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Masumoto H, Muto H, Yano K, Kurosaki Y, Niki H. The Ty1 retrotransposon harbors a DNA region that performs dual functions as both a gene silencing and chromatin insulator. Sci Rep 2024; 14:16641. [PMID: 39025990 PMCID: PMC11258251 DOI: 10.1038/s41598-024-67242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
In various eukaryotic kingdoms, long terminal repeat (LTR) retrotransposons repress transcription by infiltrating heterochromatin generated within their elements. In contrast, the budding yeast LTR retrotransposon Ty1 does not itself undergo transcriptional repression, although it is capable of repressing the transcription of the inserted genes within it. In this study, we identified a DNA region within Ty1 that exerts its silencing effect via sequence orientation. We identified a DNA region within the Ty1 group-specific antigen (GAG) gene that causes gene silencing, termed GAG silencing (GAGsi), in which the silent chromatin in the GAGsi region is created by euchromatin-specific histone modifications. A characteristic inverted repeat (IR) sequence is present at the 5' end of this region, forming a chromatin boundary between promoter-specific chromatin upstream of the IR sequence and silent chromatin downstream of the IR sequence. In addition, Esc2 and Rad57, which are involved in DNA repair, were required for GAGsi silencing. Finally, the chromatin boundary was required for the transcription of Ty1 itself. Thus, the GAGsi sequence contributes to the creation of a chromatin environment that promotes Ty1 transcription.
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Affiliation(s)
- Hiroshi Masumoto
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
| | - Hideki Muto
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Koichi Yano
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1,111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Life Science, College of Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Yohei Kurosaki
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1,111 Yata, Mishima, Shizuoka, 411-8540, Japan
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Hannon-Hatfield JA, Chen J, Bergman CM, Garfinkel DJ. Evolution of a Restriction Factor by Domestication of a Yeast Retrotransposon. Mol Biol Evol 2024; 41:msae050. [PMID: 38442736 PMCID: PMC10951436 DOI: 10.1093/molbev/msae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Transposable elements drive genome evolution in all branches of life. Transposable element insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 prime (Ty1'), a subfamily of the Ty1 family, is present in many Saccharomyces cerevisiae strains, but little is known about what controls its copy number. Here, we provide evidence that a novel gene from an exapted Ty1' sequence, domesticated restriction of Ty1' relic 2 (DRT2), encodes a restriction factor that inhibits Ty1' movement. DRT2 arose through domestication of a Ty1' GAG gene and contains the C-terminal domain of capsid, which in the related Ty1 canonical subfamily functions as a self-encoded restriction factor. Bioinformatic analysis reveals the widespread nature of DRT2, its evolutionary history, and pronounced structural variation at the Ty1' relic 2 locus. Ty1' retromobility analyses demonstrate DRT2 restriction factor functionality, and northern blot and RNA-seq analysis indicate that DRT2 is transcribed in multiple strains. Velocity cosedimentation profiles indicate an association between Drt2 and Ty1' virus-like particles or assembly complexes. Chimeric Ty1' elements containing DRT2 retain retromobility, suggesting an ancestral role of productive Gag C-terminal domain of capsid functionality is present in the sequence. Unlike Ty1 canonical, Ty1' retromobility increases with copy number, suggesting that C-terminal domain of capsid-based restriction is not limited to the Ty1 canonical subfamily self-encoded restriction factor and drove the endogenization of DRT2. The discovery of an exapted Ty1' restriction factor provides insight into the evolution of the Ty1 family, evolutionary hot-spots, and host-transposable element interactions.
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Affiliation(s)
- J Adam Hannon-Hatfield
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Casey M Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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Hénault M, Marsit S, Charron G, Landry CR. The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate. eLife 2024; 12:RP89277. [PMID: 38411604 PMCID: PMC10911583 DOI: 10.7554/elife.89277] [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] [Indexed: 02/28/2024] Open
Abstract
Transposable elements (TEs) are major contributors to structural genomic variation by creating interspersed duplications of themselves. In return, structural variants (SVs) can affect the genomic distribution of TE copies and shape their load. One long-standing hypothesis states that hybridization could trigger TE mobilization and thus increase TE load in hybrids. We previously tested this hypothesis (Hénault et al., 2020) by performing a large-scale evolution experiment by mutation accumulation (MA) on multiple hybrid genotypes within and between wild populations of the yeasts Saccharomyces paradoxus and Saccharomyces cerevisiae. Using aggregate measures of TE load with short-read sequencing, we found no evidence for TE load increase in hybrid MA lines. Here, we resolve the genomes of the hybrid MA lines with long-read phasing and assembly to precisely characterize the role of SVs in shaping the TE landscape. Highly contiguous phased assemblies of 127 MA lines revealed that SV types like polyploidy, aneuploidy, and loss of heterozygosity have large impacts on the TE load. We characterized 18 de novo TE insertions, indicating that transposition only has a minor role in shaping the TE landscape in MA lines. Because the scarcity of TE mobilization in MA lines provided insufficient resolution to confidently dissect transposition rate variation in hybrids, we adapted an in vivo assay to measure transposition rates in various S. paradoxus hybrid backgrounds. We found that transposition rates are not increased by hybridization, but are modulated by many genotype-specific factors including initial TE load, TE sequence variants, and mitochondrial DNA inheritance. Our results show the multiple scales at which TE load is shaped in hybrid genomes, being highly impacted by SV dynamics and finely modulated by genotype-specific variation in transposition rates.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université LavalQuébecCanada
- Département de biochimie, microbiologie et bioinformatique, Université LavalQuébecCanada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université LavalQuébecCanada
- Université Laval Big Data Research Center (BDRC_UL)QuébecCanada
- Département de biologie, Université LavalQuébecCanada
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Liu M, Xie XJ, Li X, Ren X, Sun J, Lin Z, Hemba-Waduge RUS, Ji JY. Transcriptional coupling of telomeric retrotransposons with the cell cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560321. [PMID: 37808851 PMCID: PMC10557779 DOI: 10.1101/2023.09.30.560321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Instead of employing telomerases to safeguard chromosome ends, dipteran species maintain their telomeres by transposition of telomeric-specific retrotransposons (TRs): in Drosophila , these are HeT-A , TART , and TAHRE . Previous studies have shown how these TRs create tandem repeats at chromosome ends, but the exact mechanism controlling TR transcription has remained unclear. Here we report the identification of multiple subunits of the transcription cofactor Mediator complex and transcriptional factors Scalloped (Sd, the TEAD homolog in flies) and E2F1-Dp as novel regulators of TR transcription and telomere length in Drosophila . Depletion of multiple Mediator subunits, Dp, or Sd increased TR expression and telomere length, while over-expressing E2F1-Dp or knocking down the E2F1 regulator Rbf1 (Retinoblastoma-family protein 1) stimulated TR transcription, with Mediator and Sd affecting TR expression through E2F1-Dp. The CUT&RUN analysis revealed direct binding of CDK8, Dp, and Sd to telomeric repeats. These findings highlight the essential role of the Mediator complex in maintaining telomere homeostasis by regulating TR transcription through E2F1-Dp and Sd, revealing the intricate coupling of TR transcription with the host cell-cycle machinery, thereby ensuring chromosome end protection and genomic stability during cell division.
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Salinero AC, Emerson S, Cormier TC, Yin J, Morse RH, Curcio MJ. Reliance of Host-Encoded Regulators of Retromobility on Ty1 Promoter Activity or Architecture. Front Mol Biosci 2022; 9:896215. [PMID: 35847981 PMCID: PMC9283973 DOI: 10.3389/fmolb.2022.896215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
The Ty1 retrotransposon family is maintained in a functional but dormant state by its host, Saccharomyces cerevisiae. Several hundred RHF and RTT genes encoding co-factors and restrictors of Ty1 retromobility, respectively, have been identified. Well-characterized examples include MED3 and MED15, encoding subunits of the Mediator transcriptional co-activator complex; control of retromobility by Med3 and Med15 requires the Ty1 promoter in the U3 region of the long terminal repeat. To characterize the U3-dependence of other Ty1 regulators, we screened a library of 188 known rhf and rtt mutants for altered retromobility of Ty1his3AI expressed from the strong, TATA-less TEF1 promoter or the weak, TATA-containing U3 promoter. Two classes of genes, each including both RHFs and RTTs, were identified. The first class comprising 82 genes that regulated Ty1his3AI retromobility independently of U3 is enriched for RHF genes that restrict the G1 phase of the cell cycle and those involved in transcriptional elongation and mRNA catabolism. The second class of 51 genes regulated retromobility of Ty1his3AI driven only from the U3 promoter. Nineteen U3-dependent regulators (U3DRs) also controlled retromobility of Ty1his3AI driven by the weak, TATA-less PSP2 promoter, suggesting reliance on the low activity of U3. Thirty-one U3DRs failed to modulate PPSP2-Ty1his3AI retromobility, suggesting dependence on the architecture of U3. To further investigate the U3-dependency of Ty1 regulators, we developed a novel fluorescence-based assay to monitor expression of p22-Gag, a restriction factor expressed from the internal Ty1i promoter. Many U3DRs had minimal effects on levels of Ty1 RNA, Ty1i RNA or p22-Gag. These findings uncover a role for the Ty1 promoter in integrating signals from diverse host factors to modulate Ty1 RNA biogenesis or fate.
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Affiliation(s)
- Alicia C. Salinero
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
| | - Simey Emerson
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Tayla C. Cormier
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - John Yin
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
| | - M. Joan Curcio
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, United States
- *Correspondence: M. Joan Curcio,
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Morse RH. Function and dynamics of the Mediator complex: novel insights and new frontiers. Transcription 2022; 13:39-52. [PMID: 35708525 PMCID: PMC9467533 DOI: 10.1080/21541264.2022.2085502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The Mediator complex was discovered in the early 1990s as a biochemically fractionated factor from yeast extracts that was necessary for activator-stimulated transcriptional activation to be observed in in vitro transcription assays. The structure of this large, multi-protein complex is now understood in great detail, and novel genetic approaches have provided rich insights into its dynamics during transcriptional activation and the mechanism by which it facilitates activated transcription. Here I review recent findings and unanswered questions regarding Mediator dynamics, the roles of individual subunits, and differences between its function in yeast and metazoan cells.
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Affiliation(s)
- Randall H Morse
- Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, United States
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Abstract
Human endogenous retroviruses (HERVs) occupy approximately 8% of the human genome. HERVs, transcribed in early embryos, are epigenetically silenced in somatic cells, except under pathological conditions. HERV-K is thought to protect embryos from exogenous viral infection. However, uncontrolled HERV-K expression in somatic cells has been implicated in several diseases. Here, we show that SOX2, which plays a key role in maintaining the pluripotency of stem cells, is critical for HERV-K LTR5Hs. HERV-K undergoes retrotransposition within producer cells in the absence of Env expression. Furthermore, we identified new HERV-K integration sites in long-term culture of induced pluripotent stem cells that express SOX2. These results suggest that the strict dependence of HERV-K on SOX2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos. IMPORTANCE Human endogenous retroviruses (HERVs) account for approximately 8% of the human genome; however, the physiological role of HERV-K remains unknown. This study found that HERV-K LTR5Hs and LTR5B were transactivated by SOX2, which is essential for maintaining and reestablishing pluripotency. HERV-K can undergo retrotransposition within producer cells without env expression, and new integration sites may affect cell proliferation. In induced pluripotent stem cells (iPSCs), genomic impairment due to HERV-K retrotransposition has been identified, but it is a rare event. Considering the retention of SOX2-responsive elements in the HERV-K long terminal repeat (LTR) for over 20 million years, we conclude that HERV-K may play important physiological roles in SOX2-expressing cells.
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Bonnet A, Chaput C, Palmic N, Palancade B, Lesage P. A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription. PLoS Genet 2021; 17:e1009889. [PMID: 34723966 PMCID: PMC8585004 DOI: 10.1371/journal.pgen.1009889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposons under tight transcriptional control.
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Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Carole Chaput
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Noé Palmic
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
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Maxwell PH. Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. Mob DNA 2020; 11:16. [PMID: 32336995 PMCID: PMC7175516 DOI: 10.1186/s13100-020-00215-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Genomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identifying potential roles to clearly demonstrating the level of impact TEs have on genome evolution and possible functions that they contribute to their host organisms. I summarize TE content and distribution in four well-characterized yeast model systems in this review: the pathogens Candida albicans and Cryptococcus neoformans, and the nonpathogenic species Saccharomyces cerevisiae and Schizosaccharomyces pombe. I compare and contrast their TE landscapes to their lifecycles, genomic features, as well as the presence and nature of RNA interference pathways in each species to highlight the valuable diversity represented by these models for functional studies of TEs. I then review the regulation and impacts of the Ty1 and Ty3 retrotransposons from Saccharomyces cerevisiae and Tf1 and Tf2 retrotransposons from Schizosaccharomyces pombe to emphasize parallels and distinctions between these well-studied elements. I propose that further characterization of TEs in the pathogenic yeasts would enable this set of four yeast species to become an excellent set of models for comparative functional studies to address outstanding questions about TE-host relationships.
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Border collies of the genome: domestication of an autonomous retrovirus-like transposon. Curr Genet 2018; 65:71-78. [PMID: 29931377 DOI: 10.1007/s00294-018-0857-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/23/2022]
Abstract
Retrotransposons often spread rapidly through eukaryotic genomes until they are neutralized by host-mediated silencing mechanisms, reduced by recombination and mutation, and lost or transformed into benevolent entities. But the Ty1 retrotransposon appears to have been domesticated to guard the genome of Saccharomyces cerevisiae.
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Curcio M. Ty1 Retrotransposition Frequency Assay Using a Chromosomal Ty1his3AI or Ty1kanMXAI Element. Bio Protoc 2018. [DOI: 10.21769/bioprotoc.3004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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