51
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Ryan FP. An alternative approach to medical genetics based on modern evolutionary biology. Part 2: retroviral symbiosis. J R Soc Med 2009; 102:324-31. [PMID: 19679734 DOI: 10.1258/jrsm.2009.090183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Frank P Ryan
- Sheffield Primary Care Trust and Department of Animal and Plant Sciences, Sheffield University, Sheffield, UK.
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52
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Varela M, Spencer TE, Palmarini M, Arnaud F. Friendly viruses: the special relationship between endogenous retroviruses and their host. Ann N Y Acad Sci 2009; 1178:157-72. [PMID: 19845636 PMCID: PMC4199234 DOI: 10.1111/j.1749-6632.2009.05002.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Endogenous retroviruses (ERVs) are present in the genome of all vertebrates and have coevolved with their hosts for millions of years. Some ERVs play a critical role in placental development, contribute to genome plasticity, and protect the host against infection of related pathogenic and exogenous retroviruses, thus some ERVs have been positively selected and maintained in the host genome. The sheep genome contains 27 endogenous retroviruses (enJSRVs) related to the pathogenic Jaagsiekte sheep retrovirus (JSRV), the causative agent of a transmissible lung cancer in sheep. enJSRVs are able to protect their host against JSRV infection by blocking different steps of the viral replication cycle. In addition, enJSRVs are absolutely required for sheep placental development. Thus, enJSRVs-JSRV provides a unique and interesting model to study the symbiotic relationship and interplay between host ERVs and evolution. This review will provide some examples of the biological functions of ERVs. In particular, the role of ERVs in reproductive biology and in protecting the host against pathogenic retrovirus infections will be emphasized using enJSRVs/JSRV and the sheep as a model.
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Affiliation(s)
- Mariana Varela
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland, UK
| | - Thomas E. Spencer
- Laboratory for Uterine Biology and Pregnancy, Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - Massimo Palmarini
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland, UK
| | - Frederick Arnaud
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland, UK
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53
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Gimenez J, Montgiraud C, Oriol G, Pichon JP, Ruel K, Tsatsaris V, Gerbaud P, Frendo JL, Evain-Brion D, Mallet F. Comparative methylation of ERVWE1/syncytin-1 and other human endogenous retrovirus LTRs in placenta tissues. DNA Res 2009; 16:195-211. [PMID: 19561344 PMCID: PMC2725788 DOI: 10.1093/dnares/dsp011] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are globally silent in somatic cells. However, some HERVs display high transcription in physiological conditions. In particular, ERVWE1, ERVFRDE1 and ERV3, three proviruses of distinct families, are highly transcribed in placenta and produce envelope proteins associated with placenta development. As silencing of repeated elements is thought to occur mainly by DNA methylation, we compared the methylation of ERVWE1 and related HERVs to appreciate whether HERV methylation relies upon the family, the integration site, the tissue, the long terminal repeat (LTR) function or the associated gene function. CpG methylation of HERV-W LTRs in placenta-associated tissues was heterogeneous but a joint epigenetic control was found for ERVWE1 5'LTR and its juxtaposed enhancer, a mammalian apparent LTR retrotransposon. Additionally, ERVWE1, ERVFRDE1 and ERV3 5'LTRs were all essentially hypomethylated in cytotrophoblasts during pregnancy, but showed distinct and stage-dependent methylation profiles. In non-cytotrophoblastic cells, they also exhibited different methylation profiles, compatible with their respective transcriptional activities. Comparative analyses of transcriptional activity and LTR methylation in cell lines further sustained a role for methylation in the control of functional LTRs. These results suggest that HERV methylation might not be family related but copy-specific, and related to the LTR function and the tissue. In particular, ERVWE1 and ERV3 could be developmentally epigenetically regulated HERVs.
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Affiliation(s)
- Juliette Gimenez
- Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMérieux, Cancer Biomarkers Research Group, 69495 Pierre Bénite cedex, France
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54
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Affiliation(s)
- Saara M. Rawn
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, and the Graduate Program in Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada; ,
| | - James C. Cross
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, and the Graduate Program in Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada; ,
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55
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Abstract
Viruses are the most abundant living entities and probably had a major role in the evolution of life, but are still defined using negative criteria. Here, we propose to divide biological entities into two groups of organisms: ribosome-encoding organisms, which include eukaryotic, archaeal and bacterial organisms, and capsid-encoding organisms, which include viruses. Other replicons (for example, plasmids and viroids) can be termed 'orphan replicons'. Based on this suggested classification system, we propose a new definition for a virus--a capsid-encoding organism that is composed of proteins and nucleic acids, self-assembles in a nucleocapsid and uses a ribosome-encoding organism for the completion of its life cycle.
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Affiliation(s)
- Didier Raoult
- Unité des Rickettsies, IRD-CNRS UMR 6236, IFR-48, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France.
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56
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Malassiné A, Frendo JL, Blaise S, Handschuh K, Gerbaud P, Tsatsaris V, Heidmann T, Evain-Brion D. Human endogenous retrovirus-FRD envelope protein (syncytin 2) expression in normal and trisomy 21-affected placenta. Retrovirology 2008; 5:6. [PMID: 18215254 PMCID: PMC2245979 DOI: 10.1186/1742-4690-5-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 01/23/2008] [Indexed: 11/25/2022] Open
Abstract
Human trophoblast expresses two fusogenic retroviral envelope proteins, the widely studied syncytin 1, encoded by HERV-W and the recently characterized syncytin 2 encoded by HERV-FRD. Here we studied syncytin 2 in normal and Trisomy 21-affected placenta associated with abnormal trophoblast differentiation. Syncytin 2 immunolocalization was restricted throughout normal pregnancy to some villous cytotrophoblastic cells (CT). During the second trimester of pregnancy, syncytin 2 was immunolocalized in some cuboidal CT in T21 placentas, whereas in normal placentas it was observed in flat CT, extending into their cytoplasmic processes. In vitro, CT isolated from normal placenta fuse and differentiate into syncytiotrophoblast. At the same time, syncytin 2 transcript levels decreased significantly with syncytiotrophoblast formation. In contrast, CT isolated from T21-affected placentas fused and differentiated poorly and no variation in syncytin 2 transcript levels was observed. Syncytin 2 expression illustrates the abnormal trophoblast differentiation observed in placenta of fetal T21-affected pregnancies.
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Affiliation(s)
- André Malassiné
- INSERM, U767, 4 avenue de l'Observatoire 75006 Paris, France.
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57
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Reiss D, Zhang Y, Mager DL. Widely variable endogenous retroviral methylation levels in human placenta. Nucleic Acids Res 2007; 35:4743-54. [PMID: 17617638 PMCID: PMC1950553 DOI: 10.1093/nar/gkm455] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
It is generally assumed that transposable elements, including endogenous retroviruses (ERVs), are silenced by DNA methylation/chromatin structure in mammalian cells. However, there have been very few experimental studies to examine the methylation status of human ERVs. In this study, we determined and compared the methylation status of the 5′ long terminal repeats (LTRs) of different copies of the human endogenous retrovirus (HERV) family HERV-E, which are inserted in various genomic contexts. We found that three HERV-E LTRs which function as alternative gene promoters in placenta are unmethylated in that tissue but heavily methylated in blood cells, where these LTRs are not active promoters. This difference is not solely due to global hypomethylation in placenta, since two general measures of methylation levels of HERV-E and HERV-K LTRs suggest only 10–15% lower overall HERV methylation in placenta compared to blood. Comparisons between methylation levels of the LTR-derived gene promoters and six random HERV-E LTRs in placenta showed that the former display significantly lower methylation levels than random LTRs. Moreover, the differences in methylation between LTRs cannot always be explained by their genomic environment, since methylation of flanking sequences can be very different from methylation of the LTR itself.
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Affiliation(s)
- Daphne Reiss
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC and Department of Medical Genetics, University of British Columbia, Canada
| | - Ying Zhang
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC and Department of Medical Genetics, University of British Columbia, Canada
| | - Dixie L. Mager
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC and Department of Medical Genetics, University of British Columbia, Canada
- *To whom correspondence should be addressed.+1-604-675-8139+1-604-877-0712
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58
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Moyes D, Griffiths DJ, Venables PJ. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends Genet 2007; 23:326-33. [PMID: 17524519 DOI: 10.1016/j.tig.2007.05.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 04/16/2007] [Accepted: 05/11/2007] [Indexed: 10/23/2022]
Abstract
Human endogenous retroviruses (HERVs) result from ancestral infection by infectious viruses over millions of years of primate evolution. Some are transcriptionally active, express proteins and therefore have the potential to cause disease. Here we review the controversial attempts to link them with cancer and autoimmunity. The main difficulty is that most HERVs investigated to date are present at the same locus in 100% of the population. However, a new class of insertionally polymorphic HERV-K family members, present in a minority of individuals, has recently been described. We propose that insertionally polymorphic HERVs could be novel genetic risk factors and hence provide a new lease of life for research into HERVs and disease.
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Affiliation(s)
- David Moyes
- The Kennedy Institute of Rheumatology, Imperial College London, London, UK
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59
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Spencer TE, Johnson GA, Bazer FW, Burghardt RC, Palmarini M. Pregnancy recognition and conceptus implantation in domestic ruminants: roles of progesterone, interferons and endogenous retroviruses. Reprod Fertil Dev 2007; 19:65-78. [PMID: 17389136 DOI: 10.1071/rd06102] [Citation(s) in RCA: 215] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The present review highlights new information on pregnancy recognition and conceptus development and implantation in sheep with respect to regulation by progesterone, interferons and endogenous retroviruses. After formation of the corpus luteum, progesterone acts on the endometrium and stimulates blastocyst growth and elongation to a filamentous conceptus (embryo/fetus and associated extra-embryonic membranes). The envelope of endogenous retroviruses related to Jaagsiekte sheep retroviruses appears to intrinsically regulate mononuclear trophectoderm cell proliferation and differentiation into trophoblast giant binucleate cells. The mononuclear trophectoderm cells of elongating sheep conceptuses secrete interferon-tau, which acts on the endometrium to prevent development of the luteolytic mechanism by inhibiting transcription of the gene for the oestrogen receptor alpha in the luminal and superficial ductal glandular epithelia. These actions prevent oestrogen-induced transcription of the oxytocin receptor gene and, therefore, oxytocin-induced luteolytic pulses of prostaglandin F2alpha. Progesterone down regulation of its receptors in luminal and glandular epithelia correlates temporally with a reduction in anti-adhesive mucin land induction of secreted galectin 15 (LGALSI5) and secreted phosphoprotein 1, which are proposed to regulate trophectoderm proliferation and adhesion. Interferon-c acts on the endometrial lumenal epithelium to induce WNT7A and to stimulate LGALS 15, cathepsin L and cystatin C, which are candidate regulators of conceptus development and implantation. The number of potential contributors to maternal recognition and establishment of pregnancy continues to grow and this highlights our limited appreciation of the complexity of the key molecules and signal transduction pathways that intersect during these key developmental processes. The goal of improving reproductive efficiency by preventing embryonic losses that occur during the peri-implantation period of pregnancy in domestic ruminants provides the challenge to increase our knowledge of endometrial function and conceptus development.
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Affiliation(s)
- Thomas E Spencer
- Center for Animal Biotechnology andGenomics, Department of Animal Science, Texas A&M University, College Station, TX 77843, USA.
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60
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Volff JN. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 2007; 28:913-22. [PMID: 16937363 DOI: 10.1002/bies.20452] [Citation(s) in RCA: 267] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Autonomous transposable elements, generally considered as junk and selfish, encode transposition proteins that can bind, copy, break, join or degrade nucleic acids as well as process or interact with other proteins. Such a repertoire of activities might be of interest for the host cell. There is indeed substantial evidence that mobile DNA can serve as a dynamic reservoir for new cellular functions. Transposable element genes encoding transposase, integrase, reverse transcriptase as well as structural and envelope proteins have been repeatedly recruited by their host during evolution in most eukaryotic lineages. Such domesticated sequences protect us against infections, are necessary for our reproduction, allow the replication of our chromosomes and control cell proliferation and death; others are essential for plant development. Many new candidates for domesticated sequences have been revealed by sequencing projects. Their functional analysis will uncover new aspects of evolutionary alchemy, the turning of junk into gold within genomes.
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Affiliation(s)
- Jean-Nicolas Volff
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, am Hubland, D-97074 Würzburg, Germany.
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61
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Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, Mager DL. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet 2006; 3:e10. [PMID: 17222062 PMCID: PMC1781489 DOI: 10.1371/journal.pgen.0030010] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 12/05/2006] [Indexed: 12/19/2022] Open
Abstract
Neuronal apoptosis inhibitory protein (NAIP, also known as BIRC1) is a member of the conserved inhibitor of apoptosis protein (IAP) family. Lineage-specific rearrangements and expansions of this locus have yielded different copy numbers among primates and rodents, with human retaining a single functional copy and mouse possessing several copies, depending on the strain. Roles for this gene in disease have been documented, but little is known about transcriptional regulation of NAIP. We show here that NAIP has multiple promoters sharing no similarity between human and rodents. Moreover, we demonstrate that multiple, domesticated long terminal repeats (LTRs) of endogenous retroviral elements provide NAIP promoter function in human, mouse, and rat. In human, an LTR serves as a tissue-specific promoter, active primarily in testis. However, in rodents, our evidence indicates that an ancestral LTR common to all rodent genes is the major, constitutive promoter for these genes, and that a second LTR found in two of the mouse genes is a minor promoter. Thus, independently acquired LTRs have assumed regulatory roles for orthologous genes, a remarkable evolutionary scenario. We also demonstrate that 5′ flanking regions of IAP family genes as a group, in both human and mouse are enriched for LTR insertions compared to average genes. We propose several potential explanations for these findings, including a hypothesis that recruitment of LTRs near NAIP or other IAP genes may represent a host-cell adaptation to modulate apoptotic responses. When retroviruses infect cells, the viral DNA inserts into the cellular genome. If this happens in gametes (egg or sperm), the viral DNA will be transmitted from parent to offspring, like all chromosomal DNA. Through evolutionary time, such infections of gametes have been so prevalent that 8%–10% of the normal human and mouse genomes are now composed of ancient viral DNA, termed endogenous retroviruses (ERVs). In human, these ERVs are mutated or “dead” but it has been shown that ERV regulatory regions can be employed by the host to help control expression of cellular genes. Here, we report on a remarkable example of this phenomenon. We demonstrate that both the human and rodent neuronal apoptosis inhibitory protein (NAIP) genes, involved in preventing cell death, use different ERV sequences to drive gene expression. Moreover, in each of the primate and rodent lineages, two separate ERVs contribute to NAIP gene expression. This repeated ERV recruitment by NAIP genes throughout evolution is very unlikely to have occurred by chance. We offer a number of potential explanations, including the intriguing possibility that it may be advantageous for anti-cell death genes like NAIP to use ERVs to control their expression. These results support the view that not all retroviral remnants in our genome are simply junk DNA.
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Affiliation(s)
- Mark T Romanish
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wynne M Lock
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Louie N. van de Lagemaat
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Catherine A Dunn
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- *To whom correspondence should be addressed. E-mail:
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62
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Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E. At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription. J Virol 2006; 80:10752-62. [PMID: 17041225 PMCID: PMC1641792 DOI: 10.1128/jvi.00871-06] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report the first genome-wide comparison of in vivo promoter activities of a group of human-specific endogenous retroviruses in healthy and cancerous germ line tissues. To this end, we employed a recently developed technique termed genomic repeat expression monitoring. We found that at least 50% of human-specific long terminal repeats (LTRs) possessed promoter activity, and many of them were up- or downregulated in a seminoma. Individual LTRs were expressed at markedly different levels, ranging from approximately 0.001 to approximately 3% of the housekeeping beta-actin gene transcript level. We demonstrated that the main factors affecting the LTR promoter activity were the LTR type (5'-proviral, 3' proviral, or solitary) and position with regard to genes. The averaged promoter strengths of solitary and 3'-proviral LTRs were almost identical in both tissues, whereas 5'-proviral LTRs displayed two- to fivefold higher promoter activities. The relative content of promoter-active LTRs in gene-rich regions was significantly higher than that in gene-poor loci. This content was maximal in those regions where LTRs "overlapped" readthrough transcripts. Although many promoter-active LTRs were mapped near known genes, no clear-cut correlation was observed between transcriptional activities of genes and neighboring LTRs. Our data also suggest a selective suppression of transcription for LTRs located in gene introns.
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Affiliation(s)
- Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia.
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63
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Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, Spencer TE. Endogenous retroviruses regulate periimplantation placental growth and differentiation. Proc Natl Acad Sci U S A 2006; 103:14390-5. [PMID: 16980413 PMCID: PMC1599973 DOI: 10.1073/pnas.0603836103] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Indexed: 12/26/2022] Open
Abstract
Endogenous retroviruses (ERVs) are fixed and abundant in the genomes of vertebrates. Circumstantial evidence suggests that ERVs play a role in mammalian reproduction, particularly placental morphogenesis, because intact ERV envelope genes were found to be expressed in the syncytiotrophoblasts of human and mouse placenta and to elicit fusion of cells in vitro. We report here in vivo and in vitro experiments finding that the envelope of a particular class of ERVs of sheep, endogenous Jaagsiekte sheep retroviruses (enJSRVs), regulates trophectoderm growth and differentiation in the periimplantation conceptus (embryo/fetus and associated extraembryonic membranes). The enJSRV envelope gene is expressed in the trophectoderm of the elongating ovine conceptus after day 12 of pregnancy. Loss-of-function experiments were conducted in utero by injecting morpholino antisense oligonucleotides on day 8 of pregnancy that blocked enJSRV envelope protein production in the conceptus trophectoderm. This approach retarded trophectoderm outgrowth during conceptus elongation and inhibited trophoblast giant binucleate cell differentiation as observed on day 16. Pregnancy loss was observed by day 20 in sheep receiving morpholino antisense oligonucleotides. In vitro inhibition of the enJSRV envelope reduced the proliferation of mononuclear trophectoderm cells isolated from day 15 conceptuses. Consequently, these results demonstrate that the enJSRV envelope regulates trophectoderm growth and differentiation in the periimplantation ovine conceptus. This work supports the hypothesis that ERVs play fundamental roles in placental morphogenesis and mammalian reproduction.
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Affiliation(s)
- Kathrin A. Dunlap
- *Center for Animal Biotechnology and Genomics, Department of Animal Science, and
| | - Massimo Palmarini
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow G61 1QH, United Kingdom
| | - Mariana Varela
- Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow G61 1QH, United Kingdom
| | - Robert C. Burghardt
- Image Analysis Laboratory, Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843; and
| | - Kanako Hayashi
- *Center for Animal Biotechnology and Genomics, Department of Animal Science, and
| | - Jennifer L. Farmer
- *Center for Animal Biotechnology and Genomics, Department of Animal Science, and
| | - Thomas E. Spencer
- *Center for Animal Biotechnology and Genomics, Department of Animal Science, and
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64
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Dahl A, Krämer F, Schnieder T. Detection of a gypsy-like sequence in the genome of the cat flea Ctenocephalides felis (Bouché 1835). Parasitol Res 2006; 100:311-6. [PMID: 16941190 DOI: 10.1007/s00436-006-0249-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Accepted: 05/29/2006] [Indexed: 10/24/2022]
Abstract
The gypsy virus of Drosophila melanogaster is the first identified retrovirus of insects. Its infectious properties have been reported, and it is able to cause diverse mutations of the phenotype in the fruit fly. As a typical endogenous retrovirus, it is transmitted vertically as part of the host genome, but horizontal transmission has also been shown for the D. melanogaster gypsy virus. Using polymerase chain reaction with degenerate primers designed from the gypsy element of Drosophila subobscura, a gypsy-like sequence was amplified from the genome of the cat flea Ctenocephalides felis in a pool of laboratory and field strains. High identities with other gypsy-like sequences of Drosophila spp. can be detected. In contrast to some of these gypsy sequences, the 410-bp fragment of C. felis possesses two deletions, which are localised in the env gene region. Because of these deletions and the lack of virus particles in C. felis, the criteria for host infectivity are not fulfilled. Nevertheless, the general detection of a gypsy-like sequence in C. felis and the capability of the ectoparasite to act as transmitter of viral diseases can be of importance for the cat flea's position in the epidemiology of diseases, which are accompanied by a higher rate of mutation.
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Affiliation(s)
- A Dahl
- Institute for Parasitology, University of Veterinary Medicine Hannover Foundation, Buenteweg 17, 30559, Hannover, Germany
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65
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Pichon JP, Bonnaud B, Cleuziat P, Mallet F. Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling. Nucleic Acids Res 2006; 34:e46. [PMID: 16554552 PMCID: PMC1409818 DOI: 10.1093/nar/gkl086] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human endogenous retroviruses (HERVs) can be divided into distinct families of tens to thousands of paralogous loci. The expression of HERV elements has been detected in all tissues tested to date, particularly germ cells, embryonic tissues and neoplastic tissues. Hence, the study of HERV expression could represent added value in cancer diagnosis. We developed a quantitative assay combining a multiplex degenerate PCR (MD-PCR) amplification, based on the relative conservation of the pol genes, and a colorimetric Oligo Sorbent Array (OLISA®). Nine HERV families were selected and amplification primers and capture probes were designed for each family. The features required to achieve efficient amplification of most of the elements of each HERV family and balanced co-amplification of all HERV families were analyzed. We found that MD-PCR reliability, i.e. equivalence of amplification and dose-effect relationship, relied on the adjustment of three critical parameters: the primer degeneracy, the relative concentration of each primer and the total amount of primers in the amplification mixture. The analysis of tumoral versus normal tissues suggests that this assay could prove useful in tumor phenotyping.
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Affiliation(s)
| | | | - Philippe Cleuziat
- Centre de Biologie Moléculaire et des Microsystèmes, bioMérieux, Parc Polytec5 rue des Berges, 38024 Grenoble Cedex 01, France
| | - François Mallet
- To whom correspondence should be addressed. Tel: +33 472 728 358; Fax: +33 472 72 8533;
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66
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Desset S, Vaury C. Transcriptional interference mediated by retrotransposons within the genome of their host: lessons from alleles of the white gene from Drosophila melanogaster. Cytogenet Genome Res 2005; 110:209-14. [PMID: 16093674 DOI: 10.1159/000084954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Accepted: 10/13/2003] [Indexed: 11/19/2022] Open
Abstract
Systematic sequencing of model genomes has accelerated our knowledge on genome structure and shown that a large proportion of intergenic regions are made up of mobile element families. Among them, retrotransposons that are mobilized via an RNA intermediate and thus do not excise during their replication cycle are certainly essential factors able to imprint novel and heritable transcriptional regulation within the genome of their host. Today, a crucial complement to the systematic sequencing data is thus to elucidate the potential role of these elements in the regulation of nearby genes, and ultimately in the evolution of eukaryotic genomes.
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Affiliation(s)
- S Desset
- INSERM U384, Faculté de Médecine, Clermont-Ferrand, France
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67
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Brandt J, Veith AM, Volff JN. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. Cytogenet Genome Res 2005; 110:307-17. [PMID: 16093683 DOI: 10.1159/000084963] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Accepted: 02/25/2004] [Indexed: 12/30/2022] Open
Abstract
A family of at least eleven genes called Mar related to long terminal repeat retrotransposons from the Ty3/gypsy group, including two genes previously identified as such, is present in human and mouse genomes. Single orthologous copies were identified for most Mar genes in different mammals. All of them have lost essential structural features necessary for autonomous retrotransposition before divergence between mouse and human. Three Mar genes also have introns at identical positions in human and mouse. Hence, Mar genes do not correspond to functional retrotransposons. Mar genes evolved under purifying selection, strongly suggesting that they are not pseudogenic relics but rather neofunctionalized retrotransposon genes. All putative Mar proteins display sequence similarity to the capsid-like domain of the Gag protein of Tf1/Sushi retrotransposons. In addition, three Mar proteins have conserved the Gag CCHC zinc finger motif, suggesting a role in nucleic acid binding. Some Mar genes have also retained from their retrotransposon origin a -1 ribosomal frameshifting between the gag-related open reading frame and a region encoding a putative aspartyl protease domain. EST analysis revealed that the majority of Mar genes are expressed in brain as well as in other tissues and organs. Some Mar proteins might function as transcription factors or be involved in the control of cell proliferation and apoptosis. Strikingly, as many as eight Mar genes are located on the X chromosome in human, mouse and other mammals, and at least two of the autosomal genes are subject to imprinting. We suggest that retrotransposons might be a source for epigenetically regulated genes. Epigenetic regulation of these neogenes might be derived from the cellular defense mechanisms having controlled their retrotransposon ancestor.
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Affiliation(s)
- J Brandt
- Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
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