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Sindhu P, Magotra A, Sindhu V, Chaudhary P. Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility. ZYGOTE 2024:1-17. [PMID: 39291610 DOI: 10.1017/s0967199424000224] [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: 09/19/2024]
Abstract
Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.
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Affiliation(s)
- Pushpa Sindhu
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Vikas Sindhu
- Department of Animal Nutrition, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Pradeep Chaudhary
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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2
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He Y, Taylor RL, Bai H, Ashwell CM, Zhao K, Li Y, Sun G, Zhang H, Song J. Transgenerational epigenetic inheritance and immunity in chickens that vary in Marek's disease resistance. Poult Sci 2023; 102:103036. [PMID: 37832188 PMCID: PMC10568563 DOI: 10.1016/j.psj.2023.103036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 10/15/2023] Open
Abstract
Marek's disease virus (MDV), a naturally oncogenic, highly contagious alpha herpesvirus, induces a T cell lymphoma in chickens that causes severe economic loss. Marek's disease (MD) outcome in an individual is attributed to genetic and environmental factors. Further investigation of the host-virus interaction mechanisms that impact MD resistance is needed to achieve greater MD control. This study analyzed genome-wide DNA methylation patterns in 2 highly inbred parental lines 63 and 72 and 5 recombinant congenic strains (RCS) C, L, M, N, and X strains from those parents. Lines 63 and 72, are MD resistant and susceptible, respectively, whereas the RCS have different combinations of 87.5% Line 63 and 12.5% Line 72. Our DNA methylation cluster showed a strong association with MD incidence. Differentially methylated regions (DMRs) between the parental lines and the 5 RCS were captured. MD-resistant and MD-susceptible markers of DNA methylation were identified as transgenerational epigenetic inheritable. In addition, the growth of v-src DNA tumors and antibody response against sheep red blood cells differed among the 2 parental lines and the RCS. Overall, our results provide very solid evidence that DNA methylation patterns are transgenerational epigenetic inheritance (TEI) in chickens and also play a vital role in MD tumorigenesis and other immune responses; the specific methylated regions may be important modulators of general immunity.
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Affiliation(s)
- Yanghua He
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822 USA; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences West Virginia University, Morgantown, WV 26508 USA
| | - Hao Bai
- Department of Joint International Research Laboratory of Agriculture and Agri-Product Safety, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Christopher M Ashwell
- Division of Animal and Nutritional Sciences West Virginia University, Morgantown, WV 26508 USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, GD 510642, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Huanmin Zhang
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA.
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3
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Ju X, Wang Z, Cai D, Bello SF, Nie Q. DNA methylation in poultry: a review. J Anim Sci Biotechnol 2023; 14:138. [PMID: 37925454 PMCID: PMC10625706 DOI: 10.1186/s40104-023-00939-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/10/2023] [Indexed: 11/06/2023] Open
Abstract
As an important epigenetic modification, DNA methylation is involved in many biological processes such as animal cell differentiation, embryonic development, genomic imprinting and sex chromosome inactivation. As DNA methylation sequencing becomes more sophisticated, it becomes possible to use it to solve more zoological problems. This paper reviews the characteristics of DNA methylation, with emphasis on the research and application of DNA methylation in poultry.
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Affiliation(s)
- Xing Ju
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China
| | - Zhijun Wang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, 666 Wusu Road, Lin'an, 311300, China
| | - Danfeng Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China
| | - Semiu Folaniyi Bello
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China
| | - Qinghua Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, 510642, China.
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4
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Birhan M, Gelaye E, Ibrahim SM, Berhane N, Abayneh T, Getachew B, Zemene A, Birie K, Deresse G, Adamu K, Dessalegn B, Gessese AT, Kinde MZ, Bitew M. Marek's disease in chicken farms from Northwest Ethiopia: gross pathology, virus isolation, and molecular characterization. Virol J 2023; 20:45. [PMID: 36890573 PMCID: PMC9997020 DOI: 10.1186/s12985-023-02003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
Marek's disease virus (MDV) is a highly contagious, immunosuppressive, and oncogenic chicken pathogen causing marek's disease (MD). In this outbreak-based study, 70 dual-purpose chickens that originated from poultry farms in Northwest Ethiopia and suspected of MD were sampled for pathological and virological study from January 2020 to June 2020. Clinically, affected chickens showed inappetence, dyspnea, depression, shrunken combs, and paralysis of legs, wings, and neck, and death. Pathologically, single or multiple greyish white to yellow tumor-like nodular lesions of various size were appreciated in visceral organs. In addition, splenomegaly, hepatomegaly, renomegaly, and sciatic nerve enlargement were observed. Twenty-seven (27) pooled clinical samples i.e. 7 pooled spleen samples and 20 pooled feathers samples were aseptically collected. Confluent monolayer of Chicken Embryo Fibroblast cells was inoculated with a suspension of pathological samples. Of this, MDV-suggestive cytopathic effects were recorded in 5 (71.42%) and 17 (85%) pooled spleen and feather samples respectively. Molecular confirmation of pathogenic MDV was conducted using conventional PCR amplifying 318 bp of ICP4 gene of MDV-1, of which, 40.9% (9/22) tested positive. In addition, 5 PCR-positive samples from various farms were sequenced further confirming the identity of MDV. The ICP4 partial gene sequences were submitted to GenBank with the following accession numbers: OP485106, OP485107, OP485108, OP485109, and OP485110. Comparative phylogenetics showed, two of the isolates from the same site, Metema, seem to be clonal complexes forming distinct cluster. The other three isolates, two from Merawi and one from Debretabor, appear to represent distinct genotypes although the isolate from Debretabor is closer to the Metema clonal complex. On the other hand, the isolates from Merawi appeared genetically far related to the rest of the 3 isolates and clustered with Indian MDV strains included in the analysis. This study presented the first molecular evidence of MDV in chicken farms from Northwest Ethiopia. Biosecurity measures should strictly be implemented to hinder the spread of the virus. Nationwide studies on molecular characteristics of MDV isolates, their pathotypes, and estimation of the economic impact associated with the disease may help justify production and use of MD vaccines within the country.
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Affiliation(s)
- Mastewal Birhan
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia.
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia.
| | | | | | - Nega Berhane
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | | | | | - Aragaw Zemene
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Kassahun Birie
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | | | | | - Bereket Dessalegn
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe Tesfaye Gessese
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Mebrie Zemene Kinde
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Molalegne Bitew
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
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5
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Yuan Y, Zheng G, You Z, Wang L, Wang Z, Sun C, Liu C, Li X, Zhao P, Wang Y, Yang N, Lian L. Integrated analysis of methylation profiles and transcriptome of MDV-infected chicken spleens reveal hypomethylation of CD4 and HMGB1 genes might promote MD tumorigenesis. Poult Sci 2023; 102:102594. [PMID: 37043960 PMCID: PMC10140160 DOI: 10.1016/j.psj.2023.102594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 02/19/2023] Open
Abstract
Marek's disease (MD) is a lymphoproliferative neoplastic disease caused by Marek's disease virus (MDV). Previous studies have showed that DNA methylation was involved in MD development, but systematic studies are still lacking. Herein, we performed whole genome bisulfite sequencing (WGBS) and RNA-seq in MDV-infected tumorous spleens (IN), noninfected spleens (NoIN), and survivor (SUR) spleens of chickens to identify the genes playing important roles in MD tumor transformation. We generated the first genome-wide DNA methylation profile of MDV-infected, noninfected, and survivor chickens. Combined the WGBS and RNA-Seq, we found that the expression of 25% differential expression genes (DEGs) were significantly correlated with methylation of CpG sites in their gene bodies or promoters. Further, we focused on the DEGs with differentially methylated regions (DMRs) on genes' body and promoter, and it showed the expression of 60% DEGs were significantly correlated with methylation of CpG sites in DMRs. Finally, we identified 8 genes, including CD4, CTLA4, DTL, HMGB1, LGMN, NUP210, RAD52, and ZAP70, and their expression was negatively correlated with methylation of DMRs in their promoters in both IN vs. NoIN and IN vs. SUR. These 8 genes showed specifically high expression in IN groups and clustered in module turquoise analyzed by WGCNA. Out of 8 genes, CD4 and HMGB1 were drop in QTLs associated with MD resistance. Thus, we overexpressed the 2 genes to simulate their high expression in the IN group and found they significantly promoted MDCC-MSB-1 cell proliferation, which revealed they might play promoting roles in MD tumorigenesis in IN due to their high expression induced by hypomethylation.
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6
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Podgorniak T, Dhanasiri A, Chen X, Ren X, Kuan PF, Fernandes J. Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics 2022; 17:1281-1298. [PMID: 35006036 PMCID: PMC9542679 DOI: 10.1080/15592294.2021.2017554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 12/18/2022] Open
Abstract
Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.
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Affiliation(s)
- Tomasz Podgorniak
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Anusha Dhanasiri
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Xianquan Chen
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xu Ren
- Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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7
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Masroor S, Aalam MT, Khan O, Tanuj GN, Gandham RK, Dhara SK, Gupta PK, Mishra BP, Dutt T, Singh G, Sajjanar BK. Effect of acute heat shock on stress gene expression and DNA methylation in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) dairy cattle. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:1797-1809. [PMID: 35796826 DOI: 10.1007/s00484-022-02320-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Environmental temperature is one of the major factors to affect health and productivity of dairy cattle. Gene expression networks within the cells and tissues coordinate stress response, metabolism, and milk production in dairy cattle. Epigenetic DNA methylations were found to mediate the effect of environment by regulating gene expression patterns. In the present study, we compared three Indian native zebu cattle, Bos indicus (Sahiwal, Tharparkar, and Hariana) and one crossbred Bos indicus × Bos taurus (Vrindavani) for stress gene expression and differences in the DNA methylation patterns. The results indicated acute heat shock to cultured PBMC affected their proliferation, stress gene expression, and DNA methylation. Interestingly, expressions of HSP70, HSP90, and STIP1 were found more pronounced in zebu cattle than the crossbred cattle. However, no significant changes were observed in global DNA methylation due to acute heat shock, even though variations were observed in the expression patterns of DNA methyltransferases (DNMT1, DNMT3a) and demethylases (TET1, TET2, and TET3) genes. The treatment 5-AzaC (5-azacitidine) that inhibit DNA methylation in proliferating PBMC caused significant increase in heat shock-induced HSP70 and STIP1 expression indicating that hypomethylation facilitated stress gene expression. Further targeted analysis DNA methylation in the promoter regions revealed no significant differences for HSP70, HSP90, and STIP1. However, there was a significant hypomethylation for BDNF in both zebu and crossbred cattle. Similarly, NR3C1 promoter region showed hypomethylation alone in crossbred cattle. Overall, the results indicated that tropically adapted zebu cattle had comparatively higher expression of stress genes than the crossbred cattle. Furthermore, DNA methylation may play a role in regulating expression of certain genes involved in stress response pathways.
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Affiliation(s)
- Sana Masroor
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Mohd Tanzeel Aalam
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Owais Khan
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gunturu Narasimha Tanuj
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Sujoy K Dhara
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Praveen K Gupta
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Bishnu Prasad Mishra
- ICAR-National Bureau of Animal Genetic Resources, Haryana, Karnal, 132001, India
| | - Triveni Dutt
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gynendra Singh
- Physiology and Climatology Division, ICAR-Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, Uttar Pradesh, India
| | - Basavaraj K Sajjanar
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India.
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8
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Dunislawska A, Pietrzak E, Wishna Kadawarage R, Beldowska A, Siwek M. Pre-hatching and post-hatching environmental factors related to epigenetic mechanisms in poultry. J Anim Sci 2021; 100:6473202. [PMID: 34932113 DOI: 10.1093/jas/skab370] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetic modifications are phenotypic changes unrelated to the modification of the DNA sequence. These modifications are essential for regulating cellular differentiation and organism development. In this case, epigenetics controls how the animal's genetic potential is used. The main epigenetic mechanisms are microRNA activity, DNA methylation and histone modification. The literature has repeatedly shown that environmental modulation has a significant influence on the regulation of epigenetic mechanisms in poultry. The aim of this review is to give an overview of the current state of the knowledge in poultry epigenetics in terms of issues relevant to overall poultry production and the improvement of the health status in chickens and other poultry species. One of the main differences between birds and mammals is the stage of embryonic development. The bird's embryo develops outside its mother, so an optimal environment of egg incubation before hatching is crucial for development. It is also the moment when many factors influence the activation of epigenetic mechanisms, i.e., incubation temperature, humidity, light, as well as in ovo treatments. Epigenome of the adult birds, might be modulated by: nutrition, supplementation and treatment, as well as modification of the intestinal microbiota. In addition, the activation of epigenetic mechanisms is influenced by pathogens (i.e., pathogenic bacteria, toxins, viruses and fungi) as well as, the maintenance conditions. Farm animal epigenetics is still a big challenge for scientists. This is a research area with many open questions. Modern methods of epigenetic analysis can serve both in the analysis of biological mechanisms and in the research and applied to production system, poultry health and welfare.
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Affiliation(s)
- A Dunislawska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - E Pietrzak
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - R Wishna Kadawarage
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - A Beldowska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - M Siwek
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
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Bednarczyk M, Dunislawska A, Stadnicka K, Grochowska E. Chicken embryo as a model in epigenetic research. Poult Sci 2021; 100:101164. [PMID: 34058565 PMCID: PMC8170499 DOI: 10.1016/j.psj.2021.101164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/27/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Epigenetics is defined as the study of changes in gene function that are mitotically or meiotically heritable and do not lead to a change in DNA sequence. Epigenetic modifications are important mechanisms that fine tune the expression of genes in response to extracellular signals and environmental changes. In vertebrates, crucial epigenetic reprogramming events occur during early embryogenesis and germ cell development. Chicken embryo, which develops external to the mother's body, can be easily manipulated in vivo and in vitro, and hence, it is an excellent model for performing epigenetic studies. Environmental factors such as temperature can affect the development of an embryo into the phenotype of an adult. A better understanding of the environmental impact on embryo development can be achieved by analyzing the direct effects of epigenetic modifications as well as their molecular background and their intergenerational and transgenerational inheritance. In this overview, the current possibility of epigenetic changes during chicken embryonic development and their effects on long-term postembryonic development are discussed.
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Affiliation(s)
- Marek Bednarczyk
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, 85-084 Bydgoszcz, Poland.
| | - Aleksandra Dunislawska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, 85-084 Bydgoszcz, Poland
| | - Katarzyna Stadnicka
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, 85-084 Bydgoszcz, Poland
| | - Ewa Grochowska
- Department of Animal Biotechnology and Genetics, UTP University of Science and Technology, 85-084 Bydgoszcz, Poland
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10
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A chicken DNA methylation clock for the prediction of broiler health. Commun Biol 2021; 4:76. [PMID: 33462334 PMCID: PMC7814119 DOI: 10.1038/s42003-020-01608-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
The domestic chicken (Gallus gallus domesticus) is the globally most important source of commercially produced meat. While genetic approaches have played an important role in the development of chicken stocks, little is known about chicken epigenetics. We have systematically analyzed the chicken DNA methylation machinery and DNA methylation landscape. While overall DNA methylation distribution was similar to mammals, sperm DNA appeared hypomethylated, which correlates with the absence of the DNMT3L cofactor in the chicken genome. Additional analysis revealed the presence of low-methylated regions, which are conserved gene regulatory elements that show tissue-specific methylation patterns. We also used whole-genome bisulfite sequencing to generate 56 single-base resolution methylomes from various tissues and developmental time points to establish an LMR-based DNA methylation clock for broiler chicken age prediction. This clock was used to demonstrate epigenetic age acceleration in animals with experimentally induced inflammation. Our study provides detailed insights into the chicken methylome and suggests a novel application of the DNA methylation clock as a marker for livestock health. Raddatz, Lyko and colleagues use whole-genome bisulfite sequencing data to generate a methylation clock for chicken. This clock was able to detect age acceleration in broiler chickens under experimentally induced inflammation.
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11
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Li-Byarlay H, Boncristiani H, Howell G, Herman J, Clark L, Strand MK, Tarpy D, Rueppell O. Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection. Front Genet 2020; 11:566320. [PMID: 33101388 PMCID: PMC7546774 DOI: 10.3389/fgene.2020.566320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022] Open
Abstract
Honey bees (Apis mellifera L.) suffer from many brood pathogens, including viruses. Despite considerable research, the molecular responses and dynamics of honey bee pupae to viral pathogens remain poorly understood. Israeli Acute Paralysis Virus (IAPV) is emerging as a model virus since its association with severe colony losses. Using worker pupae, we studied the transcriptomic and methylomic consequences of IAPV infection over three distinct time points after inoculation. Contrasts of gene expression and 5 mC DNA methylation profiles between IAPV-infected and control individuals at these time points - corresponding to the pre-replicative (5 h), replicative (20 h), and terminal (48 h) phase of infection - indicate that profound immune responses and distinct manipulation of host molecular processes accompany the lethal progression of this virus. We identify the temporal dynamics of the transcriptomic response to with more genes differentially expressed in the replicative and terminal phases than in the pre-replicative phase. However, the number of differentially methylated regions decreased dramatically from the pre-replicative to the replicative and terminal phase. Several cellular pathways experienced hyper- and hypo-methylation in the pre-replicative phase and later dramatically increased in gene expression at the terminal phase, including the MAPK, Jak-STAT, Hippo, mTOR, TGF-beta signaling pathways, ubiquitin mediated proteolysis, and spliceosome. These affected biological functions suggest that adaptive host responses to combat the virus are mixed with viral manipulations of the host to increase its own reproduction, all of which are involved in anti-viral immune response, cell growth, and proliferation. Comparative genomic analyses with other studies of viral infections of honey bees and fruit flies indicated that similar immune pathways are shared. Our results further suggest that dynamic DNA methylation responds to viral infections quickly, regulating subsequent gene activities. Our study provides new insights of molecular mechanisms involved in epigenetic that can serve as foundation for the long-term goal to develop anti-viral strategies for honey bees, the most important commercial pollinator.
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Affiliation(s)
- Hongmei Li-Byarlay
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Humberto Boncristiani
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Gary Howell
- High Performance Cluster, Office of Information Technology, North Carolina State University, Raleigh, NC, United States
| | - Jake Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Lindsay Clark
- High Performance Computing in Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Micheline K. Strand
- Army Research Office, Army Research Laboratory, Research Triangle Park, NC, United States
| | - David Tarpy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, United States
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
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12
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Sui C, Wang Q, Zhou Y, Zhang D, Yin H, Ai S. Homogeneous detection of 5-hydroxymethylcytosine based on electrochemiluminescence quenching of g-C 3N 4/MoS 2 nanosheets by ferrocenedicarboxylic acid polymer. Talanta 2020; 219:121211. [PMID: 32887114 DOI: 10.1016/j.talanta.2020.121211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 01/02/2023]
Abstract
A sensitively homogeneous electrochemiluminescence (ECL) method was developed for 5-hydroxymethylcytosine (5hmC) detection using TiO2/MoS2/g-C3N4/GCE as substrate electrode, where g-C3N4 was employed as the ECL active material, the MoS2 nanosheets were used as co-catalyst, and TiO2 was adopted as phosphate group capture reagent. To achieve the specific recognition and capture of 5hmC, the covalent reaction between -CH2OH and -SH was employed under the catalysis of HhaI methyltransferase, in which, -SH functionalized ferrocenedicarboxylic acid polymer (PFc-SH) was prepared as 5hmC capture reagent and ECL signal quencher. Then, based on the interaction between TiO2 and phosphate group of 5hmC, the target was recognized and captured on electrode, resulting in a decreased ECL response due to the quenching effect of PFc-SH. Under optimal conditions, the biosensor presented the linear range from 0.01 to 500 nM with the detection limit of 3.21 pM (S/N = 3). The steric effect on electrode surface is a bottle-neck issue restricting devised biosensors advancement. In this work, the reaction between 5hmC and PFc was carried out in the solution, which can avoid steric effect on electrode surface to keep the high activity of enzyme. In addition, the biosensor was successfully applied to detect 5hmC in genomic DNA of chicken embryo fibroblast cells and different tissues of rice seedlings.
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Affiliation(s)
- Chengji Sui
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Qian Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Dingding Zhang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Thompson RP, Nilsson E, Skinner MK. Environmental epigenetics and epigenetic inheritance in domestic farm animals. Anim Reprod Sci 2020; 220:106316. [PMID: 32094003 DOI: 10.1016/j.anireprosci.2020.106316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/26/2023]
Abstract
Epigenetics refers to molecular factors and processes around DNA that can affect genome activity and gene expression independent of DNA sequence. Epigenetic mechanisms drive developmental processes and have also been shown to be tied to disease development. Many epigenetic studies have been done using plants, rodent, and human models, but fewer have focused on domestic livestock species. The goal of this review is to present current epigenetic findings in livestock species (cattle, pigs, sheep and poultry). Much of this research examined epigenetic effects following exposure to toxicants, nutritional changes or infectious disease in those animals directly exposed, or in the offspring they produced. A limited number of studies in domestic animals have examined epigenetic transgenerational inheritance in the absence of continued exposures. One example used a porcine model to investigate the effect that feeding males a diet supplemented with micronutrients had on liver DNA methylation and muscle mass in grand-offspring (the transgenerational F2 generation). Further research into how epigenetic mechanisms affect the health and production traits of domestic livestock and their offspring is important to elucidate.
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Affiliation(s)
- Ryan P Thompson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA.
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15
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Alkie TN, Yitbarek A, Hodgins DC, Kulkarni RR, Taha-Abdelaziz K, Sharif S. Development of innate immunity in chicken embryos and newly hatched chicks: a disease control perspective. Avian Pathol 2019; 48:288-310. [PMID: 31063007 DOI: 10.1080/03079457.2019.1607966] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Newly hatched chickens are confronted by a wide array of pathogenic microbes because their adaptive immune defences have limited capabilities to control these pathogens. In such circumstances, and within this age group, innate responses provide a degree of protection. Moreover, as the adaptive immune system is relatively naïve to foreign antigens, synergy with innate defences is critical. This review presents knowledge on the ontogeny of innate immunity in chickens pre-hatch and early post-hatch and provides insights into possible interventions to modulate innate responses early in the life of the bird. As in other vertebrate species, the chicken innate immune system which include cellular mediators, cytokine and chemokine repertoires and molecules involved in antigen detection, develop early in life. Comparison of innate immune systems in newly hatched chickens and mature birds has revealed differences in magnitude and quality, but responses in younger chickens can be boosted using innate immune system modulators. Functional expression of pattern recognition receptors and several defence molecules by innate immune system cells of embryos and newly hatched chicks suggests that innate responses can be modulated at this stage of development to combat pathogens. Improved understanding of innate immune system ontogeny and functionality in chickens is critical for the implementation of sound and safe interventions to provide long-term protection against pathogens. Next-generation tools for studying genetic and epigenetic regulation of genes, functional metagenomics and gene knockouts can be used in the future to explore and dissect the contributions of signalling pathways of innate immunity and to devise more efficacious disease control strategies.
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Affiliation(s)
- Tamiru N Alkie
- a Department of Pathobiology, Ontario Veterinary College , University of Guelph , Guelph , ON , Canada
| | - Alexander Yitbarek
- a Department of Pathobiology, Ontario Veterinary College , University of Guelph , Guelph , ON , Canada
| | - Douglas C Hodgins
- a Department of Pathobiology, Ontario Veterinary College , University of Guelph , Guelph , ON , Canada
| | - Raveendra R Kulkarni
- a Department of Pathobiology, Ontario Veterinary College , University of Guelph , Guelph , ON , Canada
| | - Khaled Taha-Abdelaziz
- a Department of Pathobiology, Ontario Veterinary College , University of Guelph , Guelph , ON , Canada.,b Pathology Department, Faculty of Veterinary Medicine , Beni-Suef University , Beni-Suef , Egypt
| | - Shayan Sharif
- a Department of Pathobiology, Ontario Veterinary College , University of Guelph , Guelph , ON , Canada
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Gga-miR-130b-3p inhibits MSB1 cell proliferation, migration, invasion, and its downregulation in MD tumor is attributed to hypermethylation. Oncotarget 2018; 9:24187-24198. [PMID: 29849932 PMCID: PMC5966247 DOI: 10.18632/oncotarget.24679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/27/2018] [Indexed: 01/07/2023] Open
Abstract
Marek's disease is an oncogenic and lymphoproliferative disease of chickens caused by Marek's disease virus. Hypermethylation or hypomethylation of CpG islands in gene promoter region are involved in the initiation and progression of carcinogenesis. In this study, we analyzed differential methylation levels of upstream region of gga-miR-130b-3p gene between Marek's disease virus-infected tumorous and non-infected spleens. Around the upstream 1 kb of gga-miR-130b-3p gene, two amplicons were designed that covered 616 bp. There were forty-eight CpG sites in this region. CpG sites in this region presented higher methylation level in tumorous spleens compared with that in non-infected ones. There were eight CpG sites significantly hypermethylated in tumorous spleens. The expression level of three DNA methyltransferases including DNMT1, DNMT3a and DNMT3b increased and the expression level of Tet ten-eleven translocation protein 2 remarkably decreased in tumorous spleens. Hypermethylation in the upstream region of gga-miR-130b-3p gene might be a direct reason for its downregulation in MD tumorous tissues. Moreover, cell proliferation of Marek's disease lymphoblastoid cell line MDCC-MSB1 was remarkably inhibited at 24, 36, 48, 60 and 72 h post-gga-miR-130b-3p-agomir transfection. The transwell migration assay indicated cell number of migration was significantly lower in miRNA agomir transfection group. Matrix metalloproteinases MMP2 and MMP9 are involved in tumor invasion, and their protein levels were significantly downregulated at 72 h post-miRNA-agomir transfection. Collectively, these results indicated that hypermethylation in upstream region of gga-miR-130b-3p gene contributed to its downregulation in tumorous tissues. Gga-miR-130b-3p plays an inhibitory role in lymphomatous cell transformation.
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Global and Complement Gene-Specific DNA Methylation in Grass Carp after Grass Carp Reovirus (GCRV) Infection. Int J Mol Sci 2018; 19:ijms19041110. [PMID: 29642440 PMCID: PMC5979442 DOI: 10.3390/ijms19041110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 11/17/2022] Open
Abstract
Grass carp reovirus (GCRV) causes huge economic loss to the grass carp cultivation industry but the mechanism remains largely unknown. In this study, we investigated the global and complement gene-specific DNA methylation in grass carp after GCRV infection aimed to uncover the mechanism underlying GCRV infection. The global DNA methylation level was increased after GCRV infection. Expression levels of enzymes involved in DNA methylation including DNA methyltransferase (DNMT), ten-eleven translocation proteins (TETs), and glycine N-methyltransferase (GNMT) were significantly altered after GCRV infection. In order to investigate the relationship between the gene expression level and DNA methylation level, two representative complement genes, complement component 3 (C3) and kininogen-1 (KNG1), were selected for further analysis. mRNA expression levels of the two genes were significantly increased at 5 and 7 days after GCRV infection, whereas the DNA methylation level at the 5′ flanking regions of the two genes were down-regulated at the same time-points. Moreover, a negative correlation was detected between gene expression levels and DNA methylation levels of the two genes. Therefore, the current data revealed a global and complement gene-specific DNA methylation profile after GCRV infection. Our study would provide new insights into understanding the mechanism underlying GCRV infection.
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Bélteky J, Agnvall B, Bektic L, Höglund A, Jensen P, Guerrero-Bosagna C. Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans. Genet Sel Evol 2018; 50:13. [PMID: 29609558 PMCID: PMC5880090 DOI: 10.1186/s12711-018-0384-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
Background Domestication of animals leads to large phenotypic alterations within a short evolutionary time-period. Such alterations are caused by genomic variations, yet the prevalence of modified traits is higher than expected if they were caused only by classical genetics and mutations. Epigenetic mechanisms may also be important in driving domesticated phenotypes such as behavior traits. Gene expression can be modulated epigenetically by mechanisms such as DNA methylation, resulting in modifications that are not only variable and susceptible to environmental stimuli, but also sometimes transgenerationally stable. To study such mechanisms in early domestication, we used as model two selected lines of red junglefowl (ancestors of modern chickens) that were bred for either high or low fear of humans over five generations, and investigated differences in hypothalamic DNA methylation between the two populations. Results Twenty-two 1-kb windows were differentially methylated between the two selected lines at p < 0.05 after false discovery rate correction. The annotated functions of the genes within these windows indicated epigenetic regulation of metabolic and signaling pathways, which agrees with the changes in gene expression that were previously reported for the same tissue and animals. Conclusions Our results show that selection for an important domestication-related behavioral trait such as tameness can cause divergent epigenetic patterns within only five generations, and that these changes could have an important role in chicken domestication. Electronic supplementary material The online version of this article (10.1186/s12711-018-0384-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johan Bélteky
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Beatrix Agnvall
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Lejla Bektic
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Andrey Höglund
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Per Jensen
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden
| | - Carlos Guerrero-Bosagna
- AVIAN Behavioural Physiology and Genomics Group, IFM Biology, Linköping University, 581 83, Linköping, Sweden.
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Zhang Z, Du H, Bai L, Yang C, Li Q, Li X, Qiu M, Yu C, Jiang Z, Jiang X, Liu L, Hu C, Xia B, Xiong X, Song X, Jiang X. Whole genome bisulfite sequencing reveals unique adaptations to high-altitude environments in Tibetan chickens. PLoS One 2018; 13:e0193597. [PMID: 29561872 PMCID: PMC5862445 DOI: 10.1371/journal.pone.0193597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 02/14/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Tibetan chickens living at high altitudes show specific adaptations to high-altitude conditions, but the epigenetic modifications associated with these adaptations have not been characterized. RESULTS We investigated the genome-wide DNA methylation patterns in Tibetan chicken blood by using whole genome bisulfite sequencing. Generally, Tibetan chickens exhibited analogous methylation patterns to that of lowland chickens. A total of 3.92% of genomic cytosines were methylcytosines and 51.22% of cytosines in CG contexts were methylated, which was less than those in lowland chicken (55.69%). Moreover, the base adjacent to the methylcytosines of mCHGs in Tibetan chickens had a preference for T, which was different from that in lowland chickens. In Tibetan chickens, the methylation levels in the promoter were relatively low, while the gene body was also maintained in a hypomethylated state. DNA methylation levels in regions upstream of the transcription start site of genes were negatively correlated with the level of gene expression, and DNA methylation of gene body regions was also negatively related to gene expression. CONCLUSIONS We generated the genome-wide DNA methylation patterns in Tibetan chickens and our results will be helpful for future epigenetic studies related to adaptations to high-altitude conditions.
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Affiliation(s)
- Zengrong Zhang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Huarui Du
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | | | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Qingyun Li
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaocheng Li
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Mohan Qiu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Chunlin Yu
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Zongrong Jiang
- Ganzi Animal Science institute, Ganzi Tibetan Autonomous Prefecture, Kangding, Sichuan, China
| | - Xiaoyu Jiang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Lan Liu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Chenming Hu
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Bo Xia
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xia Xiong
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaoyan Song
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaosong Jiang
- Sichuan Animal Science Academy, Chengdu, Sichuan, China
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, China
- * E-mail:
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Protective vaccination and blood-stage malaria modify DNA methylation of gene promoters in the liver of Balb/c mice. Parasitol Res 2017; 116:1463-1477. [PMID: 28315013 DOI: 10.1007/s00436-017-5423-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/08/2017] [Indexed: 02/07/2023]
Abstract
Epigenetic mechanisms such as DNA methylation are increasingly recognized to be critical for vaccination efficacy and outcome of different infectious diseases, but corresponding information is scarcely available for host defense against malaria. In the experimental blood-stage malaria Plasmodium chabaudi, we investigate the possible effects of a blood-stage vaccine on DNA methylation of gene promoters in the liver, known as effector against blood-stage malaria, using DNA methylation microarrays. Naturally susceptible Balb/c mice acquire, by protective vaccination, the potency to survive P. chabaudi malaria and, concomitantly, modifications of constitutive DNA methylation of promoters of numerous genes in the liver; specifically, promoters of 256 genes are hyper(=up)- and 345 genes are hypo(=down)-methylated (p < 0.05). Protective vaccination also leads to changes in promoter DNA methylation upon challenge with P. chabaudi at peak parasitemia on day 8 post infection (p.i.), when 571 and 1013 gene promoters are up- and down-methylated, respectively, in relation to constitutive DNA methylation (p < 0.05). Gene set enrichment analyses reveal that both vaccination and P. chabaudi infections mainly modify promoters of those genes which are most statistically enriched with functions relating to regulation of transcription. Genes with down-methylated promoters encompass those encoding CX3CL1, GP130, and GATA2, known to be involved in monocyte recruitment, IL-6 trans-signaling, and onset of erythropoiesis, respectively. Our data suggest that vaccination may epigenetically improve parts of several effector functions of the liver against blood-stage malaria, as, e.g., recruitment of monocyte/macrophage to the liver accelerated liver regeneration and extramedullary hepatic erythropoiesis, thus leading to self-healing of otherwise lethal P. chabaudi blood-stage malaria.
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Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont SJ, Hu S, Zhou H, Li N. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics 2015; 16:851. [PMID: 26497311 PMCID: PMC4619007 DOI: 10.1186/s12864-015-2098-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/15/2015] [Indexed: 12/30/2022] Open
Abstract
Background DNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals. Avian species hold a crucial position in evolutionary history. In this study, we used whole-genome bisulfite sequencing (MethylC-seq) to generate single base methylation profiles of lungs in two genetically distinct and highly inbred chicken lines (Fayoumi and Leghorn) that differ in genetic resistance to multiple pathogens, and we explored the potential regulatory role of DNA methylation associated with immune response differences between the two chicken lines. Methods The MethylC-seq was used to generate single base DNA methylation profiles of Fayoumi and Leghorn birds. In addition, transcriptome profiling using RNA–seq from the same chickens and tissues were obtained to interrogate how DNA methylation regulates gene transcription on a genome-wide scale. Results The general DNA methylation pattern across different regions of genes was conserved compared to other species except for hyper-methylation of repeat elements, which was not observed in chicken. The methylation level of miRNA and pseudogene promoters was high, which indicates that silencing of these genes may be partially due to promoter hyper-methylation. Interestingly, the promoter regions of more recently evolved genes tended to be more highly methylated, whereas the gene body regions of evolutionarily conserved genes were more highly methylated than those of more recently evolved genes. Immune-related GO (Gene Ontology) terms were significantly enriched from genes within the differentially methylated regions (DMR) between Fayoumi and Leghorn, which implicates DNA methylation as one of the regulatory mechanisms modulating immune response differences between these lines. Conclusions This study establishes a single-base resolution DNA methylation profile of chicken lung and suggests a regulatory role of DNA methylation in controlling gene expression and maintaining genome transcription stability. Furthermore, profiling the DNA methylomes of two genetic lines that differ in disease resistance provides a unique opportunity to investigate the potential role of DNA methylation in host disease resistance. Our study provides a foundation for future studies on epigenetic modulation of host immune response to pathogens in chickens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2098-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinxiu Li
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rujiao Li
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Xiaoxiang Hu
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yiqiang Zhao
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Li Li
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chungang Feng
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaorong Gu
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Fang Liang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA. .,Department of Poultry Science, Texas A&M University, College Station, TX, 77845, USA.
| | - Ning Li
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China. .,National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China. .,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Carrillo JA, He Y, Luo J, Menendez KR, Tablante NL, Zhao K, Paulson JN, Li B, Song J. Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine. PLoS One 2015; 10:e0100476. [PMID: 26107953 PMCID: PMC4481310 DOI: 10.1371/journal.pone.0100476] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/25/2014] [Indexed: 01/08/2023] Open
Abstract
In this study we investigated the methylome of chickens immunized with Infectious laryngotracheitis (ILT) vaccine derived from chicken embryos. Methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq) method was employed in the detection of the 1,155 differentially methylated regions (DMRs) across the entire genome. After validation, we ascertained the genomic DMRs distribution and annotated them regarding genes, transcription start sites (TSS) and CpG islands. We found that global DNA methylation decreased in vaccinated birds, presenting 704 hypomethylated and 451 hypermethylated DMRs, respectively. Additionally, we performed an enrichment analysis detecting gene networks, in which cancer and RNA post-transcriptional modification appeared in the first place, followed by humoral immune response, immunological disease and inflammatory disease. The top four identified canonical pathways were EIF2 signaling, regulation of EIF4 and p70S6K signaling, axonal guidance signaling and mTOR signaling, providing new insight regarding the mechanisms of ILT etiology. Lastly, the association between DNA methylation and differentially expressed genes was examined, and detected negative correlation in seventeen of the eighteen genes.
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Affiliation(s)
- José A. Carrillo
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Yanghua He
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Juan Luo
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Kimberly R. Menendez
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Nathaniel L. Tablante
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America
| | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joseph N. Paulson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Bichun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou City, Jiangsu Province, P. R. China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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Feeney A, Nilsson E, Skinner MK. Epigenetics and transgenerational inheritance in domesticated farm animals. J Anim Sci Biotechnol 2014; 5:48. [PMID: 25810901 PMCID: PMC4373098 DOI: 10.1186/2049-1891-5-48] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/14/2014] [Indexed: 01/10/2023] Open
Abstract
Epigenetics provides a molecular mechanism of inheritance that is not solely dependent on DNA sequence and that can account for non-Mendelian inheritance patterns. Epigenetic changes underlie many normal developmental processes, and can lead to disease development as well. While epigenetic effects have been studied in well-characterized rodent models, less research has been done using agriculturally important domestic animal species. This review will present the results of current epigenetic research using farm animal models (cattle, pigs, sheep and chickens). Much of the work has focused on the epigenetic effects that environmental exposures to toxicants, nutrients and infectious agents has on either the exposed animals themselves or on their direct offspring. Only one porcine study examined epigenetic transgenerational effects; namely the effect diet micronutrients fed to male pigs has on liver DNA methylation and muscle mass in grand-offspring (F2 generation). Healthy viable offspring are very important in the farm and husbandry industry and epigenetic differences can be associated with production traits. Therefore further epigenetic research into domestic animal health and how exposure to toxicants or nutritional changes affects future generations is imperative.
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Affiliation(s)
- Amanda Feeney
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, 99164-4236 Pullman, WA USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, 99164-4236 Pullman, WA USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, 99164-4236 Pullman, WA USA
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