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Liu Y, Niu Y, Ma X, Xiang Y, Wu D, Li W, Wang T, Niu D. Porcine endogenous retrovirus: classification, molecular structure, regulation, function, and potential risk in xenotransplantation. Funct Integr Genomics 2023; 23:60. [PMID: 36790562 DOI: 10.1007/s10142-023-00984-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023]
Abstract
Xenotransplantation with porcine organs has been recognized as a promising solution to alleviate the shortage of organs for human transplantation. Porcine endogenous retrovirus (PERV), whose proviral DNAs are integrated in the genome of all pig breeds, is a main microbiological risk for xenotransplantation. Over the last decades, some advances on PERVs' studies have been achieved. Here, we reviewed the current progress of PERVs including the classification, molecular structure, regulation, function in immune system, and potential risk in xenotransplantation. We also discussed the problem of insufficient study on PERVs as well as the questions need to be answered in the future work.
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Affiliation(s)
- Yu Liu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yifan Niu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Xiang Ma
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China.,College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.,Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China
| | - Yun Xiang
- Jinhua Academy of Agricultural Sciences, Jinhua, Zhejiang, 321000, China
| | - De Wu
- Postdoctoral Research Station, Jinhua Development Zone, Jinhua, Zhejiang, 321000, China
| | - Weifen Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Tao Wang
- Nanjing Kgene Genetic Engineering Co., Ltd, Nanjing, Jiangsu, 211300, China.
| | - Dong Niu
- College of Animal Science and Technology & College of Veterinary Medicine, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China.
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Łopata K, Wojdas E, Nowak R, Łopata P, Mazurek U. Porcine Endogenous Retrovirus (PERV) - Molecular Structure and Replication Strategy in the Context of Retroviral Infection Risk of Human Cells. Front Microbiol 2018; 9:730. [PMID: 29755422 PMCID: PMC5932395 DOI: 10.3389/fmicb.2018.00730] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/28/2018] [Indexed: 12/28/2022] Open
Abstract
The xenotransplantation of porcine tissues may help overcome the shortage of human organs for transplantation. However, there are some concerns about recipient safety because the risk of porcine endogenous retrovirus (PERV) transmission to human cells remains unknown. Although, to date, no PERV infections have been noted in vivo, the possibility of such infections has been confirmed in vitro. Better understanding of the structure and replication cycle of PERVs is a prerequisite for determining the risk of infection and planning PERV-detection strategies. This review presents the current state of knowledge about the structure and replication cycle of PERVs in the context of retroviral infection risk.
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Affiliation(s)
- Krzysztof Łopata
- Department of Molecular Biology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Emilia Wojdas
- Department of Molecular Biology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland.,Department of Instrumental Analysis, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Roman Nowak
- Department of Molecular Biology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Paweł Łopata
- Department of Molecular Biology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Urszula Mazurek
- Department of Molecular Biology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
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Sokol M, Jessen KM, Pedersen FS. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. APMIS 2016; 124:127-39. [PMID: 26818267 DOI: 10.1111/apm.12477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/12/2015] [Indexed: 12/13/2022]
Abstract
Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the γ- and β-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence. The advent of deep sequencing or next-generation sequencing (NGS) has revolutionized the way researchers solve important scientific questions and develop novel hypotheses in relation to human genome regulation. We recently applied next-generation paired-end RNA-sequencing (RNA-seq) together with chromatin immunoprecipitation with sequencing (ChIP-seq) to examine ERV9 chimeric transcription in human reference cell lines from Encyclopedia of DNA Elements (ENCODE). This led to the discovery of advanced regulation mechanisms by ERV9s and other HERVs across numerous human loci including transcription of large gene-unannotated genomic regions, as well as cooperative regulation by multiple HERVs and non-LTR repeats such as Alu elements. In this article, well-established examples of human gene regulation by HERVs are reviewed followed by a description of paired-end RNA-seq, and its application in identifying chimeric transcription genome-widely. Based on integrative analyses of RNA-seq and ChIP-seq, data we then present novel examples of regulation by ERV9s of tumor suppressor genes CADM2 and SEMA3A, as well as transcription of an unannotated region. Taken together, this article highlights the high suitability of contemporary sequencing methods in future analyses of human biology in relation to evolutionary acquired retroviruses in the human genome.
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Affiliation(s)
- Martin Sokol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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He Q, Kim H, Huang R, Lu W, Tang M, Shi F, Yang D, Zhang X, Huang J, Liu D, Songyang Z. The Daxx/Atrx Complex Protects Tandem Repetitive Elements during DNA Hypomethylation by Promoting H3K9 Trimethylation. Cell Stem Cell 2016; 17:273-86. [PMID: 26340527 DOI: 10.1016/j.stem.2015.07.022] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 06/14/2015] [Accepted: 07/28/2015] [Indexed: 01/02/2023]
Abstract
In mammals, DNA methylation is essential for protecting repetitive sequences from aberrant transcription and recombination. In some developmental contexts (e.g., preimplantation embryos) DNA is hypomethylated but repetitive elements are not dysregulated, suggesting that alternative protection mechanisms exist. Here we explore the processes involved by investigating the role of the chromatin factors Daxx and Atrx. Using genome-wide binding and transcriptome analysis, we found that Daxx and Atrx have distinct chromatin-binding profiles and are co-enriched at tandem repetitive elements in wild-type mouse ESCs. Global DNA hypomethylation further promoted recruitment of the Daxx/Atrx complex to tandem repeat sequences, including retrotransposons and telomeres. Knockdown of Daxx/Atrx in cells with hypomethylated genomes exacerbated aberrant transcriptional de-repression of repeat elements and telomere dysfunction. Mechanistically, Daxx/Atrx-mediated repression seems to involve Suv39h recruitment and H3K9 trimethylation. Our data therefore suggest that Daxx and Atrx safeguard the genome by silencing repetitive elements when DNA methylation levels are low.
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Affiliation(s)
- Quanyuan He
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Hyeung Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rui Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Weisi Lu
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mengfan Tang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fengtao Shi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Dong Yang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dan Liu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
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Wolf G, Greenberg D, Macfarlan TS. Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family. Mob DNA 2015; 6:17. [PMID: 26435754 PMCID: PMC4592553 DOI: 10.1186/s13100-015-0050-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/24/2015] [Indexed: 12/17/2022] Open
Abstract
Tandem C2H2-type zinc finger proteins (ZFPs) constitute the largest transcription factor family in animals. Tandem-ZFPs bind DNA in a sequence-specific manner through arrays of multiple zinc finger domains that allow high flexibility and specificity in target recognition. In tetrapods, a large proportion of tandem-ZFPs contain Krüppel-associated-box (KRAB) repression domains, which are able to induce epigenetic silencing through the KAP1 corepressor. The KRAB-ZFP family continuously amplified in tetrapods through segmental gene duplications, often accompanied by deletions, duplications, and mutations of the zinc finger domains. As a result, tetrapod genomes contain unique sets of KRAB-ZFP genes, consisting of ancient and recently evolved family members. Although several hundred human and mouse KRAB-ZFPs have been identified or predicted, the biological functions of most KRAB-ZFP family members have gone unexplored. Furthermore, the evolutionary forces driving the extraordinary KRAB-ZFP expansion and diversification have remained mysterious for decades. In this review, we highlight recent studies that associate KRAB-ZFPs with the repression of parasitic DNA elements in the mammalian germ line and discuss the hypothesis that the KRAB-ZFP family primarily evolved as an adaptive genomic surveillance system against foreign DNA. Finally, we comment on the computational, genetic, and biochemical challenges of studying KRAB-ZFPs and attempt to predict how these challenges may be soon overcome.
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Affiliation(s)
- Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD 20892 USA
| | - David Greenberg
- The Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158 USA ; Present address: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025 USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD 20892 USA
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Buckley RM, Adelson DL. Mammalian genome evolution as a result of epigenetic regulation of transposable elements. Biomol Concepts 2015; 5:183-94. [PMID: 25372752 DOI: 10.1515/bmc-2014-0013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/27/2014] [Indexed: 12/29/2022] Open
Abstract
Transposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming - an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.
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Choi J, Kim HM, Yoon JK, Cho Y, Lee HJ, Kim KC, Kim CK, Kim GW, Kim YB. Identification of Porcine Endogenous Retrovirus (PERV) packaging sequence and development of PERV packaging viral vector system. J Microbiol 2015; 53:348-53. [PMID: 25935307 DOI: 10.1007/s12275-015-5134-0] [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: 03/11/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/11/2022]
Abstract
Studies of the retroviruses have focused on the specific interaction of the nucleocapsid protein with a packaging signal in the viral RNA as important for this selectivity, but the packaging signal in porcine endogenous retrovirus (PERV) has not been defined. Herein, we identified and analyzed this packaging signal in PERV and found hairpin structures with conserved tetranucleotides in their loops and nucleocapsid recognition sequences; both of which are key elements in the viral packaging signal of MLV. We evaluated packaging efficiency of sequence variants isolated from viral and proviral integrated genomes. All viral packaging sequences (Ψ) were identical, while five distinct packaging sequences were identified from proviral sources. One proviral sequence (Ψ1) was identical to that of the viral Ψ and had the highest packaging efficiency. Three variants (Ψ2, Ψ3, Ψ4) maintained key elements of the viral packaging signal, but had nucleotide replacements and consequently demonstrated reduced packaging efficiency. Despite of the same overall hairpin structure, the proviral variant (Ψ5) had only one GACG sequence in the hairpin loop and showed the lowest packaging efficiency other than ∆Ψ, in which the essential packaging sequence was removed. This result, thus, defined the packaging sequences in PERV and emphasized the importance of nucleotide sequence and RNA structure in the determination of packaging efficiency. In addition, we demonstrate efficient infection and gene expression from the PERV based viral vector, which may serve as a novel alternative to current retroviral expression systems.
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Affiliation(s)
- Jiwon Choi
- Department of Bioindustrial Technologies, Konkuk University, Seoul, 143-701, Korea
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Wolf G, Yang P, Füchtbauer AC, Füchtbauer EM, Silva AM, Park C, Wu W, Nielsen AL, Pedersen FS, Macfarlan TS. The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev 2015; 29:538-54. [PMID: 25737282 PMCID: PMC4358406 DOI: 10.1101/gad.252767.114] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Endogenous retroviruses (ERVs) are epigenetically silenced during development, yet the cellular factors recognizing ERVs in a sequence-specific manner remain elusive. Wolf et al. find that ZFP809 initiates the silencing of ERVs in a sequence-specific manner via recruitment of heterochromatin-inducing complexes. ERV reactivation is accompanied by an epigenetic shift from repressive to active histone modifications. ZFP809 is required to initiate ERV silencing during embryonic development but becomes largely dispensable in somatic tissues. Retroviruses have been invading mammalian germlines for millions of years, accumulating in the form of endogenous retroviruses (ERVs) that account for nearly one-tenth of the mouse and human genomes. ERVs are epigenetically silenced during development, yet the cellular factors recognizing ERVs in a sequence-specific manner remain elusive. Here we demonstrate that ZFP809, a member of the Krüppel-associated box zinc finger protein (KRAB-ZFP) family, initiates the silencing of ERVs in a sequence-specific manner via recruitment of heterochromatin-inducing complexes. ZFP809 knockout mice display highly elevated levels of ZFP809-targeted ERVs in somatic tissues. ERV reactivation is accompanied by an epigenetic shift from repressive to active histone modifications but only slight destabilization of DNA methylation. Importantly, using conditional alleles and rescue experiments, we demonstrate that ZFP809 is required to initiate ERV silencing during embryonic development but becomes largely dispensable in somatic tissues. Finally, we show that the DNA-binding specificity of ZFP809 is evolutionarily conserved in the Muroidea superfamily of rodents and predates the endogenization of retroviruses presently targeted by ZFP809 in Mus musculus. In sum, these data provide compelling evidence that ZFP809 evolved to recognize foreign DNA and establish histone modification-based epigenetic silencing of ERVs.
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Affiliation(s)
- Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Peng Yang
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Annette C Füchtbauer
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Andreia M Silva
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Chungoo Park
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Warren Wu
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Finn S Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA;
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Sokol M, Jessen KM, Pedersen FS. Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions. Retrovirology 2015; 12:32. [PMID: 25927889 PMCID: PMC4422309 DOI: 10.1186/s12977-015-0161-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/30/2015] [Indexed: 12/19/2022] Open
Abstract
Background Evidence suggests that some human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively ERVs) regulate the expression of neighboring genes in normal and disease states; e.g. the human globin locus is regulated by an ERV9 that coordinates long-range gene switching during hematopoiesis and activates also intergenic transcripts. While complex transcription regulation is associated with integration of certain exogenous retroviruses, comparable regulation sustained by ERVs is less understood. Findings We analyzed ERV transcription using ERV9 consensus sequences and publically available RNA-sequencing, chromatin immunoprecipitation with sequencing (ChIP-seq) and cap analysis gene expression (CAGE) data from ENCODE. We discovered previously undescribed and advanced transcription regulation mechanisms in several human reference cell lines. We show that regulation by ERVs involves long-ranging activations including complex RNA splicing patterns, and transcription of large unannotated regions ranging in size from several hundred kb to around 1 Mb. Moreover, regulation was found to be cooperatively sustained in some loci by multiple ERVs and also non-LTR repeats. Conclusion Our analyses show that endogenous retroviruses sustain advanced transcription regulation in human cell lines, which shows similarities to complex insertional mutagenesis effects exerted by exogenous retroviruses. By exposing previously undescribed regulation effects, this study should prove useful for understanding fundamental transcription mechanisms resulting from evolutionary acquisition of retroviral sequence in the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0161-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Sokol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK-8000, Denmark.
| | - Karen Margrethe Jessen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK-8000, Denmark.
| | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, DK-8000, Denmark.
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Garcia-Etxebarria K, Sistiaga-Poveda M, Jugo BM. Endogenous retroviruses in domestic animals. Curr Genomics 2014; 15:256-65. [PMID: 25132796 PMCID: PMC4133949 DOI: 10.2174/1389202915666140520003503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 01/15/2023] Open
Abstract
Endogenous retroviruses (ERVs) are genomic elements that are present in a wide range of vertebrates. Although the study of ERVs has been carried out mainly in humans and model organisms, recently, domestic animals have become important, and some species have begun to be analyzed to gain further insight into ERVs. Due to the availability of complete genomes and the development of new computer tools, ERVs can now be analyzed from a genome-wide viewpoint. In addition, more experimental work is being carried out to analyze the distribution, expression and interplay of ERVs within a host genome. Cats, cattle, chicken, dogs, horses, pigs and sheep have been scrutinized in this manner, all of which are interesting species in health and economic terms. Furthermore, several studies have noted differences in the number of endogenous retroviruses and in the variability of these elements among different breeds, as well as their expression in different tissues and the effects of their locations, which, in some cases, are near genes. These findings suggest a complex, intriguing relationship between ERVs and host genomes. In this review, we summarize the most important in silico and experimental findings, discuss their implications and attempt to predict future directions for the study of these genomic elements.
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Affiliation(s)
- Koldo Garcia-Etxebarria
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila. Zientzia eta Teknologia Fakultatea. Euskal Herriko Unibertsitatea (UPV/EHU). 644 Postakutxa , E-48080 Bilbao, Spain
| | - Maialen Sistiaga-Poveda
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila. Zientzia eta Teknologia Fakultatea. Euskal Herriko Unibertsitatea (UPV/EHU). 644 Postakutxa , E-48080 Bilbao, Spain
| | - Begoña Marina Jugo
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila. Zientzia eta Teknologia Fakultatea. Euskal Herriko Unibertsitatea (UPV/EHU). 644 Postakutxa , E-48080 Bilbao, Spain
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Gola J, Mazurek U. Detection of porcine endogenous retrovirus in xenotransplantation. Reprod Biol 2014; 14:68-73. [PMID: 24607257 DOI: 10.1016/j.repbio.2014.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
Abstract
Xenotransplantation can provide a virtually limitless supply of cells, tissues and organs for a variety of therapeutic procedures. Cells and tissues for use in human transplantation procedures could be supplied using material taken from pigs. However, there is a potential risk of transmission of porcine infectious agents, including porcine endogenous retroviruses (PERVs), to a novel human host, with as yet unknown consequences. Three subtypes of PERV have been identified, of which both PERV-A and PERV-B have the ability to infect human cells in vitro. The third subtype, PERV-C, does not show this ability. Recombinant PERV-A/C forms have demonstrated infectivity in human cell culture. Monitoring in xenotransplantation should comprise screening of the source pig herd (PERV-A and PERV-B level expression assessment, PERV-C detection) and screening of recipients (differentiation between PERV transmission and chimerism). The detection of PERVs includes analyses of both DNA and RNA (PCR and RT-PCR), quantitative determination of the level of PERV nucleic acids (real-time PCR and real-time RT-PCR), assessment of reverse transcriptase (RT) activity (RT assays) and viral and recipient protein detection (immunological methods). In summary, all available methods should be used in monitoring of PERVs in xenotransplantation, and caution should be exercised at all stages of monitoring. Such monitoring has enormous significance for eliminating the possibility of transmission of PERV infection, thus contributing to higher levels of safety in xenotransplantation.
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Affiliation(s)
- Joanna Gola
- Department of Molecular Biology, Medical University of Silesia, Jednosci 8, 41-200 Sosnowiec, Poland.
| | - Urszula Mazurek
- Department of Molecular Biology, Medical University of Silesia, Jednosci 8, 41-200 Sosnowiec, Poland.
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12
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Role of DNA methylation in expression and transmission of porcine endogenous retroviruses. J Virol 2013; 87:12110-20. [PMID: 23986605 DOI: 10.1128/jvi.03262-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Porcine endogenous retroviruses (PERV) represent a major safety concern in pig-to-human xenotransplantation. To date, no PERV infection of a xenograft recipient has been recorded; however, PERVs are transmissible to human cells in vitro. Some recombinants of the A and C PERV subgroups are particularly efficient in infection and replication in human cells. Transcription of PERVs has been described in most pig cells, but their sequence and insertion polymorphism in the pig genome impede identification of transcriptionally active or silenced proviral copies. Furthermore, little is known about the epigenetic regulation of PERV transcription. Here, we report on the transcriptional suppression of PERV by DNA methylation in vitro and describe heavy methylation in the majority of PERV 5' long terminal repeats (LTR) in porcine tissues. In contrast, we have detected sparsely methylated or nonmethylated proviruses in the porcine PK15 cells, which express human cell-tropic PERVs. We also demonstrate the resistance of PERV DNA methylation to inhibitors of methylation and deacetylation. Finally, we show that the high permissiveness of various human cell lines to PERV infection coincides with the inability to efficiently silence the PERV proviruses by 5'LTR methylation. In conclusion, we suggest that DNA methylation is involved in PERV regulation, and that only a minor fraction of proviruses are responsible for the PERV RNA expression and porcine cell infectivity.
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