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Lillie M, Pettersson M, Jern P. Contrasting segregation patterns among endogenous retroviruses across the koala population. Commun Biol 2024; 7:350. [PMID: 38514810 PMCID: PMC10957985 DOI: 10.1038/s42003-024-06049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Koalas (Phascolarctos cinereus) have experienced a history of retroviral epidemics leaving their trace as heritable endogenous retroviruses (ERVs) in their genomes. A recently identified ERV lineage, named phaCin-β, shows a pattern of recent, possibly current, activity with high insertional polymorphism in the population. Here, we investigate geographic patterns of three focal ERV lineages of increasing estimated ages, from the koala retrovirus (KoRV) to phaCin-β and to phaCin-β-like, using the whole-genome sequencing of 430 koalas from the Koala Genome Survey. Thousands of ERV loci were found across the population, with contrasting patterns of polymorphism. Northern individuals had thousands of KoRV integrations and hundreds of phaCin-β ERVs. In contrast, southern individuals had higher phaCin-β frequencies, possibly reflecting more recent activity and a founder effect. Overall, our findings suggest high ERV burden in koalas, reflecting historic retrovirus-host interactions. Importantly, the ERV catalogue supplies improved markers for conservation genetics in this endangered species.
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Affiliation(s)
- Mette Lillie
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-752 36, Uppsala, Sweden.
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
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2
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Jern P, Greenwood AD. Wildlife endogenous retroviruses: colonization, consequences, and cooption. Trends Genet 2024; 40:149-159. [PMID: 37985317 DOI: 10.1016/j.tig.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are yielding remarkable perspectives on long-term retrovirus-host interactions. These initial forays into broader taxonomic analysis, including sequencing of multiple individuals per species, show the incredible plasticity and variation of ERVs within and among wildlife species. This demonstrates that stochastic processes govern much of the vertebrate genome. In this review, we elaborate on discoveries pertaining to wildlife ERV origins and evolution, genome colonization, and consequences for host biology.
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Affiliation(s)
- Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany; School of Veterinary Medicine, Freie Unversität Berlin, Berlin, Germany.
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3
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Garza R, Sharma Y, Atacho DAM, Thiruvalluvan A, Abu Hamdeh S, Jönsson ME, Horvath V, Adami A, Ingelsson M, Jern P, Hammell MG, Englund E, Kirkeby A, Jakobsson J, Marklund N. Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia. Cell Rep 2023; 42:113395. [PMID: 37967557 DOI: 10.1016/j.celrep.2023.113395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/05/2023] [Accepted: 10/20/2023] [Indexed: 11/17/2023] Open
Abstract
Traumatic brain injury (TBI) is a leading cause of chronic brain impairment and results in a robust, but poorly understood, neuroinflammatory response that contributes to the long-term pathology. We used single-nuclei RNA sequencing (snRNA-seq) to study transcriptomic changes in different cell populations in human brain tissue obtained acutely after severe, life-threatening TBI. This revealed a unique transcriptional response in oligodendrocyte precursors and mature oligodendrocytes, including the activation of a robust innate immune response, indicating an important role for oligodendroglia in the initiation of neuroinflammation. The activation of an innate immune response correlated with transcriptional upregulation of endogenous retroviruses in oligodendroglia. This observation was causally linked in vitro using human glial progenitors, implicating these ancient viral sequences in human neuroinflammation. In summary, this work provides insight into the initiating events of the neuroinflammatory response in TBI, which has therapeutic implications.
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Affiliation(s)
- Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Diahann A M Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Arun Thiruvalluvan
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Sami Abu Hamdeh
- Department of Neuroscience, Neurosurgery, Uppsala University, Uppsala, Sweden
| | - Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Vivien Horvath
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden; Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine and Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Krembil Brain Institute, University Health Network, Toronto, ON, Canada
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Molly Gale Hammell
- Institute for Systems Genetics, Department of Neuroscience and Physiology, NYU Langone Health, New York, NY 10016, USA; Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10003, USA
| | - Elisabet Englund
- Department of Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden
| | - Agnete Kirkeby
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark; Department of Experimental Medical Science, Wallenberg Center for Molecular Medicine and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden.
| | - Niklas Marklund
- Department of Clinical Sciences Lund, Neurosurgery, Lund University, Skåne University Hospital, Lund, Sweden
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Hill J, Lillie M, Pettersson ME, Rubin CJ, Grant BR, Grant PR, Andersson L, Jern P. Spatiotemporal variations in retrovirus-host interactions among Darwin's finches. Nat Commun 2022; 13:6033. [PMID: 36229469 PMCID: PMC9562234 DOI: 10.1038/s41467-022-33723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches. Endogenous retroviruses (ERV) are inherited remains of retroviruses that have colonized host genomes during evolution. Here the authors observe considerable species-specific ERV variation among Darwin’s finches, reflecting historic retrovirus-host interactions.
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Affiliation(s)
- Jason Hill
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
| | - Mette Lillie
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
| | - Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.,Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - B Rosemary Grant
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Peter R Grant
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
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Çınar Ç, Wesseldijk L, Karinen A, Jern P, Tybur J. Sex differences in the genetic and environmental underpinnings of meat and plant preferences. Food Qual Prefer 2022. [DOI: 10.1016/j.foodqual.2021.104421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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6
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Edvardsen RB, Wallerman O, Furmanek T, Kleppe L, Jern P, Wallberg A, Kjærner-Semb E, Mæhle S, Olausson SK, Sundström E, Harboe T, Mangor-Jensen R, Møgster M, Perrichon P, Norberg B, Rubin CJ. Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut. PLoS Genet 2022; 18:e1010011. [PMID: 35134055 PMCID: PMC8824383 DOI: 10.1371/journal.pgen.1010011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/22/2021] [Indexed: 01/29/2023] Open
Abstract
Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly from a male and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed that all chromosomes exhibit heterochiasmy, i.e. male-only and female-only meiotic recombination regions (MRR/FRR). We show that FRR/MRR intervals differ in nucleotide diversity and repeat class content and that this is true also for other Pleuronectidae species. We further show that remnants of a Gypsy-like transposable element insertion on chr13 promotes early male specific expression of gonadal somatic cell derived factor (gsdf). Less than 4.5 MYA, this male-determining element evolved on an autosomal FRR segment featuring pre-existing male meiotic recombination barriers, thereby creating a Y chromosome. Our findings indicate that heterochiasmy may facilitate the evolution of genetic sex determination systems relying on linkage of sexually antagonistic loci to a sex-determining factor. Even closely related fish species can have different sex chromosomes, but this turn-over of sex determination systems is poorly understood. Here, we used large-scale genome sequencing to determine the DNA sequence of the Atlantic halibut chromosomes and compared sequencing data from males and females to identify the sex chromosomes. We show that males have much higher gene activity of the gene gonadal somatic cell derived factor (gsdf), which is located on the sex chromosomes and has a role in testicular development. The genome contains many mobile DNA sequences, transposable elements (TEs), one placed in front of gsdf, enhancing its activity. This made gsdf the sex determining factor, thereby creating a new Y-chromosome. We further describe how all Atlantic halibut chromosomes behave similar to sex chromosomes in that most regions only recombine in one sex. This phenomenon may contribute to the rapid turn-over of genetic sex determination systems in fish. Our results highlight the molecular events creating a new Y-chromosome and show that the new Atlantic halibut Y was formed less than 4.5 million years ago. Future studies in Atlantic halibut and closely related species can shed light on mechanisms contributing to sex chromosome evolution in fish.
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Affiliation(s)
| | | | | | - Lene Kleppe
- Institute of Marine Research, Bergen, Norway
| | | | | | | | - Stig Mæhle
- Institute of Marine Research, Bergen, Norway
| | | | | | | | | | | | | | | | - Carl-Johan Rubin
- Institute of Marine Research, Bergen, Norway
- Uppsala University, Uppsala, Sweden
- * E-mail: (RBE); (C-JR)
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Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
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8
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Jönsson ME, Garza R, Sharma Y, Petri R, Södersten E, Johansson JG, Johansson PA, Atacho DA, Pircs K, Madsen S, Yudovich D, Ramakrishnan R, Holmberg J, Larsson J, Jern P, Jakobsson J. Activation of endogenous retroviruses during brain development causes an inflammatory response. EMBO J 2021; 40:e106423. [PMID: 33644903 PMCID: PMC8090857 DOI: 10.15252/embj.2020106423] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for an inflammatory response, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9‐based gene disruption of the epigenetic co‐repressor protein Trim28, we found a dynamic H3K9me3‐dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain. Neuronal ERV expression was linked to activated microglia and the presence of ERV‐derived proteins in aggregate‐like structures. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in an inflammatory response.
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Affiliation(s)
- Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Rebecca Petri
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Erik Södersten
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Pia A Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann Am Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sofia Madsen
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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Pettersson ME, Jern P. ZBED6 binding motifs correlate with endogenous retroviruses and Syncytin genes. Virus Evol 2020; 7:veaa083. [PMID: 33859827 PMCID: PMC8035546 DOI: 10.1093/ve/veaa083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Retroviruses have infiltrated vertebrate germlines for millions of years as inherited endogenous retroviruses (ERVs). Mammalian genomes host large numbers of ERVs and transposable elements (TEs), including retrotransposons and DNA transposons, that contribute to genomic innovation and evolution as coopted genes and regulators of diverse functions. To explore features distinguishing coopted ERVs and TEs from other integrations, we focus on the potential role of ZBED6 and repeated ERV domestication as repurposed Syncytin genes. The placental mammal-specific ZBED6 is a DNA transposon-derived transcription regulator and we demonstrate that its binding motifs are associated with distinct Syncytins and that ZBED6 binding motifs are 2- to 3-fold more frequent in ERVs than in flanking DNA. Our observations suggest that ZBED6 could contribute an extended regulatory role of genomic expression, utilizing ERVs as platforms for genomic innovation and evolution.
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Affiliation(s)
- Mats E Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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10
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Li J, Davis BW, Jern P, Dorshorst BJ, Siegel PB, Andersson L. Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken. Mob DNA 2019; 10:38. [PMID: 31467598 PMCID: PMC6712707 DOI: 10.1186/s13100-019-0181-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of CYP19A1 encoding aromatase that converts androgens to estrogen and thereby inhibits the development of male-specific plumage. A long terminal repeat (LTR) from an uncharacterized endogenous retrovirus (ERV) insertion was found in an isoform of the CYP19A1 transcript from henny feathering chicken. However, the complete sequence and the genomic position of the insertion were not determined. Results We used publicly available whole genome sequence data to determine the flanking sequences of the ERV, and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region, was detected partially in an aromatase transcript, which present a plausible explanation for ectopic expression of aromatase in non-ovarian tissues underlying the henny feathering phenotype. Conclusions We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5’end of CYP19A1. The presence of this ERV showed complete concordance with the henny feathering phenotype both within a pedigree segregating for this phenotype and across breeds. Electronic supplementary material The online version of this article (10.1186/s13100-019-0181-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingyi Li
- 1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Brian W Davis
- 1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Patric Jern
- 2Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Ben J Dorshorst
- 4Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061 USA
| | - Paul B Siegel
- 4Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061 USA
| | - Leif Andersson
- 1Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA.,2Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.,3Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-7507 Uppsala, Sweden
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11
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Medstrand P, Jern P. Obituary: Jonas Blomberg (1944–2019). Retrovirology 2019. [PMCID: PMC6419368 DOI: 10.1186/s12977-019-0469-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
More than half of the genomic landscape in humans and many other organisms is composed of repetitive DNA, which mostly derives from transposable elements (TEs) and viruses. Recent technological advances permit improved assessment of the repetitive content across genomes and newly developed molecular assays have revealed important roles of TEs and viruses in host genome evolution and organization. To update on our current understanding of TE biology and to promote new interdisciplinary strategies for the TE research community, leading experts gathered for the 2nd Uppsala Transposon Symposium on October 4–5, 2018 in Uppsala, Sweden. Using cutting-edge single-molecule and single-cell approaches, research on TEs and other repeats has entered a new era in biological and biomedical research.
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13
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Gunst A, Werner M, Waldorp L, Laan E, Källström M, Jern P. 009 Comparing symptom networks of women with reduced, increased, and stable sexual desire. J Sex Med 2018. [DOI: 10.1016/j.jsxm.2018.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Gunst A, Ventus D, Arver S, Dhejne C, Görts-Öberg K, Zamore-Söderström E, Jern P. 015 A randomized, wait list-controlled trial suggests that two psychobehavioral interventions are effective for women’s hypoactive sexual desire. J Sex Med 2018. [DOI: 10.1016/j.jsxm.2018.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Ventus D, Gunst A, Arver S, Dhejne C, Görts Öberg K, Zamore-Söderström E, Jern P. 521 Vibrator-assisted start-stop exercises in conjunction with body awareness training improve premature ejaculation symptoms: a randomized waiting list controlled study. J Sex Med 2018. [DOI: 10.1016/j.jsxm.2018.04.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Brattås PL, Jönsson ME, Fasching L, Nelander Wahlestedt J, Shahsavani M, Falk R, Falk A, Jern P, Parmar M, Jakobsson J. TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells. Cell Rep 2017; 18:1-11. [PMID: 28052240 DOI: 10.1016/j.celrep.2016.12.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022] Open
Abstract
Endogenous retroviruses (ERVs), which make up 8% of the human genome, have been proposed to participate in the control of gene regulatory networks. In this study, we find a region- and developmental stage-specific expression pattern of ERVs in the developing human brain, which is linked to a transcriptional network based on ERVs. We demonstrate that almost 10,000, primarily primate-specific, ERVs act as docking platforms for the co-repressor protein TRIM28 in human neural progenitor cells, which results in the establishment of local heterochromatin. Thereby, TRIM28 represses ERVs and consequently regulates the expression of neighboring genes. These results uncover a gene regulatory network based on ERVs that participates in control of gene expression of protein-coding transcripts important for brain development.
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Affiliation(s)
- Per Ludvik Brattås
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Liana Fasching
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Jenny Nelander Wahlestedt
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Mansoureh Shahsavani
- Department of Neuroscience, Karolinska Institute, Retziusväg 8, 171 77 Stockholm, Sweden
| | - Ronny Falk
- Department of Neuroscience, Karolinska Institute, Retziusväg 8, 171 77 Stockholm, Sweden
| | - Anna Falk
- Department of Neuroscience, Karolinska Institute, Retziusväg 8, 171 77 Stockholm, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden.
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17
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Gunst A, Ventus D, Kärnä A, Salo P, Jern P. Female sexual function varies over time and is dependent on partner-specific factors: a population-based longitudinal analysis of six sexual function domains. Psychol Med 2017; 47:341-352. [PMID: 27766993 DOI: 10.1017/s0033291716002488] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Most studies examining female sexual functions (FSFs) have used cross-sectional designs, not allowing for studying temporal stability and possible relationships between different FSFs over time. Our aim was to study these relationships using a longitudinal approach. METHOD The study sample consisted of 2173 Finnish women from two large-scale, population-based data collections 7 years apart. The Female Sexual Function Index was used. Analyses were further conducted separately for women in different relationship constellations. RESULTS Standardized autoregressive paths ranged from 0.136 (sexual satisfaction) to 0.447 (orgasm function) in the full sample, suggesting that most of the variance in FSF was explained by something other than previous function. Orgasm, desire and satisfaction were the strongest predictors of other functions in the full sample and for women in the same relationship at both time points (higher orgasm function predicted higher function in other domains; greater sexual desire and satisfaction predicted lower function in other domains), however, with small effects sizes. For single women, orgasm function and sexual desire were the only significant autoregressive paths. Significant unidirectional cross-domain paths were found for women in the same relationship at both time points. One significant cross-domain path, not confirmed as unidirectional, was found for single women. CONCLUSIONS FSFs varied considerably over 7 years and relationship status was of importance when assessing temporal stability and cross-domain effects. Our results advocate tailored psychobehavioural treatment interventions for female sexual dysfunctions that take partner-specific factors into account.
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Affiliation(s)
- A Gunst
- Department of Psychology,University of Turku,Turku,Finland
| | - D Ventus
- Department of Psychology,Åbo Akademi University,Turku,Finland
| | - A Kärnä
- Independent Researcher,Turku,Finland
| | - P Salo
- Department of Psychology,University of Turku,Turku,Finland
| | - P Jern
- Department of Psychology,University of Turku,Turku,Finland
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18
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Martinez Barrio A, Lamichhaney S, Fan G, Rafati N, Pettersson M, Zhang H, Dainat J, Ekman D, Höppner M, Jern P, Martin M, Nystedt B, Liu X, Chen W, Liang X, Shi C, Fu Y, Ma K, Zhan X, Feng C, Gustafson U, Rubin CJ, Sällman Almén M, Blass M, Casini M, Folkvord A, Laikre L, Ryman N, Ming-Yuen Lee S, Xu X, Andersson L. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. eLife 2016; 5. [PMID: 27138043 PMCID: PMC4854517 DOI: 10.7554/elife.12081] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/06/2016] [Indexed: 01/04/2023] Open
Abstract
Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.
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Affiliation(s)
- Alvaro Martinez Barrio
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Guangyi Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.,BGI-Shenzhen, Shenzen, China
| | - Nima Rafati
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - He Zhang
- BGI-Shenzhen, Shenzen, China.,College of Physics, Qingdao University, Qingdao, China
| | - Jacques Dainat
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden
| | - Diana Ekman
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marc Höppner
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Björn Nystedt
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Xin Liu
- BGI-Shenzhen, Shenzen, China
| | | | | | | | - Yuanyuan Fu
- BGI-Shenzhen, Shenzen, China.,School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | | | | | - Chungang Feng
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ulla Gustafson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Markus Sällman Almén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Martina Blass
- Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden
| | - Arild Folkvord
- Department of Biology, University of Bergen, Bergen, Norway.,Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway.,Institute of Marine Research, Bergen, Norway
| | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nils Ryman
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Xun Xu
- BGI-Shenzhen, Shenzen, China
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States
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19
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Delhomme N, Sundström G, Zamani N, Lantz H, Lin YC, Hvidsten TR, Höppner MP, Jern P, Van de Peer Y, Lundeberg J, Grabherr MG, Street NR. Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLoS One 2015; 10:e0139080. [PMID: 26413905 PMCID: PMC4586145 DOI: 10.1371/journal.pone.0139080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant’s phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.
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Affiliation(s)
- Nicolas Delhomme
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Görel Sundström
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Neda Zamani
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Henrik Lantz
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden
| | - Yao-Cheng Lin
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium
| | - Torgeir R. Hvidsten
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Marc P. Höppner
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Joakim Lundeberg
- School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Manfred G. Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden
| | - Nathaniel R. Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- * E-mail:
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20
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Kierczak M, Jabłońska J, Forsberg SKG, Bianchi M, Tengvall K, Pettersson M, Scholz V, Meadows JRS, Jern P, Carlborg Ö, Lindblad-Toh K. cgmisc: enhanced genome-wide association analyses and visualization. Bioinformatics 2015; 31:3830-1. [PMID: 26249815 PMCID: PMC4653382 DOI: 10.1093/bioinformatics/btv426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED High-throughput genotyping and sequencing technologies facilitate studies of complex genetic traits and provide new research opportunities. The increasing popularity of genome-wide association studies (GWAS) leads to the discovery of new associated loci and a better understanding of the genetic architecture underlying not only diseases, but also other monogenic and complex phenotypes. Several softwares are available for performing GWAS analyses, R environment being one of them. RESULTS We present cgmisc, an R package that enables enhanced data analysis and visualization of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of the existing software. It also provides several tools for advanced visualization of genomic data and utilizes the power of the R language to aid in preparation of publication-quality figures. Some of the package functions are specific for the domestic dog (Canis familiaris) data. AVAILABILITY AND IMPLEMENTATION The package is operating system-independent and is available from: https://github.com/cgmisc-team/cgmisc CONTACT marcin.kierczak@imbim.uu.se. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marcin Kierczak
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and
| | - Jagoda Jabłońska
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Simon K G Forsberg
- Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Katarina Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and
| | - Veronika Scholz
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Örjan Carlborg
- Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Broad Institute of MIT and Harvard, Boston, MA, USA
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21
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Fasching L, Kapopoulou A, Sachdeva R, Petri R, Jönsson ME, Männe C, Turelli P, Jern P, Cammas F, Trono D, Jakobsson J. TRIM28 represses transcription of endogenous retroviruses in neural progenitor cells. Cell Rep 2014; 10:20-8. [PMID: 25543143 PMCID: PMC4434221 DOI: 10.1016/j.celrep.2014.12.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/28/2014] [Accepted: 12/01/2014] [Indexed: 01/16/2023] Open
Abstract
TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs) results in high-level expression of two groups of endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain.
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Affiliation(s)
- Liana Fasching
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Adamandia Kapopoulou
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rohit Sachdeva
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Rebecca Petri
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Christian Männe
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Florence Cammas
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U896, Université Montpellier; Institut Régional du Cancer Montpellier, Montpellier 34298, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden.
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22
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Abstract
Genomic data provide an excellent resource to improve understanding of retrovirus evolution and the complex relationships among viruses and their hosts. In conjunction with broad-scale in silico screening of vertebrate genomes, this resource offers an opportunity to complement data on the evolution and frequency of past retroviral spread and so evaluate future risks and limitations for horizontal transmission between different host species. Here, we develop a methodology for extracting phylogenetic signal from large endogenous retrovirus (ERV) datasets by collapsing information to facilitate broad-scale phylogenomics across a wide sample of hosts. Starting with nearly 90,000 ERVs from 60 vertebrate host genomes, we construct phylogenetic hypotheses and draw inferences regarding the designation, host distribution, origin, and transmission of the Gammaretrovirus genus and associated class I ERVs. Our results uncover remarkable depths in retroviral sequence diversity, supported within a phylogenetic context. This finding suggests that current infectious exogenous retrovirus diversity may be underestimated, adding credence to the possibility that many additional exogenous retroviruses may remain to be discovered in vertebrate taxa. We demonstrate a history of frequent horizontal interorder transmissions from a rodent reservoir and suggest that rats may have acted as important overlooked facilitators of gammaretrovirus spread across diverse mammalian hosts. Together, these results demonstrate the promise of the methodology used here to analyze large ERV datasets and improve understanding of retroviral evolution and diversity for utilization in wider applications.
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Affiliation(s)
- Alexander Hayward
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden
| | - Manfred Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedical Centre, SE-75123 Uppsala, Sweden
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23
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Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG. Unsupervised genome-wide recognition of local relationship patterns. BMC Genomics 2013; 14:347. [PMID: 23706020 PMCID: PMC3669000 DOI: 10.1186/1471-2164-14-347] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 05/08/2013] [Indexed: 12/05/2022] Open
Abstract
Background Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion. Results We developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems. Conclusions Saguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro’s utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.
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Affiliation(s)
- Neda Zamani
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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24
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Hayward A, Ghazal A, Andersson G, Andersson L, Jern P. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. PLoS One 2013; 8:e59940. [PMID: 23533661 PMCID: PMC3606216 DOI: 10.1371/journal.pone.0059940] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022] Open
Abstract
ZBED genes originate from domesticated hAT DNA transposons and encode regulatory proteins of diverse function in vertebrates. Here we reveal the evolutionary relationship between ZBED genes and demonstrate that they are derived from at least two independent domestication events in jawed vertebrate ancestors. We show that ZBEDs form two monophyletic clades, one of which has expanded through several independent duplications in host lineages. Subsequent diversification of ZBED genes has facilitated regulation of multiple diverse fundamental functions. In contrast to known examples of transposable element exaptation, our results demonstrate a novel unprecedented capacity for the repeated utilization of a family of transposable element-derived protein domains sequestered as regulators during the evolution of diverse host gene functions in vertebrates. Specifically, ZBEDs have contributed to vertebrate regulatory innovation through the donation of modular DNA and protein interacting domains. We identify that C7ORF29, ZBED2, 3, 4, and ZBEDX form a monophyletic group together with ZBED6, that is distinct from ZBED1 genes. Furthermore, we show that ZBED5 is related to Buster DNA transposons and is phylogenetically separate from other ZBEDs. Our results offer new insights into the evolution of regulatory pathways, and suggest that DNA transposons have contributed to regulatory complexity during genome evolution in vertebrates.
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Affiliation(s)
- Alexander Hayward
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (AH); (PJ)
| | - Awaisa Ghazal
- Science for Life Laboratory, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Andersson
- Science for Life Laboratory, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (AH); (PJ)
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Groenen MAM, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LAF, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RPMA, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JGR, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012; 491:393-8. [PMID: 23151582 PMCID: PMC3566564 DOI: 10.1038/nature11622] [Citation(s) in RCA: 947] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/27/2012] [Indexed: 01/03/2023]
Abstract
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.
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Johansson A, Bergman H, Corander J, Waldman ID, Karrani N, Salo B, Jern P, Algars M, Sandnabba K, Santtila P, Westberg L. Alcohol and aggressive behavior in men--moderating effects of oxytocin receptor gene (OXTR) polymorphisms. Genes Brain Behav 2011; 11:214-21. [PMID: 22008269 DOI: 10.1111/j.1601-183x.2011.00744.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We explored if the disposition to react with aggression while alcohol intoxicated was moderated by polymorphic variants of the oxytocin receptor gene (OXTR). Twelve OXTR polymorphisms were genotyped in 116 Finnish men [aged 18-30, M = 22.7, standard deviation (SD) = 2.4] who were randomly assigned to an alcohol condition in which they received an alcohol dose of 0.7 g pure ethanol/kg body weight or a placebo condition. Aggressive behavior was measured using a laboratory paradigm in which it was operationalized as the level of aversive noise administered to a fictive opponent. No main effects of the polymorphisms on aggressive behavior were found after controlling for multiple testing. The interactive effects between alcohol and two of the OXTR polymorphisms (rs4564970 and rs1488467) on aggressive behavior were nominally significant and remained significant for the rs4564970 when controlled for multiple tests. To the best of our knowledge, this is the first experimental study suggesting interactive effects of specific genetic variants and alcohol on aggressive behavior in humans.
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Affiliation(s)
- A Johansson
- Department of Psychology and Logopedics Department of Mathematics, Abo Akademi University, Turku, Finland
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Martínez Barrio Á, Ekerljung M, Jern P, Benachenhou F, Sperber GO, Bongcam-Rudloff E, Blomberg J, Andersson G. The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. PLoS One 2011; 6:e19832. [PMID: 21589882 PMCID: PMC3093408 DOI: 10.1371/journal.pone.0019832] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 04/18/2011] [Indexed: 11/25/2022] Open
Abstract
Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra- and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred.
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Affiliation(s)
- Álvaro Martínez Barrio
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Marie Ekerljung
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Patric Jern
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Farid Benachenhou
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran O. Sperber
- Department of Neuroscience, Physiology, Uppsala University, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jonas Blomberg
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Benachenhou F, Jern P, Oja M, Sperber G, Blikstad V, Somervuo P, Kaski S, Blomberg J. Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data. PLoS One 2009; 4:e5179. [PMID: 19365549 PMCID: PMC2664473 DOI: 10.1371/journal.pone.0005179] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 03/10/2009] [Indexed: 01/06/2023] Open
Abstract
Background Retroviral LTRs, paired or single, influence the transcription of both retroviral and non-retroviral genomic sequences. Vertebrate genomes contain many thousand endogenous retroviruses (ERVs) and their LTRs. Single LTRs are difficult to detect from genomic sequences without recourse to repetitiveness or presence in a proviral structure. Understanding of LTR structure increases understanding of LTR function, and of functional genomics. Here we develop models of orthoretroviral LTRs useful for detection in genomes and for structural analysis. Principal Findings Although mutated, ERV LTRs are more numerous and diverse than exogenous retroviral (XRV) LTRs. Hidden Markov models (HMMs), and alignments based on them, were created for HML- (human MMTV-like), general-beta-, gamma- and lentiretroviruslike LTRs, plus a general-vertebrate LTR model. Training sets were XRV LTRs and RepBase LTR consensuses. The HML HMM was most sensitive and detected 87% of the HML LTRs in human chromosome 19 at 96% specificity. By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found. HMM consensus sequences had a conserved modular LTR structure. Target site duplications (TG-CA), TATA (occasionally absent), an AATAAA box and a T-rich region were prominent features. Most of the conservation was located in, or adjacent to, R and U5, with evidence for stem loops. Several of the long HML LTRs contained long ORFs inserted after the second A rich module. HMM consensus alignment allowed comparison of functional features like transcriptional start sites (sense and antisense) between XRVs and ERVs. Conclusion The modular conserved and redundant orthoretroviral LTR structure with three A-rich regions is reminiscent of structurally relaxed Giardia promoters. The five HMMs provided a novel broad range, repeat-independent, ab initio LTR detection, with prospects for greater generalisation, and insight into LTR structure, which may aid development of LTR-targeted pharmaceuticals.
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Affiliation(s)
- Farid Benachenhou
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Patric Jern
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Merja Oja
- Helsinki Institute for Information Technology, Department of Computer Science, University of Helsinki and Laboratory of Computer and Information Science, Helsinki University of Technology, Helsinki, Finland
| | - Göran Sperber
- Unit of Physiology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Vidar Blikstad
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Panu Somervuo
- Helsinki Institute for Information Technology, Department of Computer Science, University of Helsinki and Laboratory of Computer and Information Science, Helsinki University of Technology, Helsinki, Finland
| | - Samuel Kaski
- Helsinki Institute for Information Technology, Department of Computer Science, University of Helsinki and Laboratory of Computer and Information Science, Helsinki University of Technology, Helsinki, Finland
| | - Jonas Blomberg
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- * E-mail:
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Jern P, Russell RA, Pathak VK, Coffin JM. Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance. PLoS Pathog 2009; 5:e1000367. [PMID: 19343218 PMCID: PMC2659435 DOI: 10.1371/journal.ppat.1000367] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 03/05/2009] [Indexed: 12/17/2022] Open
Abstract
The role of APOBEC3 (A3) protein family members in inhibiting retrovirus infection and mobile element retrotransposition is well established. However, the evolutionary effects these restriction factors may have had on active retroviruses such as HIV-1 are less well understood. An HIV-1 variant that has been highly G-to-A mutated is unlikely to be transmitted due to accumulation of deleterious mutations. However, G-to-A mutated hA3G target sequences within which the mutations are the least deleterious are more likely to survive selection pressure. Thus, among hA3G targets in HIV-1, the ratio of nonsynonymous to synonymous changes will increase with virus generations, leaving a footprint of past activity. To study such footprints in HIV-1 evolution, we developed an in silico model based on calculated hA3G target probabilities derived from G-to-A mutation sequence contexts in the literature. We simulated G-to-A changes iteratively in independent sequential HIV-1 infections until a stop codon was introduced into any gene. In addition to our simulation results, we observed higher ratios of nonsynonymous to synonymous mutation at hA3G targets in extant HIV-1 genomes than in their putative ancestral genomes, compared to random controls, implying that moderate levels of A3G-mediated G-to-A mutation have been a factor in HIV-1 evolution. Results from in vitro passaging experiments of HIV-1 modified to be highly susceptible to hA3G mutagenesis verified our simulation accuracy. We also used our simulation to examine the possible role of A3G-induced mutations in the origin of drug resistance. We found that hA3G activity could have been responsible for only a small increase in mutations at known drug resistance sites and propose that concerns for increased resistance to other antiviral drugs should not prevent Vif from being considered a suitable target for development of new drugs. The search for new drugs to battle HIV-1 infections is a continuing struggle. APOBEC3G proteins have been shown to deaminate C-residues in HIV-1 minus strand DNA during its synthesis, resulting in G-to-A mutations in the RNA genome. The HIV-1 Vif protein has evolved to counteract APOBEC3G and thereby escape these frequently deleterious mutations, making Vif an attractive target for new drugs. However, a partial block of Vif could result in an increased although low-level HIV-1 G-to-A mutation rate. Here we investigated APOBEC3G mutation footprints in HIV-1 evolution and the potential risk for known drug resistance from sublethal G-to-A mutations. Using computer simulations, the accuracies of which were verified by infection experiments, we detected evolutionary APOBEC3G mutation footprints in the HIV-1 genome. We predict that the risk that APOBEC3G-induced G-to-A mutations will cause drug resistance is very low. We therefore propose that concerns for increased resistance to other antiviral drugs should not prevent Vif from being considered a suitable target for development of new drugs.
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Affiliation(s)
- Patric Jern
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Rebecca A. Russell
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Abstract
For millions of years, retroviral infections have challenged vertebrates, occasionally leading to germline integration and inheritance as ERVs, genetic parasites whose remnants today constitute some 7% to 8% of the human genome. Although they have had significant evolutionary side effects, it is useful to view ERVs as fossil representatives of retroviruses extant at the time of their insertion into the germline and not as direct players in the evolutionary process itself. Expression of particular ERVs is associated with several positive physiological functions as well as certain diseases, although their roles in human disease as etiological agents, possible contributing factors, or disease markers-well demonstrated in animal models-remain to be established. Here we discuss ERV contributions to host genome structure and function, including their ability to mediate recombination, and physiological effects on the host transcriptome resulting from their integration, expression, and other events.
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Affiliation(s)
- Patric Jern
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
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Witting K, Santtila P, Rijsdijk F, Varjonen M, Jern P, Johansson A, von der Pahlen B, Alanko K, Sandnabba NK. Correlated genetic and non-shared environmental influences account for the co-morbidity between female sexual dysfunctions. Psychol Med 2009; 39:115-127. [PMID: 18366817 DOI: 10.1017/s0033291708003206] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Previous studies have shown moderate heritability for female orgasm. So far, however, no study has addressed the pattern of genetic and environmental influences on diverse sexual dysfunctions in women, nor how genetic and environmental factors contribute to the associations between them. METHOD The sample was drawn from the Genetics of Sex and Aggression (GSA) sample and consisted of 6, 446 female twins (aged 18-43 years) and 1994 female siblings (aged 18-49 years). The participants responded to the Female Sexual Function Index (FSFI), either by post or online. RESULTS Model fitting analyses indicated that individual differences on all six subdomains of the FSFI (desire, arousal, lubrication, orgasm, satisfaction, and pain) were primarily due to non-shared (individual-specific) environmental influences. Genetic influences were modest but significant, whereas shared environmental influences were not significant. A correlated factors model including additive and non-additive genetic and non-shared environmental effects proved to have the best fit and suggested that both correlated additive and non-additive genetic factors and unique environmental factors underlie the co-occurrence of the sexual function problems. CONCLUSIONS The findings suggest that female sexual dysfunctions are separate entities with some shared aetiology. They also indicate that there is a genetic susceptibility for sexual dysfunctions. The unique experiences of each individual are, however, the main factors determining if, and which, dysfunction develops.
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Affiliation(s)
- K Witting
- Centre of Excellence for Behaviour Genetics, Department of Psychology, Abo Akademi University, Finland.
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Abstract
In this issue of Cell Host & Microbe, OhAinle et al., 2008 report that APOBEC3H, a potent innate retroviral restriction factor in primates, lost its function twice independently during recent evolution in humans, stressing an ever present trade-off between benefit and cost of protection against pathogens.
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Affiliation(s)
- Patric Jern
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
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Santtila P, Sandnabba NK, Jern P, Varjonen M, Witting K, von der Pahlen B. Recreational use of erectile dysfunction medication may decrease confidence in ability to gain and hold erections in young males. Int J Impot Res 2007; 19:591-6. [PMID: 17657209 DOI: 10.1038/sj.ijir.3901584] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We aimed to estimate the frequency of recreational use of erectile dysfunction medication (EDM) and to identify any adverse effects on confidence in gaining and holding erections resulting from such use. In addition, we explored differences in erectile function and sexual behavior between recreational and medicinal users of EDM to control for the possibility of recreational users having but not admitting erectile dysfunction. A subset from the Genetics of Sex and Aggression population-based sample of 4428 males with a mean age of 29.51 (s.d.=6.77) years provided information on their use of EDM, erectile function during first intercourse and currently, sexual behavior and confidence in their ability to gain and hold erections. There were 2.6% (n=115) recreational and 0.9% (n=39) medicinal users of EDM. Recreational users had currently significantly lower confidence in their erectile ability than non-users even though they had significantly better erectile function and significantly more unrestricted sexual behavior as well as had more confidence when initiating sexual activity. More frequent use of EDM was associated with significantly less confidence in erectile ability among the recreational users. We conclude that recreational users of EDM may be vulnerable for becoming psychologically dependent on pharmacologically induced erection.
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Affiliation(s)
- P Santtila
- Department of Psychology, Center of Excellence in Behavior Genetics, Abo Akademi University, Turku, Finland.
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Abstract
Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector© (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection of chains of conserved retroviral motifs fulfilling distance constraints and (iii) attempted reconstruction of original retroviral protein sequences, combining alignment, codon statistics and properties of protein ends. Other features are prediction of additional open reading frames, automated database collection, graphical presentation and automatic classification. ReTe favors elements >1000-bp long due to its dependence on order of and distances between retroviral fragments. It detects single or low-copy-number elements. ReTe assigned a ‘retroviral’ score of 890–2827 to 10 exogenous retroviruses from seven genera, and accurately predicted their genes. In a simulated model, ReTe was robust against mutational decay. The human genome was analyzed in 1–2 days on a LINUX cluster. Retroviral sequences were detected in divergent vertebrate genomes. Most ReTe detected chains were coincident with Repeatmasker output and the HERVd database. ReTe did not report most of the evolutionary old HERV-L related and MalR sequences, and is not yet tailored for single LTR detection. Nevertheless, ReTe rationally detects and annotates many retroviral sequences.
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Affiliation(s)
- Göran O. Sperber
- Department of Neuroscience, Physiology and Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala and Department of Biology and Chemical Engineering, Mälardalens Högskola, Eskilstuna, Sweden
| | - Tove Airola
- Department of Neuroscience, Physiology and Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala and Department of Biology and Chemical Engineering, Mälardalens Högskola, Eskilstuna, Sweden
| | - Patric Jern
- Department of Neuroscience, Physiology and Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala and Department of Biology and Chemical Engineering, Mälardalens Högskola, Eskilstuna, Sweden
| | - Jonas Blomberg
- Department of Neuroscience, Physiology and Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala and Department of Biology and Chemical Engineering, Mälardalens Högskola, Eskilstuna, Sweden
- *To whom correspondence should be addressed.+46 18 611 55 93+46 18 55 10 12
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Jern P, Sperber GO, Blomberg J. Divergent patterns of recent retroviral integrations in the human and chimpanzee genomes: probable transmissions between other primates and chimpanzees. J Virol 2006; 80:1367-75. [PMID: 16415014 PMCID: PMC1346942 DOI: 10.1128/jvi.80.3.1367-1375.2006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. We screened both the human genome (version hg16) and the chimpanzee genome (version PanTro1) for ERVs and conducted a phylogenetic analysis of recent integrations. We found a number of recent integrations within both genomes. They segregated into four groups. Two larger gammaretrovirus-like groups (PtG1 and PtG2) occurred in chimpanzees but not in humans. The PtG sequences were most similar to two baboon ERVs and a macaque sequence but neither to other chimpanzee ERVs nor to any human gammaretrovirus-like ERVs. The pattern was consistent with cross-species transfer via predation. This appears to be an example of horizontal transfer of retroviruses with occasional fixation in the germ line.
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Affiliation(s)
- Patric Jern
- Section of Virology, Department of Medical Sciences, Uppsala University, Academic Hospital, Dag Hammarskjolds v. 17, SE-751 85 Uppsala, Sweden.
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Forsman A, Yun Z, Hu L, Uzhameckis D, Jern P, Blomberg J. Development of broadly targeted human endogenous gammaretroviral pol-based real time PCRs Quantitation of RNA expression in human tissues. J Virol Methods 2005; 129:16-30. [PMID: 15967513 DOI: 10.1016/j.jviromet.2005.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/24/2005] [Accepted: 04/05/2005] [Indexed: 10/25/2022]
Abstract
Endogenous retroviral sequences (ERVs) are dynamic genomic components with profound influences on gene expression and genomic structure. Their extent of expression is not well known. Several broadly targeted real-time reverse transcription PCR (QPCRs) systems for surveillance of RNA expression of the major groups of human gammaretroviral ERVs were constructed. The highly conserved reverse transcriptase (RT) and integrase (IN) domains of the pol gene were used as targets for the PCRs, which were both probe-based (TaqMan) and probe-less (SYBR Green). Different levels of primer and probe degeneracy, with or without inosine, were tested. Several of the PCRs had sensitivities of a few HERV nucleic acid copies per PCR reaction. Specificities were approximately as expected from the fit of primers and probes. Gammaretroviral HERV RNA expression was studied in different human tissues. Each HERV group had a specific pattern of expression. HERV-E was highly expressed in testis, HERV-I/T in brain and testis, HERV-H in brain and testis, while HERV-W was highly expressed in placenta. Gammaretroviral RNA was not detected in plasma from 50 blood donors in saliva from 20 persons. In conclusion, a set of tools for investigation of gammaretroviral HERV RNA expression was created.
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Affiliation(s)
- Anna Forsman
- Section of Virology, Department of Medical Sciences, Academic Hospital, Uppsala University, 751 85 Uppasala, Sweden
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Jern P, Sperber GO, Blomberg J. Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2005; 2:50. [PMID: 16092962 PMCID: PMC1224870 DOI: 10.1186/1742-4690-2-50] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 08/10/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Endogenous retroviral sequences (ERVs) are integral parts of most eukaryotic genomes and vastly outnumber exogenous retroviruses (XRVs). ERVs with a relatively complete structure were retrieved from the genetic archives of humans and chickens, diametrically opposite representatives of vertebrate retroviruses (over 3300 proviruses), and analyzed, using a bioinformatic program, RetroTector, developed by us. This rich source of proviral information, accumulated in a local database, and a collection of XRV sequences from the literature, allowed the reconstruction of a Pol based phylogenetic tree, more extensive than previously possible. The aim was to find traits useful for classification and evolutionary studies of retroviruses. Some of these traits have been used by others, but they are here tested in a wider context than before. RESULTS In the ERV collection we found sequences similar to the XRV-based genera: alpha-, beta-, gamma-, epsilon- and spumaretroviruses. However, the occurrence of intermediates between them indicated an evolutionary continuum and suggested that taxonomic changes eventually will be necessary. No delta or lentivirus representatives were found among ERVs. Classification based on Pol similarity is congruent with a number of structural traits. Acquisition of dUTPase occurred three times in retroviral evolution. Loss of one or two NC zinc fingers appears to have occurred several times during evolution. Nucleotide biases have been described earlier for lenti-, delta- and betaretroviruses and were here confirmed in a larger context. CONCLUSION Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny. "Global" genomic properties useful in phylogenies are i.) translational strategy, ii.) number of Gag NC zinc finger motifs, iii.) presence of Pro N-terminal dUTPase (dUTPasePro), iv.) presence of Pro C-terminal G-patch and v.) presence of a GPY/F motif in the Pol integrase (IN) C-terminal domain. "Local" retroviral genomic properties useful for delineation of lower level taxa are i.) host species range, ii.) nucleotide compositional bias and iii.) LTR lengths.
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Affiliation(s)
- Patric Jern
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran O Sperber
- Unit of Physiology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Jonas Blomberg
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Abstract
Recently, we identified and classified 926 human endogenous retrovirus H (HERV-H)-like proviruses in the human genome. In this paper, we used the information to, in silico, reconstruct a putative ancestral HERV-H. A calculated consensus sequence was nearly open in all genes. A few manual adjustments resulted in a putative 9-kb HERV-H provirus with open reading frames (ORFs) in gag, pro, pol, and env. Long terminal repeats (LTRs) differed by 1.1%, indicating proximity to an integration event. The gag ORF was extended upstream of the normal myristylation start site. There was a long leader (including a "pre-gag" ORF) region positioned like the N terminus of murine leukemia virus (MLV) "glyco-Gag," potentially encoding a proline- and serine-rich domain remotely similar to MLV pp12. Another ORF, starting inside the 5' LTR, had no obvious similarity to known protein domains. Unlike other hitherto described gammaretroviruses, the reconstructed Gag had two zinc finger motifs. Alternative splicing of sequences related to the HERV-H consensus was confirmed using dbEST data. env transcripts were most prevalent in colon tumors, but also in normal testis. We found no evidence for full length env transcripts in the dbEST. HERV-H had a markedly skewed nucleotide composition, disfavoring guanine and favoring cytidine. We conclude that the HERV-H consensus shared a gene arrangement common to gammaretroviruses with gag separated by stop codon from pro-pol in the same reading frame, while env resides in another reading frame. There was also alternative splicing. HERV-H consensus yielded new insights in gammaretroviral evolution and will be useful as a model in studies on expression and function.
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Affiliation(s)
- Patric Jern
- Section of Virology, Department of Medical Sciences, Uppsala University, Academic Hospital, Dag Hammarskjolds v. 17, SE-751 85 Uppsala, Sweden.
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Jern P, Sperber GO, Blomberg J. Definition and variation of human endogenous retrovirus H. Virology 2004; 327:93-110. [PMID: 15327901 DOI: 10.1016/j.virol.2004.06.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 06/02/2004] [Accepted: 06/16/2004] [Indexed: 10/26/2022]
Abstract
We defined the abundant human endogenous retrovirus group HERV-H based on pol similarity. Among 3661 pol-containing elements, 1124 integrations were similar to HERV-H RGH2 pol using translated pol sequences. A clustering procedure lessened these to 234 representatives, amenable to detailed study. Among the 1124, 926 clustered into HERV-H and 106 into adjacent HERV-H-like, the remainder being more distant to HERV-H. The HERV-H group was divided into RTVLH2-like (705 elements) and RGH2-like (77 elements) subgroups. Among 926 HERV-H, LTR differences were 1-33%, 10% had env, 78% had gag, 66% had a histidine primer binding site (PBS), and 3% (both subgroups) had a phenylalanine PBS. Allelic differences in env were studied using a convenient temperature gradient gel electrophoresis (TGGE) method and a genomic single nucleotide polymorphism (SNP) search. A pattern of abundant defective elements and less abundant less defective ones led us to formulate a "midwife" master model where more complete elements help the others in trans to transpose.
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Affiliation(s)
- Patric Jern
- Section of Virology, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden.
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Abstract
Human endogenous retroviruses (HERVs) are estimated to represent at least 1% of the human genome. An HERV-H env SU sequence (HERV-H19) was used to screen the high-throughput (htgs) and nonredundant (nr) databases for other HERV-H SU open reading frames (ORFs) and thus possible functional proteins. Using PCR with primers derived from HERV-H19 SU, we also obtained several new sequences with ORFs from a human DNA sample. In a phylogenetic analysis, ORF-containing sequences clustered with HERV-H sequences from chromosomes 1 and 2. SU ORF- and non-SU ORF-containing elements had about the same difference between 5' and 3' long terminal repeats (LTRs) (about 4%), indicating a similar time of integration. SU ORF sequences had a moderately high number of synonymous-versus-nonsynonymous mutations, which indicates a selection for maintenance of the HERV-H SU ORFs.
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Affiliation(s)
- Patric Jern
- Section of Virology, Department of Medical Science, Uppsala University, SE-751 85 Uppsala, Sweden.
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