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Altgilbers S, Dierks C, Klein S, Weigend S, Kues WA. Quantitative analysis of CRISPR/Cas9-mediated provirus deletion in blue egg layer chicken PGCs by digital PCR. Sci Rep 2022; 12:15587. [PMID: 36114266 PMCID: PMC9481566 DOI: 10.1038/s41598-022-19861-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/06/2022] [Indexed: 11/08/2022] Open
Abstract
Primordial germ cells (PGCs), the precursors of sperm and oocytes, pass on the genetic material to the next generation. The previously established culture system of chicken PGCs holds many possibilities for functional genomics studies and the rapid introduction of desired traits. Here, we established a CRISPR/Cas9-mediated genome editing protocol for the genetic modification of PGCs derived from chickens with blue eggshell color. The sequence targeted in the present report is a provirus (EAV-HP) insertion in the 5'-flanking region of the SLCO1B3 gene on chromosome 1 in Araucana chickens, which is supposedly responsible for the blue eggshell color. We designed pairs of guide RNAs (gRNAs) targeting the entire 4.2 kb provirus region. Following transfection of PGCs with the gRNA, genomic DNA was isolated and analyzed by mismatch cleavage assay (T7EI). For absolute quantification of the targeting efficiencies in homozygous blue-allele bearing PGCs a digital PCR was established, which revealed deletion efficiencies of 29% when the wildtype Cas9 was used, and 69% when a high-fidelity Cas9 variant was employed. Subsequent single cell dilutions of edited PGCs yielded 14 cell clones with homozygous deletion of the provirus. A digital PCR assay proved the complete absence of this provirus in cell clones. Thus, we demonstrated the high efficiency of the CRISPR/Cas9 system in introducing a large provirus deletion in chicken PGCs. Our presented workflow is a cost-effective and rapid solution for screening the editing success in transfected PGCs.
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Affiliation(s)
- Stefanie Altgilbers
- Department of Biotechnology, Stem Cell Physiology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany.
| | - Claudia Dierks
- Department of Breeding and Genetic Resources, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Sabine Klein
- Department of Biotechnology, Stem Cell Physiology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Steffen Weigend
- Department of Breeding and Genetic Resources, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
| | - Wilfried A Kues
- Department of Biotechnology, Stem Cell Physiology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535, Neustadt, Germany
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2
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He S, Zheng G, Zhou D, Li G, Zhu M, Du X, Zhou J, Cheng Z. Clonal anergy of CD117 +chB6 + B cell progenitors induced by avian leukosis virus subgroup J is associated with immunological tolerance. Retrovirology 2019; 16:1. [PMID: 30602379 PMCID: PMC6317241 DOI: 10.1186/s12977-018-0463-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The pathogenesis of immunological tolerance caused by avian leukosis virus subgroup J (ALV-J), an oncogenic retrovirus, is largely unknown. RESULTS In this study, the development, differentiation, and immunological capability of B cells and their progenitors infected with ALV-J were studied both morphologically and functionally by using a model of ALV-J congenital infection. Compared with posthatch infection, congenital infection of ALV-J resulted in severe immunological tolerance, which was identified as the absence of detectable specific antivirus antibodies. In congenitally infected chickens, immune organs, particularly the bursa of Fabricius, were poorly developed. Moreover, IgM-and IgG-positive cells and total immunoglobulin levels were significantly decreased in these chickens. Large numbers of bursa follicles with no differentiation into cortex and medulla indicated that B cell development was arrested at the early stage. Flow cytometry analysis further confirmed that ALV-J blocked the differentiation of CD117+chB6+ B cell progenitors in the bursa of Fabricius. Furthermore, both the humoral immunity and the immunological capability of B cells and their progenitors were significantly suppressed, as assessed by (a) the antibody titres against sheep red blood cells and the Marek's disease virus attenuated serotype 1 vaccine; (b) the proliferative response of B cells against thymus-independent antigen lipopolysaccharide (LPS) in the spleen germinal centres; and (c) the capacities for proliferation, differentiation and immunoglobulin gene class-switch recombination of B cell progenitors in response to LPS and interleukin-4(IL-4) in vitro. CONCLUSIONS These findings suggested that the anergy of B cells in congenitally infected chickens is caused by the developmental arrest and dysfunction of B cell progenitors, which is an important factor for the immunological tolerance induced by ALV-J.
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Affiliation(s)
- Shuhai He
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
- College of Husbandry and Veterinary, Xinyang Agriculture and Forestry University, Xinyang, 464000 China
| | - Gaoying Zheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
| | - Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
| | - Mingjun Zhu
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
| | - Xusheng Du
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
| | - Jing Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai’an, 271018 China
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3
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Sacco MA, Nair VK. Prototype endogenous avian retroviruses of the genus Gallus. J Gen Virol 2014; 95:2060-2070. [PMID: 24903328 DOI: 10.1099/vir.0.066852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ancient endogenous retroviruses (ERVs), designated endogenous avian retrovirus (EAVs), are present in all Gallus spp. including the chicken, and resemble the modern avian sarcoma and leukosis viruses (ASLVs). The EAVs comprise several distinct retroviruses, including EAV-0, EAV-E51 and EAV-HP, as well as a putative member previously named the avian retrotransposon of chickens (ART-CH). Thus far, only the EAV-HP elements have been well characterized. Here, we determined sequences of representative EAV-0 and EAV-E51 proviruses by cloning and data mining of the 2011 assembly of the Gallus gallus genome. Although the EAV-0 elements are primarily deleted in the env region, we identified two complete EAV-0 env genes within the G. gallus genome and prototype elements sharing identity with an EAV-E51-related clone previously designated EAV-E33. Prototype EAV-0, EAV-E51 and EAV-E33 gag, pol and env gene sequences used for phylogenetic analysis of deduced proteins showed that the EAVs formed three distinct clades, with EAV-0 sharing the last common ancestor with the ASLVs. The EAV-E51 clade showed the greatest level of divergence compared with other EAVs or ASLVs, suggesting that these ERVs represented exogenous retroviruses that evolved and integrated into the germline over a long period of time. Moreover, the degree of divergence between the chicken and red jungle fowl EAV-E51 sequences suggested that they were more ancient than the other EAVs and may have diverged through mutations that accumulated post-integration. Finally, we showed that the ART-CH elements were chimeric defective ERVs comprising portions of EAV-E51 and EAV-HP rather than authentic retrotransposons.
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Affiliation(s)
- Melanie Ann Sacco
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA
| | - Venugopal K Nair
- Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, UK
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Wragg D, Mwacharo JM, Alcalde JA, Wang C, Han JL, Gongora J, Gourichon D, Tixier-Boichard M, Hanotte O. Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl. PLoS One 2013; 8:e71393. [PMID: 23990950 PMCID: PMC3747184 DOI: 10.1371/journal.pone.0071393] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/02/2013] [Indexed: 12/03/2022] Open
Abstract
Oocyan or blue/green eggshell colour is an autosomal dominant trait found in native chickens (Mapuche fowl) of Chile and in some of their descendants in European and North American modern breeds. We report here the identification of an endogenous avian retroviral (EAV-HP) insertion in oocyan Mapuche fowl and European breeds. Sequencing data reveals 100% retroviral identity between the Mapuche and European insertions. Quantitative real-time PCR analysis of European oocyan chicken indicates over-expression of the SLCO1B3 gene (P<0.05) in the shell gland and oviduct. Predicted transcription factor binding sites in the long terminal repeats (LTR) indicate AhR/Ar, a modulator of oestrogen, as a possible promoter/enhancer leading to reproductive tissue-specific over-expression of the SLCO1B3 gene. Analysis of all jungle fowl species Gallus sp. supports the retroviral insertion to be a post-domestication event, while identical LTR sequences within domestic chickens are in agreement with a recent de novo mutation.
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Affiliation(s)
- David Wragg
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Joram M. Mwacharo
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
| | - José A. Alcalde
- Pontificia Universidad Catolica de Chile, Facultad de Agronomia e Ingenieria Forestal, Santiago, Chile
| | - Chen Wang
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jaime Gongora
- The University of Sydney, Faculty of Veterinary Science, Sydney, New South Wales, Australia
| | - David Gourichon
- Institut National de la Recherche Agronomique, UE1295 Poultry Experimental Platform of Tours, Nouzilly, France
| | - Michèle Tixier-Boichard
- Institut National de la Recherche Agronomique, AgroParisTech, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Olivier Hanotte
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
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Yang YY, Qin AJ, Liang XY, Tong SM. Expression of endogenous retrovirus ev/J gp85 gene and analysis of its immunoreactivity in comparison with exogenous viral protein. Virol Sin 2008. [DOI: 10.1007/s12250-008-2971-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Tarlinton R, Meers J, Hanger J, Young P. Real-time reverse transcriptase PCR for the endogenous koala retrovirus reveals an association between plasma viral load and neoplastic disease in koalas. J Gen Virol 2005; 86:783-787. [PMID: 15722540 DOI: 10.1099/vir.0.80547-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Koala retrovirus (KoRV) is a newly described endogenous retrovirus and is unusual in that inserts comprise a full-length replication competent genome. As koalas are known to suffer from an extremely high incidence of leukaemia/lymphoma, the association between this retrovirus and disease in koalas was examined. Using quantitative real-time reverse transcriptase PCR it was demonstrated that KoRV RNA levels in plasma are significantly increased in animals suffering from leukaemia or lymphoma when compared with healthy animals. Increased levels of KoRV were also seen for animals with clinical chlamydiosis. A significant positive association between viral RNA levels and age was also demonstrated. Real-time PCR demonstrated as much as 5 log variation in KoRV proviral DNA levels in genomic DNA extracted from whole blood from different animals. Taken together these data indicate that KoRV is an active endogenous retrovirus and suggests that it may be causally linked to neoplastic disease in koalas.
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Affiliation(s)
- Rachael Tarlinton
- Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, St Lucia 4072, Queensland, Australia
| | - Joanne Meers
- School of Veterinary Science, University of Queensland, St Lucia 4072, Queensland, Australia
| | - Jon Hanger
- Dreamworld, Coomera, Queensland, Australia
| | - Paul Young
- Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, St Lucia 4072, Queensland, Australia
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Sacco MA, Howes K, Smith LP, Nair VK. Assessing the roles of endogenous retrovirus EAV-HP in avian leukosis virus subgroup J emergence and tolerance. J Virol 2004; 78:10525-35. [PMID: 15367619 PMCID: PMC516401 DOI: 10.1128/jvi.78.19.10525-10535.2004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian leukosis virus (ALV) subgroup J is thought to have emerged through a recombination event between an unknown exogenous ALV and the endogenous retrovirus elements designated EAV-HP. All EAV-HP elements identified to date in the chicken genome show large deletions, including that of the entire pol gene. Here we report the identification of four segregating chicken EAV-HP proviruses with complete pol genes, one of which shows exceptionally high sequence identity and a close phylogenetic relationship with ALV-J with respect to the env gene. Embryonic expression of EAV-HP env has been suggested as a factor associated with immunological tolerance induction in a proportion of ALV-J-infected meat-type chickens. In support of this, env gene transcripts expressed from two of the four newly identified EAV-HP proviruses were demonstrated in chicken embryos. However, when ALV-J-infected outbred meat-type chickens were assessed, the presence of intact EAV-HP proviruses failed to directly correlate with ALV-J tolerance. This association was further examined using F(2) progeny of two inbred lines of layer chicken that differed in EAV-HP status and immunological responses to ALV-J. Immunological tolerance developed in a small proportion of F(2) progeny birds, reflecting the expected phenotypic ratio for inheritance of a double-recessive genotype; however, the status of tolerance did not show any direct correlation with the presence of the intact EAV-HP sequence. Nevertheless, identification of an intact chicken EAV-HP locus showing a uniquely close relationship to the ALV-J prototype clone HPRS-103 in the env region provides the strongest evidence of its contribution to the emergence of ALV-J by recombination.
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MESH Headings
- Animals
- Avian Leukosis/immunology
- Avian Leukosis/virology
- Avian Leukosis Virus/classification
- Avian Leukosis Virus/genetics
- Avian Leukosis Virus/immunology
- Base Sequence
- Chick Embryo
- Chickens/virology
- DNA, Viral/chemistry
- DNA, Viral/isolation & purification
- Endogenous Retroviruses/genetics
- Endogenous Retroviruses/immunology
- Evolution, Molecular
- Gene Expression Regulation, Viral
- Genes, env
- Genes, pol
- Molecular Sequence Data
- Phylogeny
- Proviruses/genetics
- RNA, Messenger/analysis
- RNA, Messenger/isolation & purification
- RNA, Viral/analysis
- RNA, Viral/isolation & purification
- Recombination, Genetic
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Melanie A Sacco
- Institute for Animal Health, Compton, Newbury, Berkshire, United Kingdom.
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Abstract
The retroviral capacity for integration into the host genome can give rise to endogenous retroviruses (ERVs): retroviral sequences that are transmitted vertically as part of the host germ line, within which they may continue to replicate and evolve. ERVs represent both a unique archive of ancient viral sequence information and a dynamic component of host genomes. As such they hold great potential as informative markers for studies of both virus evolution and host genome evolution. Numerous novel ERVs have been described in recent years, particularly as genome sequencing projects have advanced. This review discusses the evolution of ERV lineages, considering the processes by which ERV distribution and diversity is generated. The diversity of ERVs isolated so far is summarised in terms of both their distribution across host taxa, and their relationships to recognised retroviral genera. Finally the relevance of ERVs to studies of genome evolution, host disease and viral ecology is considered, and recent findings discussed.
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Affiliation(s)
- Robert Gifford
- Department of Biological Sciences, Imperial College, Silwood Park, Buckhurst Road, Ascot Berkshire, SL5 7PY, UK
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Sacco MA, Venugopal K. Segregation of EAV-HP ancient endogenous retroviruses within the chicken population. J Virol 2001; 75:11935-8. [PMID: 11689680 PMCID: PMC114785 DOI: 10.1128/jvi.75.23.11935-11938.2001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian leukosis virus subgroup J (ALV-J), an exogenous avian retrovirus, is thought to have evolved by recombination with the highly identical env gene of the endogenous avian retrovirus EAV-HP. Embryonic expression of EAV-HP env has been suggested to be associated with the induction of immunological tolerance, a feature observed in a significant proportion of meat-type chickens infected with ALV-J. In support of this hypothesis, we demonstrate that EAV-HP loci, some of which could be associated with tolerance, are still segregating within the chicken population.
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Affiliation(s)
- M A Sacco
- Institute for Animal Health, Compton, Newbury, Berkshire RG20 7NN, United Kingdom
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