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Chen M, Yang C, Zhai X, Wang C, Liu M, Zhang B, Guo X, Wang Y, Li H, Liu Y, Han J, Wang X, Li J, Jia L, Li L. Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome. Viruses 2024; 16:892. [PMID: 38932184 PMCID: PMC11209481 DOI: 10.3390/v16060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Endogenous retroviruses (ERVs) are related to long terminal repeat (LTR) retrotransposons, comprising gene sequences of exogenous retroviruses integrated into the host genome and inherited according to Mendelian law. They are considered to have contributed greatly to the evolution of host genome structure and function. We previously characterized HERV-K HML-9 in the human genome. However, the biological function of this type of element in the genome of the chimpanzee, which is the closest living relative of humans, largely remains elusive. Therefore, the current study aims to characterize HML-9 in the chimpanzee genome and to compare the results with those in the human genome. Firstly, we report the distribution and genetic structural characterization of the 26 proviral elements and 38 solo LTR elements of HML-9 in the chimpanzee genome. The results showed that the distribution of these elements displayed a non-random integration pattern, and only six elements maintained a relatively complete structure. Then, we analyze their phylogeny and reveal that the identified elements all cluster together with HML-9 references and with those identified in the human genome. The HML-9 integration time was estimated based on the 2-LTR approach, and the results showed that HML-9 elements were integrated into the chimpanzee genome between 14 and 36 million years ago and into the human genome between 18 and 49 mya. In addition, conserved motifs, cis-regulatory regions, and enriched PBS sequence features in the chimpanzee genome were predicted based on bioinformatics. The results show that pathways significantly enriched for ERV LTR-regulated genes found in the chimpanzee genome are closely associated with disease development, including neurological and neurodevelopmental psychiatric disorders. In summary, the identification, characterization, and genomics of HML-9 presented here not only contribute to our understanding of the role of ERVs in primate evolution but also to our understanding of their biofunctional significance.
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Affiliation(s)
- Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan 430068, China;
| | - Caiqin Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Chunlei Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Mengying Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bohan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xing Guo
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yanglan Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
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Wang C, Zhai X, Wang S, Zhang B, Yang C, Song Y, Li H, Liu Y, Han J, Wang X, Li J, Chen M, Jia L, Li L. Comprehensive characterization of ERV-K (HML-8) in the chimpanzee genome revealed less genomic activity than humans. Front Cell Infect Microbiol 2024; 14:1349046. [PMID: 38456081 PMCID: PMC10918009 DOI: 10.3389/fcimb.2024.1349046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024] Open
Abstract
Endogenous retroviruses (ERVs) originate from ancestral germline infections caused by exogenous retroviruses. Throughout evolution, they have become fixed within the genome of the animals into which they were integrated. As ERV elements coevolve with the host, they are normally epigenetically silenced and can become upregulated in a series of physiological and pathological processes. Generally, a detailed ERV profile in the host genome is critical for understanding the evolutionary history and functional performance of the host genome. We previously characterized and cataloged all the ERV-K subtype HML-8 loci in the human genome; however, this has not been done for the chimpanzee, the nearest living relative of humans. In this study, we aimed to catalog and characterize the integration of HML-8 in the chimpanzee genome and compare it with the integration of HML-8 in the human genome. We analyzed the integration of HML-8 and found that HML-8 pervasively invaded the chimpanzee genome. A total of 76 proviral elements were characterized on 23/24 chromosomes, including detailed elements distribution, structure, phylogeny, integration time, and their potential to regulate adjacent genes. The incomplete structure of HML-8 proviral LTRs will undoubtedly affect their activity. Moreover, the results indicated that HML-8 integration occurred before the divergence between humans and chimpanzees. Furthermore, chimpanzees include more HML-8 proviral elements (76 vs. 40) and fewer solo long terminal repeats (LTR) (0 vs. 5) than humans. These results suggested that chimpanzee genome activity is less than the human genome and that humans may have a better ability to shape and screen integrated proviral elements. Our work is informative in both an evolutionary and a functional context for ERVs.
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Affiliation(s)
- Chunlei Wang
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiuli Zhai
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Shibo Wang
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Caiqin Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanmei Song
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lin Li
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Li C, Qian Q, Yan C, Lu M, Li L, Li P, Fan Z, Lei W, Shang K, Wang P, Wang J, Lu T, Huang Y, Yang H, Wei H, Han J, Xiao J, Chen F. HervD Atlas: a curated knowledgebase of associations between human endogenous retroviruses and diseases. Nucleic Acids Res 2024; 52:D1315-D1326. [PMID: 37870452 PMCID: PMC10767980 DOI: 10.1093/nar/gkad904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs), as remnants of ancient exogenous retrovirus infected and integrated into germ cells, comprise ∼8% of the human genome. These HERVs have been implicated in numerous diseases, and extensive research has been conducted to uncover their specific roles. Despite these efforts, a comprehensive source of HERV-disease association still needs to be added. To address this gap, we introduce the HervD Atlas (https://ngdc.cncb.ac.cn/hervd/), an integrated knowledgebase of HERV-disease associations manually curated from all related published literature. In the current version, HervD Atlas collects 60 726 HERV-disease associations from 254 publications (out of 4692 screened literature), covering 21 790 HERVs (21 049 HERV-Terms and 741 HERV-Elements) belonging to six types, 149 diseases and 610 related/affected genes. Notably, an interactive knowledge graph that systematically integrates all the HERV-disease associations and corresponding affected genes into a comprehensive network provides a powerful tool to uncover and deduce the complex interplay between HERVs and diseases. The HervD Atlas also features a user-friendly web interface that allows efficient browsing, searching, and downloading of all association information, research metadata, and annotation information. Overall, the HervD Atlas is an essential resource for comprehensive, up-to-date knowledge on HERV-disease research, potentially facilitating the development of novel HERV-associated diagnostic and therapeutic strategies.
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Affiliation(s)
- Cuidan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Qiheng Qian
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenghao Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Lu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Pan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuojing Fan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wenyan Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Shang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peihan Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Lu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Huang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hongwei Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Haobin Wei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing100101, China
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Liu M, Jia L, Guo X, Zhai X, Li H, Liu Y, Han J, Zhang B, Wang X, Li T, Wang Y, Li J, Yu C, Li L. Identification and Characterization of the HERV-K (HML-8) Group of Human Endogenous Retroviruses in the Genome. AIDS Res Hum Retroviruses 2023; 39:176-194. [PMID: 36656667 DOI: 10.1089/aid.2022.0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Human endogenous retroviruses (HERVs) can be vertically transmitted in a Mendelian fashion, are stably maintained in the human genome, and are estimated to constitute ∼8% of the genome. HERVs affect human physiology and pathology through their provirus-encoded protein or long terminal repeat (LTR) element effect. Characterization of the genomic distribution is an essential step to understanding the relationships between endogenous retrovirus expression and diseases. However, the poor characterization of human MMTV-like (HML)-8 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, the definition of an accurate and updated HERV-K HML-8 genomic map is urgently needed. In this study, we report the results of a comprehensive analysis of HERV-K HML-8 sequence presence and distribution within the human genome and hominoids, with a detailed description of the different structural and phylogenetic aspects characterizing the group. A total of 40 proviruses and 5 solo LTR elements for human were characterized, which included a detailed description of provirus structure, integration time, potentially regulated genes, transcription factor-binding sites, and primer-binding site features. Besides, 9 chimpanzee sequences, 8 gorilla sequences, and 10 orangutan sequences belonging to the HML-8 subgroup were identified. The integration time results showed that the HML-8 elements were integrated into the primate lineage around 35 and 42 million years ago (mya), during primates evolutionary speciation. Overall, the results clarified the composition of the HML-8 groups, providing an exhaustive background for subsequent functional studies.
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Affiliation(s)
- Mengying Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xing Guo
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China.,Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Xiuli Zhai
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China.,Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanglan Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Scognamiglio S, Grandi N, Pessiu E, Tramontano E. Identification, comprehensive characterization, and comparative genomics of the HERV-K(HML8) integrations in the human genome. Virus Res 2023; 323:198976. [PMID: 36309315 PMCID: PMC10194239 DOI: 10.1016/j.virusres.2022.198976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Around 8% of the human genome is composed by Human Endogenous Retroviruses (HERVs), ancient viral sequences inherited from the primate germ line after their infection by now extinct retroviruses. Given the still underexplored physiological and pathological roles of HERVs, it is fundamental to increase our information about the genomic composition of the different groups, to lay reliable foundation for functional studies. Among HERVs, the most characterized elements belong to the beta-like superfamily HERV-K, comprising 10 groups (HML1-10) with HML2 being the most recent and studied one. Among HMLs, the HML8 group is the only one still lacking a comprehensive genomic description. In the present work, we investigated HML8 sequences' distribution in the human genome (GRCh38/hg38), identifying 23 novel proviruses and characterizing the overall 78 HML8 proviruses in terms of genome structure, phylogeny, and integration pattern. HML8 elements were significantly enriched in human chromosomes 8 and X (p<0.005) while chromosomes 17 and 20 showed fewer integrations than expected (p<0.025 and p<0.005, respectively). Phylogenetic analyses classified HML8 members into 3 clusters, corresponding to the three LTR types MER11A, MER11B and MER11C. Besides different LTR types, common signatures in the internal structure suggested the potential existence of three different ancestral HML8 variants. Accordingly, time of integration estimation coupled with comparative genomics revealed that these three clusters have a different time of integration in the primates' genome, with MER11C elements being significantly younger than MER11A- and MER11B associated proviruses (p<0.005 and p<0.05, respectively). Approximately 30% of the HML8 elements were found co-localized within human genes, sometimes in exonic portions and with the same orientation, deserving further studies for their possible effects on gene expression. Overall, we provide the first detailed picture of the HML8 group distribution and variety among the genome, creating the backbone for the specific analysis of their transcriptional activity in healthy and diseased conditions.
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Affiliation(s)
- Sante Scognamiglio
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari 09042, Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari 09042, Italy
| | - Eleonora Pessiu
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari 09042, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, Laboratory of Molecular Virology, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari 09042, Italy; Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari 09042, Italy.
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Jia L, Liu M, Yang C, Li H, Liu Y, Han J, Zhai X, Wang X, Li T, Li J, Zhang B, Yu C, Li L. Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome. Retrovirology 2022; 19:11. [PMID: 35676699 PMCID: PMC9178832 DOI: 10.1186/s12977-022-00596-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) result from ancestral infections caused by exogenous retroviruses that became incorporated into the germline DNA and evolutionarily fixed in the human genome. HERVs can be transmitted vertically in a Mendelian fashion and be stably maintained in the human genome, of which they are estimated to comprise approximately 8%. HERV-K (HML1-10) transcription has been confirmed to be associated with a variety of diseases, such as breast cancer, lung cancer, prostate cancer, melanoma, rheumatoid arthritis, and amyotrophic lateral sclerosis. However, the poor characterization of HML-9 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, a precise and updated HERV-K HML-9 genomic map is urgently needed to better evaluate the role of these elements in human health. RESULTS We report a comprehensive analysis of the presence and distribution of HERV-K HML-9 elements within the human genome, with a detailed characterization of the structural and phylogenetic properties of the group. A total of 23 proviruses and 47 solo LTR elements were characterized, with a detailed description of the provirus structure, integration time, potential regulated genes, transcription factor binding sites (TFBS), and primer binding site (PBS) features. The integration time results showed that the HML-9 elements found in the human genome integrated into the primate lineage between 17.5 and 48.5 million years ago (mya). CONCLUSION The results provide a clear characterization of HML-9 and a comprehensive background for subsequent functional studies.
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Affiliation(s)
- Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Mengying Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Caiqin Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Xiuli Zhai
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071 China
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Grandi N, Pisano MP, Pessiu E, Scognamiglio S, Tramontano E. HERV-K(HML7) Integrations in the Human Genome: Comprehensive Characterization and Comparative Analysis in Non-Human Primates. BIOLOGY 2021; 10:biology10050439. [PMID: 34069102 PMCID: PMC8156875 DOI: 10.3390/biology10050439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
Simple Summary The human genome is not human at all, but it includes a multitude of sequences inherited from ancient viral infections that affected primates’ germ line. These elements can be seen as the fossils of now-extinct retroviruses, and are called Human Endogenous Retroviruses (HERVs). View as “junk DNA” for a long time, HERVs constitute 4 times the amount of DNA needed to produce all cellular proteins, and growing evidence indicates their crucial role in primate brain evolution, placenta development, and innate immunity shaping. HERVs are also intensively studied for a pathological role, even if the incomplete knowledge about their exact number and genomic position has thus far prevented any causal association. Among possible relevant HERVs, the HERV-K supergroup is of particular interest, including some of the oldest (HML5) as well as youngest (HML2) integrations. Among HERV-Ks, the HML7 group still lack a detailed description, and the present work thus aimed to identify and characterize all HML7 elements in the human genome. Results showed that the HML7 group includes 23 elements and an additional 160 “scars” of past infection that invaded in primates mostly between 20 and 30 million years ago, providing an exhaustive background to study their impact on human pathophysiology. Abstract Endogenous Retroviruses (ERVs) are ancient relics of infections that affected the primate germ line and constitute about 8% of our genome. Growing evidence indicates that ERVs had a major role in vertebrate evolution, being occasionally domesticated by the host physiology. In addition, human ERV (HERV) expression is highly investigated for a possible pathological role, even if no clear associations have been reported yet. In fact, on the one side, the study of HERV expression in high-throughput data is a powerful and promising tool to assess their actual dysregulation in diseased conditions; but, on the other side, the poor knowledge about the various HERV group genomic diversity and individual members somehow prevented the association between specific HERV loci and a given molecular mechanism of pathogenesis. The present study is focused on the HERV-K(HML7) group that—differently from the other HERV-K members—still remains poorly characterized. Starting from an initial identification performed with the software RetroTector, we collected 23 HML7 proviral insertions and about 160 HML7 solitary LTRs that were analyzed in terms of genomic distribution, revealing a significant enrichment in chromosome X and the frequent localization within human gene introns as well as in pericentromeric and centromeric regions. Phylogenetic analyses showed that HML7 members form a monophyletic group, which based on age estimation and comparative localization in non-human primates had its major diffusion between 20 and 30 million years ago. Structural characterization revealed that besides 3 complete HML7 proviruses, the other group members shared a highly defective structure that, however, still presents recognizable functional domains, making it worth further investigation in the human population to assess the presence of residual coding potential.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy; (M.P.P.); (E.P.); (S.S.); (E.T.)
- Correspondence:
| | - Maria Paola Pisano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy; (M.P.P.); (E.P.); (S.S.); (E.T.)
| | - Eleonora Pessiu
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy; (M.P.P.); (E.P.); (S.S.); (E.T.)
| | - Sante Scognamiglio
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy; (M.P.P.); (E.P.); (S.S.); (E.T.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy; (M.P.P.); (E.P.); (S.S.); (E.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Cagliari, Italy
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8
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Pisano MP, Grandi N, Tramontano E. High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. Viruses 2020; 12:E633. [PMID: 32545287 PMCID: PMC7354619 DOI: 10.3390/v12060633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023] Open
Abstract
Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.
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Affiliation(s)
- Maria Paola Pisano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Cagliari, Italy
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9
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Grandi N, Pisano MP, Demurtas M, Blomberg J, Magiorkinis G, Mayer J, Tramontano E. Identification and characterization of ERV-W-like sequences in Platyrrhini species provides new insights into the evolutionary history of ERV-W in primates. Mob DNA 2020; 11:6. [PMID: 32021657 PMCID: PMC6995185 DOI: 10.1186/s13100-020-0203-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W (HERV-W) sequences is investigated for a pathological role in various human diseases. Results We previously characterized ERV-W group genomic sequences in human and non-human Catarrhini species. We now investigated ERV-W-like sequences in the parvorder Platyrrhini, especially regarding two species with complete genome assemblies, namely marmoset (Callithrix jacchus) and squirrel monkey (Saimiri boliviensis). We identified in both species proviral sequences, annotated as ERV1–1 in respective genome assemblies, sharing high sequence similarities with Catarrhini ERV-W. A total of 130 relatively intact proviruses from the genomes of marmoset and squirrel monkey were characterized regarding their structural and evolutionarily relationships with Catarrhini ERV-W elements. Platyrrhini ERV-W sequences share several structural features with Catarrhini ERV-W elements and are closely related phylogenetically with the latter as well as with other ERV-W-related gammaretrovirus-like ERVs. The ERV-W group colonized Platyrrhini primates of both Callitrichidae and Atelidae lineages, with provirus formations having occurred mostly between 25 and 15 mya. Two LTR subgroups were associated with monophyletic proviral bodies. A pre-gag region appears to be a sequence feature common to the ERV-W group: it harbors a putative intron sequence that is missing in some ERV-W loci, holding a putative ORF as well. The presence of a long pre-gag portion was confirmed among all gammaretroviral ERV analyzed, suggesting a role in the latter biology. It is noteworthy that, contrary to Catarrhini ERV-W, there was no evidence of L1-mediated mobilization for Platyrrhini ERV-W sequences. Conclusions Our data establish that ERV-W is not exclusive to Catarrhini primates but colonized both parvorders of Simiiformes, providing further insight into the evolution of ERV-W and the colonization of primate genomes.
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Affiliation(s)
- Nicole Grandi
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Maria Paola Pisano
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Martina Demurtas
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy
| | - Jonas Blomberg
- 2Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Jens Mayer
- 4Department of Hygiene, Epidemiology, and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Enzo Tramontano
- 1Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, Monserrato, Cagliari Italy.,5Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Cagliari Italy
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10
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Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 2019; 16:6. [PMID: 30845962 PMCID: PMC6407205 DOI: 10.1186/s12977-019-0468-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/20/2023] Open
Abstract
Background Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. Results We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Conclusions Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abigail S Jarosz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Robert J Gifford
- Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Malika L Day
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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11
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Savage AL, Schumann GG, Breen G, Bubb VJ, Al-Chalabi A, Quinn JP. Retrotransposons in the development and progression of amyotrophic lateral sclerosis. J Neurol Neurosurg Psychiatry 2019; 90:284-293. [PMID: 30305322 PMCID: PMC6518469 DOI: 10.1136/jnnp-2018-319210] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023]
Abstract
Endogenous retrotransposon sequences constitute approximately 42% of the human genome, and mobilisation of retrotransposons has resulted in rearrangements, duplications, deletions, novel transcripts and the introduction of new regulatory domains throughout the human genome. Both germline and somatic de novo retrotransposition events have been involved in a range of human diseases, and there is emerging evidence for the modulation of retrotransposon activity during the development of specific diseases. Particularly, there is unequivocal consensus that endogenous retrotransposition can occur in neuronal lineages. This review addresses our current knowledge of the different mechanisms through which retrotransposons might influence the development of and predisposition to amyotrophic lateral sclerosis.
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Affiliation(s)
- Abigail L Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Gerome Breen
- Social, Genetic, and Developmental Psychiatry Research Centre, King's College London, London, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.,King's College Hospital, London, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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12
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Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proc Natl Acad Sci U S A 2018; 115:8609-8614. [PMID: 30082403 PMCID: PMC6112702 DOI: 10.1073/pnas.1807598115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endogenous retroviruses (ERVs) are proviral sequences that result from host germ-line invasion by exogenous retroviruses. The majority of ERVs are degraded. Using the koala retrovirus (KoRV) as a model system, we demonstrate that recombination with an ancient koala retroelement disables KoRV, and that recombination occurs frequently and early in the invasion process. Recombinant KoRVs (recKoRVs) are then able to proliferate in the koala germ line. This may in part explain the generally degraded nature of ERVs in vertebrate genomes and suggests that degradation via recombination is one of the earliest processes shaping retroviral genomic invasions. Endogenous retroviruses (ERVs) are proviral sequences that result from colonization of the host germ line by exogenous retroviruses. The majority of ERVs represent defective retroviral copies. However, for most ERVs, endogenization occurred millions of years ago, obscuring the stages by which ERVs become defective and the changes in both virus and host important to the process. The koala retrovirus, KoRV, only recently began invading the germ line of the koala (Phascolarctos cinereus), permitting analysis of retroviral endogenization on a prospective basis. Here, we report that recombination with host genomic elements disrupts retroviruses during the earliest stages of germ-line invasion. One type of recombinant, designated recKoRV1, was formed by recombination of KoRV with an older degraded retroelement. Many genomic copies of recKoRV1 were detected across koalas. The prevalence of recKoRV1 was higher in northern than in southern Australian koalas, as is the case for KoRV, with differences in recKoRV1 prevalence, but not KoRV prevalence, between inland and coastal New South Wales. At least 15 additional different recombination events between KoRV and the older endogenous retroelement generated distinct recKoRVs with different geographic distributions. All of the identified recombinant viruses appear to have arisen independently and have highly disrupted ORFs, which suggests that recombination with existing degraded endogenous retroelements may be a means by which replication-competent ERVs that enter the germ line are degraded.
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13
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Bergallo M, Daprà V, Novelli M, Rassu M, Montanari P, Galliano I, Quaglino P, Fierro MT. Is HERV-K and HERV-W expression regulated by mir-155 in Sézary Syndrome? GIORN ITAL DERMAT V 2018; 155:477-482. [PMID: 29582620 DOI: 10.23736/s0392-0488.18.05897-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND According to the latest update, 2578 unique mature miRNAs are currently annotated in the human genome and participate in the regulation of multiple events, such as cellular proliferation or apoptosis. A previous study analyzing global miRNA expression patterns in GH cells (high HERV-K versus low) showed that two miRNAs (miR-663 and miR-638) are differentially regulated and exhibit expression parallel to that of HERV-K. The aim of this study was to evaluate HERV-K and -W pol gene and mir-155 expression in SS patients and possible relationship between them. METHODS The comparison between SS patients and healthy donor showed a significant difference in terms of mir-155 expression P=0.0003 as previously reported by our groups. RESULTS We demonstrated that HERV-K and -W pol gene expression was significantly higher in SS patients vs. healthy donor as previously reported by our groups. Our correlation data suggest that miR-155 are not directly involved in regulating the HERVs. CONCLUSIONS Furthermore, further studies including other cohorts of pathology with mir-155 and HERVs involvement such as inflammatory diseases are needed to investigate the role of mir-155 in the cross-activations of HERVs.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy -
| | - Valentina Daprà
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Mauro Novelli
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Marco Rassu
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy
| | - Pietro Quaglino
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Maria T Fierro
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
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14
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Grandi N, Cadeddu M, Blomberg J, Mayer J, Tramontano E. HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. BMC Evol Biol 2018; 18:6. [PMID: 29351742 PMCID: PMC5775608 DOI: 10.1186/s12862-018-1125-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/14/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after their exogenous counterparts went extinct. Among human ERVs (HERVs), the HERV-W group is of particular interest for our physiology and pathology. A HERV-W provirus in locus 7q21.2 has been coopted during evolution to exert an essential role in placenta, and the group expression has been tentatively linked to Multiple Sclerosis and other diseases. Following up on a detailed analysis of 213 HERV-W insertions in the human genome, we now investigated the ERV-W group genomic spread within primate lineages. RESULTS We analyzed HERV-W orthologous loci in the genome sequences of 12 non-human primate species belonging to Simiiformes (parvorders Catarrhini and Platyrrhini), Tarsiiformes and to the most primitive Prosimians. Analysis of HERV-W orthologous loci in non-human Catarrhini primates revealed species-specific insertions in the genomes of Chimpanzee (3), Gorilla (4), Orangutan (6), Gibbon (2) and especially Rhesus Macaque (66). Such sequences were acquired in a retroviral fashion and, in the majority of cases, by L1-mediated formation of processed pseudogenes. There were also a number of LTR-LTR homologous recombination events that occurred subsequent to separation of Catarrhini sub-lineages. Moreover, we retrieved 130 sequences in Marmoset and Squirrel Monkeys (family Cebidae, Platyrrhini parvorder), identified as ERV1-1_CJa based on RepBase annotations, which appear closely related to the ERV-W group. Such sequences were also identified in Atelidae and Pitheciidae, representative of the other Platyrrhini families. In contrast, no ERV-W-related sequences were found in genome sequence assemblies of Tarsiiformes and Prosimians. CONCLUSIONS Overall, our analysis now provides a detailed picture of the ERV-W sequences colonization of the primate lineages genomes, revealing the exact dynamics of ERV-W locus formations as well as novel insights into the evolution and origin of the group.
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Affiliation(s)
- Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jens Mayer
- Institute of Human Genetics, University of Saarland, Homburg, Germany
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
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15
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Bergallo M, Pinon M, Galliano I, Montanari P, Daprà V, Gambarino S, Calvo PL. Epstein Barr virus induces HERV-K and HERV-W expression in pediatrics liver transplant recipients? Minerva Pediatr 2015; 72:145-148. [PMID: 26677952 DOI: 10.23736/s0026-4946.16.04472-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Human endogenous retrovirus (HER Vs) constitute approximately 8% of the human genome. Induction of HER V transcription is possible under certain circumstances, and may have a possible role in some pathological conditions. Aim of the present study was to verify whether HER V-W and K activation by Epstein Barr Virus (EBV) might occur also in vivo, during EBV infection, in pediatric liver transplant recipients. METHODS A total of 35 pediatric liver transplant (LT) patients who received LT at the University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital were included. The samples were grouped in EBV negative and positive. RESULTS We found that HER V-K, and HER V-W expression levels showed no differences between the two groups (P=0.533 HERV-W and P=0.6017 HERV-K). There was not was a significant difference P=0.1894 and 0.1705 for HERV-W and -K respectively when we compared transplant recipients' group with high EBV viral load vs. others transplant recipients. CONCLUSIONS Our data suggest that EBV does not facilitate in-vivo HERV activation.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy - .,Laboratory of Citoimmunodiagnostics, Città della Salute e della Scienza, Regina Margherita Children's Hospital, Turin, Italy -
| | - Michele Pinon
- Unit of Pediatric Gastroenterology and Hepatology, Molinette Hospital, Città della Salute e della Scienza, University of Turin, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy.,Laboratory of Citoimmunodiagnostics, Città della Salute e della Scienza, Regina Margherita Children's Hospital, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Medical School, University of Turin, Turin, Italy.,Laboratory of Citoimmunodiagnostics, Città della Salute e della Scienza, Regina Margherita Children's Hospital, Turin, Italy
| | - Valentina Daprà
- Laboratory of Citoimmunodiagnostics, Città della Salute e della Scienza, Regina Margherita Children's Hospital, Turin, Italy
| | - Stefano Gambarino
- Laboratory of Citoimmunodiagnostics, Città della Salute e della Scienza, Regina Margherita Children's Hospital, Turin, Italy
| | - Pier L Calvo
- Unit of Pediatric Gastroenterology and Hepatology, Molinette Hospital, Città della Salute e della Scienza, University of Turin, Turin, Italy
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16
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Tsangaras K, Mayer J, Alquezar-Planas DE, Greenwood AD. An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data. Viruses 2015; 7:6089-107. [PMID: 26610552 PMCID: PMC4664997 DOI: 10.3390/v7112927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/11/2015] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Transcriptome analysis of polar bear (Ursus maritimus) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. Closely related sequences were identified by PCR analysis of brown bear (Ursus arctos) and black bear (Ursus americanus) but were absent in non-Ursinae bear species. The virus was therefore designated UrsusERV. Two distinct groups of LTRs were observed including a recombinant ERV that contained one LTR belonging to each group indicating that genomic invasions by at least two UrsusERV variants have recently occurred. Age estimates based on proviral LTR divergence and conservation of integration sites among ursids suggest the viral group is only a few million years old. The youngest provirus was polar bear specific, had intact open reading frames (ORFs) and could potentially encode functional proteins. Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. The young age estimates and lineage specificity of the virus suggests UrsusERV is a recent cross species transmission from an unknown reservoir and places the viral group among the youngest of ERVs identified in mammals.
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Affiliation(s)
- Kyriakos Tsangaras
- Department of Translational Genetics, The Cyprus Institute of Neurology and Genetics, 6 International Airport Ave., 2370 Nicosia, Cyprus.
| | - Jens Mayer
- Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, 66421 Homburg, Germany.
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research Berlin, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research Berlin, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
- Department of Veterinary Medicine, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany.
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Bergallo M, Galliano I, Montanari P, Gambarino S, Mareschi K, Ferro F, Fagioli F, Tovo PA, Ravanini P. CMV induces HERV-K and HERV-W expression in kidney transplant recipients. J Clin Virol 2015; 68:28-31. [PMID: 26071331 DOI: 10.1016/j.jcv.2015.04.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND Human endogenous retrovirus (HERVs) constitute approximately 8% of the human genome. Induction of HERV transcription is possible under certain circumstances, and may have a possible role in some pathological conditions. OBJECTIVES The aim of this study was to evaluate HERV-K and -W pol gene expression in kidney transplant recipients and to investigate the possible relationship between HERVs gene expression and CMV infection in these patients. STUDY DESIGN Thirty-three samples of kidney transplant patients and twenty healthy blood donors were used to analyze, HERV-K and -W pol gene RNA expression by relative quantitative relative Real-Time PCR. RESULT We demonstrated that HERVs pol gene expression levels were higher in kidney transplant recipients than in healthy subjects. Moreover, HERV-K and -W pol gene expression was significantly higher in the group of kidney transplant recipients with high CMV viral load than in the groups with no or moderate CMV viral load. CONCLUSION Our data suggest that CMV may facilitate in vivo HERV activation.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy; Laboratory of Citoimmunodiagnostics, University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy; Laboratory of Citoimmunodiagnostics, University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy; Laboratory of Citoimmunodiagnostics, University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Stefano Gambarino
- Laboratory of Citoimmunodiagnostics, University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Katia Mareschi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy; Pediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Francesca Ferro
- Laboratory of Citoimmunodiagnostics, University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Franca Fagioli
- Pediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Pier-Angelo Tovo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy; Laboratory of Citoimmunodiagnostics, University Hospital City of Science and Health of Turin, Regina Margherita Children's Hospital, Turin, Italy.
| | - Paolo Ravanini
- Laboratory of Molecular Virology, Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy.
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Assinger A, Yaiw KC, Göttesdorfer I, Leib-Mösch C, Söderberg-Nauclér C. Human cytomegalovirus (HCMV) induces human endogenous retrovirus (HERV) transcription. Retrovirology 2013; 10:132. [PMID: 24219971 PMCID: PMC3842806 DOI: 10.1186/1742-4690-10-132] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Emerging evidence suggests that human cytomegalovirus (HCMV) is highly prevalent in tumours of different origin. This virus is implied to have oncogenic and oncomodulatory functions, through its ability to control host gene expression. Human endogenous retroviruses (HERV) are also frequently active in tumours of different origin, and are supposed to contribute as cofactors to cancer development. Due to the high prevalence of HCMV in several different tumours, and its ability to control host cell gene expression, we sought to define whether HCMV may affect HERV transcription. FINDINGS Infection of 3 established cancer cell lines, 2 primary glioblastoma cells, endothelial cells from 3 donors and monocytes from 4 donors with HCMV (strains VR 1814 or TB40/F) induced reverse transcriptase (RT) activity in all cells tested, but the response varied between donors. Both, gammaretrovirus-related class I elements HERV-T, HERV-W, HERV-F and ERV-9, and betaretrovirus-related class II elements HML-2 - 4 and HML-7 - 8, as well as spuma-virus related class III elements of the HERV-L group were up-regulated in response to HCMV infection in GliNS1 cells. Up-regulation of HERV activity was more pronounced in cells harbouring active HCMV infection, but was also induced by UV-inactivated virus. The effect was only slightly affected by ganciclovir treatment and was not controlled by the IE72 or IE86 HCMV genes. CONCLUSIONS Within this brief report we show that HCMV infection induces HERV transcriptional activity in different cell types.
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Affiliation(s)
| | | | | | | | - Cecilia Söderberg-Nauclér
- Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
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19
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Hohn O, Hanke K, Bannert N. HERV-K(HML-2), the Best Preserved Family of HERVs: Endogenization, Expression, and Implications in Health and Disease. Front Oncol 2013; 3:246. [PMID: 24066280 PMCID: PMC3778440 DOI: 10.3389/fonc.2013.00246] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022] Open
Abstract
Retroviruses that have the ability to infect germ line cells can become an integral and inherited part of the host genome. About 8% of the human chromosomal DNA consists of sequences derived from infections by retroviruses that presumably circulated 2-40 millions of years ago, and some elements are actually much older. Post-insertional recombinations, deletions, and mutations have rendered all known human endogenous retroviruses (HERVs) non-infectious. However some, particularly the most recently acquired proviruses of the HERV-K(HML-2) family, can expresses viral proteins and produce viral particles. In this review we will first discuss the major aspects of the endogenization process and peculiarities of the different HERV-K families. We will then focus on the genes and proteins encoded by HERV-K(HML-2) as well as inactivation of these proviruses by postinsertional mutations and their inhibition by antiretroviral factors. After describing the evolutionary interplay between host and endogenous retrovirus we will delve deeper into the currently limited understanding of HERV-K and its possible association with disease, particularly tumorigenesis.
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Affiliation(s)
- Oliver Hohn
- Division for HIV and Other Retroviruses, Robert Koch Institute , Berlin , Germany
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20
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Cegolon L, Salata C, Weiderpass E, Vineis P, Palù G, Mastrangelo G. Human endogenous retroviruses and cancer prevention: evidence and prospects. BMC Cancer 2013; 13:4. [PMID: 23282240 PMCID: PMC3557136 DOI: 10.1186/1471-2407-13-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 12/02/2012] [Indexed: 12/05/2022] Open
Abstract
Background Cancer is a significant and growing problem worldwide. While this increase may, in part, be attributed to increasing longevity, improved case notifications and risk-enhancing lifestyle (such as smoking, diet and obesity), hygiene-related factors resulting in immuno-regulatory failure may also play a major role and call for a revision of vaccination strategies to protect against a range of cancers in addition to infections. Discussion Human endogenous retroviruses (HERVs) are a significant component of a wider family of retroelements that constitutes part of the human genome. They were originated by the integration of exogenous retroviruses into the human genome millions of years ago. HERVs are estimated to comprise about 8% of human DNA and are ubiquitous in somatic and germinal tissues. Physiologic and pathologic processes are influenced by some biologically active HERV families. HERV antigens are only expressed at low levels by the host, but in circumstances of inappropriate control their genes may initiate or maintain pathological processes. Although the precise mechanism leading to abnormal HERVs gene expression has yet to be clearly elucidated, environmental factors seem to be involved by influencing the human immune system. HERV-K expression has been detected in different types of tumors. Among the various human endogenous retroviral families, the K series was the latest acquired by the human species. Probably because of its relatively recent origin, the HERV-K is the most complete and biologically active family. The abnormal expression of HERV-K seemingly triggers pathological processes leading to melanoma onset, but also contributes to the morphological and functional cellular modifications implicated in melanoma maintenance and progression. The HERV-K-MEL antigen is encoded by a pseudo-gene incorporated in the HERV-K env-gene. HERV-K-MEL is significantly expressed in the majority of dysplastic and normal naevi, as well as other tumors like sarcoma, lymphoma, bladder and breast cancer. An amino acid sequence similar to HERV-K-MEL, recognized to cause a significant protective effect against melanoma, is shared by the antigenic determinants expressed by some vaccines such as BCG, vaccinia virus and the yellow fever virus. HERV-K are also reactivated in the majority of human breast cancers. Monoclonal and single-chain antibodies against the HERV-K Env protein recently proved capable of blocking the proliferation of human breast cancer cells in vitro, inhibiting tumor growth in mice bearing xenograft tumors. Summary A recent epidemiological study provided provisional evidence of how melanoma risk could possibly be reduced if the yellow fever virus vaccine (YFV) were received at least 10 years before, possibly preventing tumor initiation rather than culling melanoma cells already compromised. Further research is recommended to confirm the temporal pattern of this protection and eliminate/attenuate the potential role of relevant confounders as socio-economic status and other vaccinations. It appears also appropriate to examine the potential protective effect of YFV against other malignancies expressing high levels of HERV-K antigens, namely breast cancer, sarcoma, lymphoma and bladder cancer. Tumor immune-therapy, as described for the monoclonal antibodies against breast cancer, is indeed considered more complex and less advantageous than immune-prevention. Cellular immunity possibly triggered by vaccines as for YFV might also be involved in anti-cancer response, in addition to humoral immunity.
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Affiliation(s)
- Luca Cegolon
- Department of Molecular Medicine, Padua University, Padua, Italy.
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21
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Sin HS, Koh E, Taya M, IIjima M, Sugimoto K, Maeda Y, Yoshida A, Iwamoto T, Namiki M. A Novel Y Chromosome Microdeletion With the Loss of an Endogenous Retrovirus Related, Testis Specific Transcript in AZFb Region. J Urol 2011; 186:1545-52. [DOI: 10.1016/j.juro.2011.05.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Indexed: 02/08/2023]
Affiliation(s)
- Ho-Su Sin
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Eitetsu Koh
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Masaki Taya
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Masashi IIjima
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Kazuhiro Sugimoto
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Yuji Maeda
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | | | - Teruaki Iwamoto
- Division of Male Infertility, Center for Infertility and IVF, International University of Health and Welfare, Nasushiobara, Japan
| | - Mikio Namiki
- Departments of Integrative Cancer Therapy and Urology, Andrology Unit, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
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22
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Mayer J, Blomberg J, Seal RL. A revised nomenclature for transcribed human endogenous retroviral loci. Mob DNA 2011; 2:7. [PMID: 21542922 PMCID: PMC3113919 DOI: 10.1186/1759-8753-2-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 05/04/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. A hitherto unknown proportion of ERV loci are transcribed and thus contribute to the human transcriptome. A small proportion of these loci encode functional proteins. As the role of ERVs in normal and diseased biological processes is not yet established, transcribed ERV loci are of particular interest. As more transcribed ERV loci are likely to be identified in the near future, the development of a systematic nomenclature is important to ensure that all information on each locus can be easily retrieved. RESULTS Here we present a revised nomenclature of transcribed human endogenous retroviral loci that sorts loci into groups based on Repbase classifications. Each symbol is of the format ERV + group symbol + unique number. Group symbols are based on a mixture of Repbase designations and well-supported symbols used in the literature. The presented guidelines will allow newly identified loci to be easily incorporated into the scheme. CONCLUSIONS The naming system will be employed by the HUGO Gene Nomenclature Committee for naming transcribed human ERV loci. We hope that the system will contribute to clarifying a certain aspect of a sometimes confusing nomenclature for human endogenous retroviruses. The presented system may also be employed for naming transcribed loci of human non-ERV repeat loci.
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Affiliation(s)
- Jens Mayer
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
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23
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Sin HS, Koh E, Kim DS, Murayama M, Sugimoto K, Maeda Y, Yoshida A, Namiki M. Human endogenous retrovirus K14C drove genomic diversification of the Y chromosome during primate evolution. J Hum Genet 2010; 55:717-25. [DOI: 10.1038/jhg.2010.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Villarreal LP. The source of self: genetic parasites and the origin of adaptive immunity. Ann N Y Acad Sci 2009; 1178:194-232. [PMID: 19845639 DOI: 10.1111/j.1749-6632.2009.05020.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stable colonization of the host by viruses (genetic parasites) can alter the systems of host identity and provide immunity against related viruses. To attain the needed stability, some viruses of prokaryotes (P1 phage) use a strategy called an addiction module. The linked protective and destructive gene functions of an addiction module insures both virus persistence but will also destroy cells that interrupt this module and thereby prevent infection by competitors. Previously, I have generalized this concept to also include persistent and lytic states of virus infection, which can be considered as a virus addiction module. Such states often involve defective viruses. In this report, I examine the origin of the adaptive immune system from the perspective of a virus addiction module. The likely role of both endogenous and exogenous retroviruses, DNA viruses, and their defective elements is considered in the origin of all the basal components of adaptive immunity (T-cell receptor, RAG-mediated gene rearrangement, clonal lymphocyte proliferation, antigen surface presentation, apoptosis, and education of immune cells). It is concluded that colonization by viruses and their defectives provides a more coherent explanation for the origin of adaptive immunity.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.
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25
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Blomberg J, Benachenhou F, Blikstad V, Sperber G, Mayer J. Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene 2009; 448:115-23. [PMID: 19540319 DOI: 10.1016/j.gene.2009.06.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 06/09/2009] [Accepted: 06/12/2009] [Indexed: 01/27/2023]
Abstract
The genomes of many species are crowded with repetitive mobile sequences. In the case of endogenous retroviruses (ERVs) there is, for various reasons, considerable confusion regarding names assigned to families/groups of ERVs as well as individual ERV loci. Human ERVs have been studied in greater detail, and naming of HERVs in the scientific literature is somewhat confusing not just to the outsider. Without guidelines, confusion for ERVs in other species will also probably increase if those ERVs are studied in greater detail. Based on previous experience, this review highlights some of the problems when naming and classifying ERVs, and provides some guidance for detecting and characterizing ERV sequences. Because of the close relationship between ERVs and exogenous retroviruses (XRVs) it is reasonable to reconcile their classification with that of XRVs. We here argue that classification should be based on a combination of similarity, structural features, (inferred) function, and previous nomenclature. Because the RepBase system is widely employed in genome annotation, RepBase designations should be considered in further taxonomic efforts. To lay a foundation for a phylogenetically based taxonomy, further analyses of ERVs in many hosts are needed. A dedicated, permanent, international consortium would best be suited to integrate and communicate our current and future knowledge on repetitive, mobile elements in general to the scientific community.
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Affiliation(s)
- Jonas Blomberg
- Section of Virology, Department of Medical Sciences, Academic Hospital, 75185 Uppsala, Sweden.
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26
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The activation of human endogenous retrovirus K (HERV-K) is implicated in melanoma cell malignant transformation. Exp Cell Res 2009; 315:849-62. [PMID: 19167380 DOI: 10.1016/j.yexcr.2008.12.023] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 11/18/2008] [Accepted: 12/27/2008] [Indexed: 12/11/2022]
Abstract
Melanoma development is a multi-step process arising from a series of genetic and epigenetic events. Although the sequential stages involved in progression from melanocytes to malignant melanoma are clearly defined, our current understanding of the mechanisms leading to melanoma onset is still incomplete. Growing evidence show that the activation of endogenous retroviral sequences might be involved in transformation of melanocytes as well as in the increased ability of melanoma cells to escape immune surveillance. Here we show that human melanoma cells in vitro undergo a transition from adherent to a more malignant, non-adherent phenotype when exposed to stress conditions. Melanoma-derived non-adherent cells are characterized by an increased proliferative potential and a decreased expression of both HLA class I molecules and Melan-A/MART-1 antigen, similarly to highly malignant cells. These phenotypic and functional modifications are accompanied by the activation of human endogenous retrovirus K expression (HERV-K) and massive production of viral-like particles. Down-regulation of HERV-K expression by RNA interference prevents the transition from the adherent to the non-adherent growth phenotype in low serum. These results implicate HERV-K in at least some critical steps of melanoma progression.
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Impact of endogenous intronic retroviruses on major histocompatibility complex class II diversity and stability. J Virol 2008; 82:6667-77. [PMID: 18448532 DOI: 10.1128/jvi.00097-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major histocompatibility complex (MHC) represents a multigene family that is known to display allelic and gene copy number variations. Primate species such as humans, chimpanzees (Pan troglodytes), and rhesus macaques (Macaca mulatta) show DRB region configuration polymorphism at the population level, meaning that the number and content of DRB loci may vary per haplotype. Introns of primate DRB alleles differ significantly in length due to insertions of transposable elements as long endogenous retrovirus (ERV) and human ERV (HERV) sequences in the DRB2, DRB6, and DRB7 pseudogenes. Although the integration of intronic HERVs resulted sooner or later in the inactivation of the targeted genes, the fixation of these endogenous retroviral segments over long time spans seems to have provided evolutionary advantage. Intronic HERVs may have integrated in a sense or an antisense manner. On the one hand, antisense-oriented retroelements such as HERV-K14I, observed in intron 2 of the DRB7 genes in humans and chimpanzees, seem to promote stability, as configurations/alleles containing these hits have experienced strong conservative selection during primate evolution. On the other hand, the HERVK3I present in intron 1 of all DRB2 and/or DRB6 alleles tested so far integrated in a sense orientation. The data suggest that multigenic regions in particular may benefit from sense introgressions by HERVs, as these elements seem to promote and maintain the generation of diversity, whereas these types of integrations may be lethal in monogenic systems, since they are known to influence transcript regulation negatively.
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Abstract
The capacity to integrate into the chromosomal DNA of germ-line cells has endowed retroviruses with the potential to be vertically transmitted from generation to generation and eventually become fixed in the genomes of the entire population. This has been independently accomplished by several ancient retroviruses that invaded the genomes of our early and more recent primate and hominoid ancestors. Some of the inherited elements then proliferated in the genome, resulting in a number of lineages with complex phylogenetic patterns. Although the vast majority of chromosomally integrated retroelements have suffered inactivating mutations and deletions, a significant impact on various aspects of human biology has been recently revealed and evidence for the present activity of at least one human endogenous retrovirus family continues to accumulate.
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Martina Y, Kurian S, Cherqui S, Evanoff G, Wilson C, Salomon DR. Pseudotyping of porcine endogenous retrovirus by xenotropic murine leukemia virus in a pig islet xenotransplantation model. Am J Transplant 2005; 5:1837-47. [PMID: 15996230 DOI: 10.1111/j.1600-6143.2005.00978.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The potential of porcine endogenous retrovirus (PERV) as a human pathogen, particularly as a public health risk, is a major concern for xenotransplantation. In vitroPERV transmission to human cells is well established. Evidence from human/pig hematopoietic chimeras in immunodeficient mice suggests PERV transmission from pig to human cells in vivo. However, recently Yang et al. demonstrated in such a model that PERV-C, a nonhuman-tropic class, could be transmitted via pseudotyping by xenotropic murine leukemia virus (X-MLV). We developed a mouse pig islet xenotransplant model, where pig and human cells are located in physically separate compartments, to directly assess PERV transmission from a functional pig xenograft. X-MLV efficiently pseudotypes all three classes of PERV, including PERV-A and -B that are known to productively infect human cell lines and PERV-C that is normally not infectious for human cells. Pseudotyping also extends PERV's natural tropism to nonpermissive, nonhuman primate cells. X-MLV is activated locally by the surgical procedure involved in the tissue transplants. Thus, the presence and activation of endogenous X-MLV in immunodeficient mice limits the clinical significance of previous reports of in vivo PERV transmission from pig tissues to human cells.
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Affiliation(s)
- Yuri Martina
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
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