficiency of these two mechanisms in the maintenance of cellular function and life span. Telomerase-null cells that used recombination to elongate telomeres were able to maintain relatively stable chromosomes; however, they exhibited a shortened replicative life span which may represent a novel aging pathway. Reintroduction of telomerase inhibited telomere recombination and restored the replicative life span of these cells, implying that telomerase is superior to telomere recombination in the regulation of yeast replicative life span.
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Affiliation(s)
- Xiao-Fen Chen
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Fei-Long Meng
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- * E-mail:
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43
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Kirwan M, Dokal I. Dyskeratosis congenita, stem cells and telomeres. Biochim Biophys Acta Mol Basis Dis 2009; 1792:371-9. [PMID: 19419704 PMCID: PMC2686081 DOI: 10.1016/j.bbadis.2009.01.010] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 01/15/2009] [Accepted: 01/15/2009] [Indexed: 12/26/2022]
Abstract
Dyskeratosis congenita (DC) is a multi-system disorder which in its classical form is characterised by abnormalities of the skin, nails and mucous membranes. In approximately 80% of cases, it is associated with bone marrow dysfunction. A variety of other abnormalities (including bone, brain, cancer, dental, eye, gastrointestinal, immunological and lung) have also been reported. Although first described almost a century ago it is the last 10 years, following the identification of the first DC gene (DKC1) in 1998, in which there has been rapid progress in its understanding. Six genes have been identified, defects in which cause different genetic subtypes (X-linked recessive, autosomal dominant, autosomal recessive) of DC. The products of these genes encode components that are critical for telomere maintenance; either because they are core constituents of telomerase (dyskerin, TERC, TERT, NOP10 and NHP2) or are part of the shelterin complex that protects the telomeric end (TIN2). These advances have also highlighted the connection between the more “cryptic/atypical” forms of the disease including aplastic anaemia and idiopathic pulmonary fibrosis. Equally, studies on this disease have demonstrated the critical importance of telomeres in human cells (including stem cells) and the severe consequences of their dysfunction. In this context DC and related diseases can now be regarded as disorders of “telomere and stem cell dysfunction”.
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Affiliation(s)
- Michael Kirwan
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK.
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44
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Capkova Frydrychova R, Biessmann H, Mason JM. Regulation of telomere length in Drosophila. Cytogenet Genome Res 2009; 122:356-64. [PMID: 19188706 DOI: 10.1159/000167823] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2008] [Indexed: 01/20/2023] Open
Abstract
Telomeres in all organisms must perform the same vital functions to ensure cell viability: to act as a protective chromosome cap that distinguishes natural chromosome ends from DNA double strand breaks, and to balance the loss of DNA from the chromosome end due to incomplete DNA replication. Most eukaryotes rely on a specialized reverse transcriptase, telomerase, to generate short repeats at the chromosome end to maintain chromosome length. Drosophila, however, uses retrotransposons that target telomeres. Transposition of these elements may be controlled by small RNAs and spreading of silent chromatin from the telomere associated sequence, both of which limit the retrotransposon expression level. Proteins binding to the retrotransposon array, such as HP1 and PROD, may also modulate transcription. It is not clear however, that simply increasing transcript levels of the telomeric retrotransposons is sufficient to increase transposition. The chromosome cap may control the ability of the telomere-specific elements to attach to chromosome ends. As in other organisms, chromosomes can be elongated by gene conversion. Although the mechanism is not known, HP1, a component of the cap, and the Ku proteins are key components in this pathway.
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Affiliation(s)
- R Capkova Frydrychova
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709-2233, USA
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45
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Eissenberg JC, Reuter G. Cellular mechanism for targeting heterochromatin formation in Drosophila. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 273:1-47. [PMID: 19215901 DOI: 10.1016/s1937-6448(08)01801-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Near the end of their 1990 historical perspective article "60 Years of Mystery," Spradling and Karpen (1990) observe: "Recent progress in understanding variegation at the molecular level has encouraged some workers to conclude that the heterochromatization model is essentially correct and that position-effect variegation can now join the mainstream of molecular biology." In the 18 years since those words were written, heterochromatin and its associated position effects have indeed joined the mainstream of molecular biology. Here, we review the findings that led to our current understanding of heterochromatin formation in Drosophila and the mechanistic insights into heterochromatin structural and functional properties gained through molecular genetics and cytology.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
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46
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Kern AD, Begun DJ. Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans. Genetics 2008; 179:1021-7. [PMID: 18505885 PMCID: PMC2429855 DOI: 10.1534/genetics.107.078345] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 04/08/2008] [Indexed: 12/22/2022] Open
Abstract
Although Drosophila melanogaster has been the subject of intensive analysis of polymorphism and divergence, little is known about the distribution of variation at the most distal regions of chromosomes arms. Here we report a survey of genetic variation on the tip of 3L in D. melanogaster and D. simulans. Levels of single nucleotide polymorphism in the most distal euchromatic sequence are approximately one order of magnitude less than that typically observed in genomic regions of normal crossing over, consistent with what might be expected under models of linked selection in regions of low crossing over. However, despite this reduced level of nucleotide variation, we found abundant deletion polymorphism. These deletions create at least three gene presence/absence polymorphisms within D. melanogaster: the putative G-protein coupled receptor mthl-8 (which is the most distal known or predicted gene on 3L) and the unannotated mRNAs AY060886 and BT006009. Strikingly, D. simulans is also segregating deletions that cause mthl8 presence/absence polymorphism. Breakpoint sequencing and tests of correlations with segregating SNPs in D. melanogaster suggest that each deletion is unique. Cloned breakpoint sequences revealed the presence of Het-A elements just distal to unique, canonical euchromatic sequences. This pattern suggests a model in which repeated telomeric deficiencies cause deletions of euchromatic sequence followed by subsequent "healing" by retrotranposition of Het-A elements. These data reveal the dominance of telomeric dynamics on the evolution of closely linked sequences in Drosophila.
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Affiliation(s)
- Andrew D Kern
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95060, USA.
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Villasante A, Abad JP, Planelló R, Méndez-Lago M, Celniker SE, de Pablos B. Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase. Genome Res 2007; 17:1909-18. [PMID: 17989257 DOI: 10.1101/gr.6365107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Drosophila telomeres do not have arrays of simple telomerase-generated G-rich repeats. Instead, Drosophila maintains its telomeres by occasional transposition of specific non-long terminal repeat (non-LTR) retrotransposons to chromosome ends. The genus Drosophila provides a superb model system for comparative telomere analysis. Here we present an evolutionary study of Drosophila telomeric elements to ascertain the significance of telomeric retrotransposons (TRs) in the maintenance of Drosophila telomeres. PCR and in silico surveys in the sibling species of Drosophila melanogaster and in more distantly related species show that multiple TRs maintain telomeres in Drosophila. In addition to TRs with two open reading frames (ORFs) capable of autonomous transposition, there are deleted telomeric retrotransposons that have lost their ORF2, which we refer to as half telomeric-retrotransposons (HTRs). The phylogenetic relationship among these telomeric elements is congruent with the phylogeny of the species, suggesting that they have been vertically inherited from a common ancestor. Our results suggest that an existing non-LTR retrotransposon was recruited to perform the cellular function of telomere maintenance.
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Affiliation(s)
- Alfredo Villasante
- Centro de Biología Molecular Severo Ochoa, Cantoblanco, 28049 Madrid, Spain.
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Abstract
I have been fascinated by chromosomes for longer than I care to mention; their beautiful structure, cell-type-specific changes in morphology, and elegant movements delight me. Shortly before I began graduate study, the development of nucleic acid hybridization made it possible to compare two nucleic acids whether or not their sequences were known. From this stemmed a progression of development in tools and techniques that continues to enhance our understanding of how chromosomes function. As my PhD project I contributed to this progression by developing in situ hybridization, a technique for hybridization to nucleic acids within their cellular context. Early studies with this technique initiated several lines of research, two of which I describe here, that I have pursued to this day. First, analysis of RNA populations by hybridization to polytene chromosomes (a proto-microarray-type experiment) led us to characterize levels of regulation during heat shock beyond those recognizable by puffing studies. We found also that one still-undeciphered major heat shock puff encodes a novel set of RNAs for which we propose a regulatory role. Second, localization of various multicopy DNA sequences has suggested roles for them in chromosome structure: Most recently we have found that Drosophila telomeres consist of and are maintained by special non-LTR (long terminal repeat) retrotransposons.
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Affiliation(s)
- Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Melnikova L, Biryukova I, Kan T, Georgiev P. Long-distance interactions between regulatory elements are suppressed at the end of a terminally deficient chromosome in Drosophila melanogaster. Chromosoma 2007; 117:41-50. [PMID: 17876596 DOI: 10.1007/s00412-007-0124-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 08/12/2007] [Accepted: 08/13/2007] [Indexed: 01/13/2023]
Abstract
In Drosophila melanogaster, broken chromosome ends behave as real telomeres and are believed to be covered with telomere-specific chromatin. It has been shown previously that the telomeric chromatin represses normal activity of enhancers that regulate yellow expression in wings and body cuticle. In this paper, we have found that a modified yellow promoter is fully active in the wing and body cuticle when it is located at the chromosome end, which is evidence that the telomeric chromatin does not repress transcription. Substitution of the yellow core promoter region, including TATA and Inr, with the promoter regions of the eve, hsp70 (TATA-containing), and white (TATA-less) promoters does not affect the ability of the promoter to be cis- or trans-activated by the yellow enhancers if the heterologous promoter is located at a distance of about 6 kb from the chromosome end. The best characterized Drosophila insulator found in the gypsy retrotransposon can specifically repress the yellow promoter at a distance when one component of the insulator complex, Mod(mdg4)-67.2 protein, is inactive. We have also found that, in the mod(mdg4) mutant background, the gypsy insulator can repress the heterologous promoters, indicating that the core promoter elements are not critical for specificity of repression. However, long-distance functional enhancer-promoter and gypsy-promoter interactions were suppressed when the distance between the yellow promoter and the end of the deficient chromosome was less than 6 kb. These results suggest that Drosophila telomeric chromatin does not generally repress transcription but is somehow involved in suppression of some long-distance interactions between regulatory elements.
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Affiliation(s)
- Larisa Melnikova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov st, Moscow, 119334, Russia
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Simmons MJ, Ryzek DF, Lamour C, Goodman JW, Kummer NE, Merriman PJ. Cytotype regulation by telomeric P elements in Drosophila melanogaster: evidence for involvement of an RNA interference gene. Genetics 2007; 176:1945-55. [PMID: 17603126 PMCID: PMC1950604 DOI: 10.1534/genetics.106.066746] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 04/23/2007] [Indexed: 11/18/2022] Open
Abstract
P elements inserted at the left telomere of the X chromosome evoke the P cytotype, a maternally inherited condition that regulates the P-element family in the Drosophila germline. This regulation is completely disrupted in stocks heterozygous for mutations in aubergine, a gene whose protein product is involved in RNA interference. However, cytotype is not disrupted in stocks heterozygous for mutations in two other RNAi genes, piwi and homeless (spindle-E), or in a stock heterozygous for a mutation in the chromatin protein gene Enhancer of zeste. aubergine mutations exert their effects in the female germline, where the P cytotype is normally established and through which it is maintained. These effects are transmitted maternally to offspring of both sexes independently of the mutations themselves. Lines derived from mutant aubergine stocks reestablish the P cytotype quickly, unlike lines derived from stocks heterozygous for a mutation in Suppressor of variegation 205, the gene that encodes the telomere-capping protein HP1. Cytotype regulation by telomeric P elements may be tied to a system that uses RNAi to regulate the activities of telomeric retrotransposons in Drosophila.
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Affiliation(s)
- Michael J Simmons
- Department of Genetics, Cell Biology, and Development, 250 BioScience Center, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108-1095, USA.
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