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Yi M, Asgenbaatar N, Wang X, Ulaangerel T, Shen Y, Wen X, Du M, Dong X, Dugarjav M, Bou G. Different expression patterns of DNA methyltransferases during horse testis development. Gene 2024; 920:148531. [PMID: 38705424 DOI: 10.1016/j.gene.2024.148531] [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: 02/22/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
DNA methyltransferases (DNMTs) are important epigenetic modification during spermatogenesis. To further evaluate the pattern of DNMTs in horse testes during development, we investigated the expression and localization of DNMT1, DNMT3a and DNMT3b at different time points. The qRT-PCR results showed that DNMT1 expression was maintained in testes tissue from 6-month-old (0.5y) to 2-year-old (2y) of age and decreased after 3-year-old (3y) (P < 0.01). The expression levels of DNMT3a and DNMT3b peaked in testes tissue at 3y (P < 0.01). At 4-year-old (4y), the expression of DNMT3a and DNMT3b was decreased and became similar to that at 0.5y. Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development. Further molecular biological studies are needed to understand the implications of the expression patterns of these DNMTs in horse testes.
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Affiliation(s)
- Minna Yi
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Nairag Asgenbaatar
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China; Da Bei Nong group rumination technology rumination acadamy Haidian District, Beijing, China
| | - Xisheng Wang
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China; Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Tseweendolmaa Ulaangerel
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Yingchao Shen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Wen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Ming Du
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoling Dong
- Da Bei Nong group rumination technology rumination acadamy Haidian District, Beijing, China; China Agricultural University, Beijing, China
| | - Manglai Dugarjav
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
| | - Gerelchimeg Bou
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
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Vasileva F, Hristovski R, Font-Lladó R, Georgiev G, Sacot A, López-Ros V, Calleja-González J, Barretina-Ginesta J, López-Bermejo A, Prats-Puig A. Physical Exercise-Induced DNA Methylation in Disease-Related Genes in Healthy Adults-A Systematic Review With Bioinformatic Analysis. J Strength Cond Res 2024; 38:384-393. [PMID: 38088908 DOI: 10.1519/jsc.0000000000004686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
ABSTRACT Vasileva, F, Hristovski, R, Font-Lladó, R, Georgiev, G, Sacot, A, López-Ros, V, Calleja-González, J, Barretina-Ginesta, J, López-Bermejo, A, and Prats-Puig, A. Physical exercise-induced DNA methylation in disease-related genes in healthy adults-A systematic review with bioinformatic analysis. J Strength Cond Res 38(2): 384-393, 2024-This study aimed to systematically review the existing literature regarding physical exercise (PE) and DNA methylation (DNAm) in healthy adults. Specific goals were to (a) identify differently methylated genes (DMGs) after PE intervention, their imprinting status, chromosome and genomic location, function, and related diseases; and (b) to screen for core genes and identify methylation changes of the core genes that can be modified by PE intervention. Our search identified 2,869 articles from which 8 were finally included. We identified 1851 DMGs ( p < 0.05) after PE intervention, although 45 of them were imprinted. Aerobic exercise (AE) seems to induce more DNA hypermethylation rather than hypomethylation, whereas anaerobic exercise (AN) seems to induce more DNA hypomethylation rather than hypermethylation. Aerobic exercise induced highest % of methylation changes on chromosome 6, whereas AN and mixed type (MT) on chromosome 1. Mixed type induced higher % of methylation changes close to transcription start site in comparison to AE and AN. After PE intervention, DMGs were mainly involved in fat metabolism, cell growth, and neuronal differentiation, whereas diseases regulated by those genes were mainly chronic diseases (metabolic, cardiovascular, neurodegenerative). Finally, 19 core genes were identified among DMGs, all related to protein metabolism. In conclusion, our findings may shed some light on the mechanisms explaining PE-induced health benefits such as the potential role that PE-induced DNAm may have in disease prevention and disease treatment.
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Affiliation(s)
- Fidanka Vasileva
- University School of Health and Sport, University of Girona, Girona, Spain
- Pediatric Endocrinology Research Group, Girona Institute for Biomedical Research, Girona, Spain
| | - Robert Hristovski
- Faculty of Physical Education, Sport and Health, University Ss. Cyril and Methodius, Skopje, Republic of North Macedonia
| | - Raquel Font-Lladó
- University School of Health and Sport, University of Girona, Girona, Spain
- Research Group of Culture and Education, Institute of Educational Research, University of Girona, Girona, Spain
| | - Georgi Georgiev
- Faculty of Physical Education, Sport and Health, University Ss. Cyril and Methodius, Skopje, Republic of North Macedonia
| | - Arnau Sacot
- University School of Health and Sport, University of Girona, Girona, Spain
- Basquet Girona, Girona, Spain
| | - Víctor López-Ros
- University School of Health and Sport, University of Girona, Girona, Spain
- Chair of Sport and Physical Education-Centre of Olympic Studies, University of Girona, Girona, Spain
| | - Julio Calleja-González
- Department of Physical Education and Sport, Faculty of Education and Sport, University of the Basque Country, Vitoria, Spain
| | | | - Abel López-Bermejo
- Pediatric Endocrinology Research Group, Girona Institute for Biomedical Research, Girona, Spain
- Pediatric Endocrinology, Dr. Josep Girona Hospital, Girona, Spain
- Department of Medical Sciences, University of Girona, Girona, Spain; and
| | - Anna Prats-Puig
- University School of Health and Sport, University of Girona, Girona, Spain
- Research Group of Clinical Anatomy, Embryology and Neuroscience, Department of Medical Sciences, University of Girona, Girona, Spain
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Cappelli K, Mecocci S, Porceddu A, Albertini E, Giontella A, Miglio A, Silvestrelli M, Verini Supplizi A, Marconi G, Capomaccio S. Genome-wide epigenetic modifications in sports horses during training as an adaptation phenomenon. Sci Rep 2023; 13:18786. [PMID: 37914824 PMCID: PMC10620398 DOI: 10.1038/s41598-023-46043-w] [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: 07/06/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
With his bicentennial breeding history based on athletic performance, the Thoroughbred horse can be considered the equine sport breed. Although genomic and transcriptomic tools and knowledge are at the state of the art in equine species, the epigenome and its modifications in response to environmental stimuli, such as training, are less studied. One of the major epigenetic modifications is cytosine methylation at 5' of DNA molecules. This crucial biochemical modification directly mediates biological processes and, to some extent, determines the organisms' phenotypic plasticity. Exercise indeed affects the epigenomic state, both in humans and in horses. In this study, we highlight, with a genome-wide analysis of methylation, how the adaptation to training in the Thoroughbred can modify the methylation pattern throughout the genome. Twenty untrained horses, kept under the same environmental conditions and sprint training regimen, were recruited, collecting peripheral blood at the start of the training and after 30 and 90 days. Extracted leukocyte DNA was analyzed with the methylation content sensitive enzyme ddRAD (MCSeEd) technique for the first time applied to animal cells. Approximately one thousand differently methylated genomic regions (DMRs) and nearby genes were called, revealing that methylation changes can be found in a large part of the genome and, therefore, referable to the physiological adaptation to training. Functional analysis via GO enrichment was also performed. We observed significant differences in methylation patterns throughout the training stages: we hypothesize that the methylation profile of some genes can be affected early by training, while others require a more persistent stimulus.
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Affiliation(s)
- Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Samanta Mecocci
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy.
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy.
| | - Andrea Porceddu
- Department of Agraria, University of Sassari, 06123, Sassari, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Arianna Miglio
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Andrea Verini Supplizi
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
| | - Gianpiero Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, 06123, Perugia, Italy
- Sports Horse Research Center (CRCS), University of Perugia, 06123, Perugia, Italy
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Reißmann M, Rajavel A, Kokov ZA, Schmitt AO. Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability. Genes (Basel) 2023; 14:1982. [PMID: 38002925 PMCID: PMC10671444 DOI: 10.3390/genes14111982] [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: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses (Equus caballus) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1, CCL5, CD40LG, FOS, IL1R2, IL20RA, and IL22RA2, on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2, GYG1, HIF1A, MOGAT1, PFKFB3, PLIN5, SIK1, and STBD1.
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Affiliation(s)
- Monika Reißmann
- Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Zaur A. Kokov
- Institute of Physics and Mathematics, Kabardino-Balkarian State University, Chernyshevsky 173, Nalchik 360004, Russia;
| | - Armin O. Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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6
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Orellana-Guerrero D, Uribe-Salazar JM, El-Sheikh Ali H, Scoggin KE, Ball B, Daels P, Finno CJ, Dini P. Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation. Int J Mol Sci 2023; 24:ijms24087084. [PMID: 37108254 PMCID: PMC10139181 DOI: 10.3390/ijms24087084] [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: 03/04/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The placenta is a temporary organ that is essential for the survival of the fetus, with a lifelong effect on the health of both the offspring and the dam. The functions of the placenta are controlled by its dynamic gene expression during gestation. In this study, we aimed to investigate the equine placental DNA methylome as one of the fundamental mechanisms that controls the gene expression dynamic. Chorioallantois samples from four (4M), six (6M), and ten (10M) months of gestation were used to map the methylation pattern of the placenta. Globally, methylation levels increased toward the end of gestation. We identified 921 differentially methylated regions (DMRs) between 4M and 6M, 1225 DMRs between 4M and 10M, and 1026 DMRs between 6M and 10M. A total of 817 genes carried DMRs comparing 4M and 6M, 978 comparing 4M and 10M, and 804 comparing 6M and 10M. We compared the transcriptomes between the samples and found 1381 differentially expressed genes (DEGs) when comparing 4M and 6M, 1428 DEGs between 4M and 10M, and 741 DEGs between 6M and 10M. Finally, we overlapped the DEGs and genes carrying DMRs (DMRs-DEGs). Genes exhibiting (a) higher expression, low methylation and (b) low expression, high methylation at different time points were identified. The majority of these DMRs-DEGs were located in introns (48.4%), promoters (25.8%), and exons (17.7%) and were involved in changes in the extracellular matrix; regulation of epithelial cell migration; vascularization; and regulation of minerals, glucose, and metabolites, among other factors. Overall, this is the first report highlighting the dynamics in the equine placenta methylome during normal pregnancy. The findings presented serve as a foundation for future studies on the impact of abnormal methylation on the outcomes of equine pregnancies.
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Affiliation(s)
- Daniela Orellana-Guerrero
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | | | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
- College of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Barry Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Peter Daels
- Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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7
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Liu L, Zhang Y, Ma H, Cao H, Liu W. Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses. Gene 2023; 856:147143. [PMID: 36574934 DOI: 10.1016/j.gene.2022.147143] [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: 07/28/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Horse Milk has important quantitative characteristics and high economic value. However, the DNA methylation regulators involved in horse milk traits have not been clarified. To explore the important role of genome-wide DNA methylation in regulating equine milk yield, this study systematically investigated the genome-wide DNA methylation profiles of Kazakh horse blood by comparing a high-production group (HP, average daily milk yield of 7.5 kg) and low-production group (LP, average daily milk yield of 3.2 kg) using deep whole-genome bisulfite sequencing. First, both groups showed similar proportions of methylation at CpG sites. Subsequently, we identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG, 480 DMRs of CHH and 8268 DMR-related genes (DMGs). GO and KEGG analyses revealed that some DMGs were involved in regulating milk and milk component formation. By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlapping genes were obtained. Finally, we found that 9 DMGs are likely involved in milk production by Kazakh horses.
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Affiliation(s)
- Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yunting Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haiyu Ma
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
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8
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Li Q, Yan RF, Yang YX, Mi CL, Jia YL, Wang TY. Stabilizing and Anti-Repressor Elements Effectively Increases Transgene Expression in Transfected CHO Cells. Front Bioeng Biotechnol 2022; 10:840600. [PMID: 35721852 PMCID: PMC9199445 DOI: 10.3389/fbioe.2022.840600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are currently the most widely used host cells for recombinant therapeutic protein (RTP) production. Currently, the RTP yields need to increase further to meet the market needs and reduce costs. In this study, three stabilizing and anti-repressor (SAR) elements from the human genome were selected, including human SAR7, SAR40, and SAR44 elements. SAR elements were cloned upstream of the promoter in the eukaryotic vector, followed by transfection into CHO cells, and were screened under G418 pressure. Flow cytometry was used to detect enhanced green fluorescent protein (eGFP) expression levels. The gene copy numbers and mRNA expression levels were determined through quantitative real-time PCR. Furthermore, the effect of the stronger SAR elements on adalimumab was investigated. The results showed that transgene expression levels in the SAR-containing vectors were higher than that of the control vector, and SAR7 and SAR40 significantly increased and maintained the long-term expression of the transgene in CHO cells. In addition, the transgene expression level increase was related with gene copy numbers and mRNA expression levels. Collectively, SAR elements can enhance the transgene expression and maintain the long-term expression of a transgene in transfected CHO cells, which may be used to increase recombinant protein production in CHO cells.
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Affiliation(s)
- Qin Li
- School of Basic Medicine, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Rui-Fang Yan
- School of Basic Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yong-Xiao Yang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Chun-Liu Mi
- School of Basic Medicine, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Yan-Long Jia
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- School of Basic Medicine, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
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9
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Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep. Animals (Basel) 2022; 12:ani12111399. [PMID: 35681863 PMCID: PMC9179529 DOI: 10.3390/ani12111399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary DNA methylation is an important epigenetic modification and plays an important role in the regulation of gene expression. The study of DNA methylation will help to explore the effects of epigenetic modifications, other than DNA sequence variation, on biological phenotypes and physiological functions, promoting the revolution of livestock selection and breeding practices. DairyMeade sheep (thin-tailed) and Mongolian sheep (fat-tailed) have large differences in their dairy and meat production performances, as well as their tail phenotype, thus providing us with good materials for genomic DNA methylation studies. The below results provided a genome-wide DNA methylation landscape of muscle and tail-fat tissues between DairyMeade sheep and Mongolian sheep and a series of differentiated methylation regions (DMRs) in which CAMK2D may play a crucial role in fat metabolism and meat quality traits. These results may help us to understand how DNA methylation affects the economic traits of domestic animals like sheep. Abstract This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement.
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10
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Dagra A, Barpujari A, Bauer SZ, Olowofela BO, Mohamed S, McGrath K, Robinson C, Robicsek S, Snyder A, Lucke-Wold B. Epigenetics of Neurotrauma. NEUROLOGY (CHICAGO, ILL.) 2022; 2:42-47. [PMID: 36507115 PMCID: PMC9732507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epigenetic changes have been linked to a host of disease states. Besides the physiological function of epigenetic changes in regulating cellular function, recent data indicates that key changes in epigenetic activity also play an important pathophysiologic role following neurotrauma specifically. Such manifestations occur through the activation or silencing of different genes. Histone methylation has emerged as a critical component of this process and can be selectively modulated after injury. Pre-clinical studies have resulted in key discoveries regarding specific methylation sites of interest. This focused review highlights some of these early findings and their relationship to clinical outcomes. These findings suggest areas of future investigation and discovery in the quest to develop ideal biomarkers and methods to utilize them in developing therapeutic interventions.
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Affiliation(s)
- A Dagra
- College of Medicine, University of Florida, USA
| | - A Barpujari
- College of Liberal Arts and Sciences, University of Florida, USA
| | - SZ Bauer
- College of Medicine, University of Nevada, USA
| | | | - S Mohamed
- College of Medicine, University of Florida, USA
| | - K McGrath
- College of Medicine, University of Florida, USA
| | - C Robinson
- Departments of Neurology and Neuroscience, McKnight Brain Institute, University of Florida, USA
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, and Brain Injury Rehabilitation and Neuroresilience Center, University of Florida, USA
| | - S Robicsek
- Department of Anesthesiology, University of Florida, USA
| | - A Snyder
- Department of Neuropsychology, University of Florida, USA
| | - B Lucke-Wold
- Department of Neurosurgery, University of Florida, USA
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Lee W, Mun S, Choi SY, Oh DY, Park YS, Han K. Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse. Animals (Basel) 2021; 11:ani11071924. [PMID: 34203473 PMCID: PMC8300358 DOI: 10.3390/ani11071924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary In modern times, horse breeds, mostly in horse racing, are the Thoroughbred varieties obtained by breeding three Godolphin Arabians with British mares in England. Especially in Jeju Island, Korea, Jeju horses have been introduced from Mongolia since the 13th century. They have contributed a lot to the agricultural community, but their population has been rapidly decreasing due to rapid agricultural industrialization. Therefore, we sympathize with Jeju horse-specific genetic variation and compare and analyze evolutionary correlations by utilizing Whole Genome Sequencing analysis to evaluate the genetic diversity of Jeju horses and preserve genetic information. We explored Jeju horse-specific genetic differences through a comparative analysis of large-capacity genomic data between the public database and a Thoroughbred variety. In order to adapt to the barren external environment, it is predicted that Jeju horses have experienced strong positive selection in the direction of accumulating many genetic variations, enough to cause functional differences in the eqCD1a6 gene to have an efficient immune function. In addition, we further validate the Jeju horse-specific single nucleotide polymorphisms in the aqCD1a6 gene by employing the digital PCR method, a diagnostic technique for genetic variations. Abstract The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species.
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Affiliation(s)
- Wooseok Lee
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
| | - Seyoung Mun
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
| | - Song-Yi Choi
- Department of Pathology, Colleage of Medicine, Chungnam National University, Daejeon 34134, Korea;
| | - Dong-Yep Oh
- Livestock Research Institute, Gyeongsangbuk-Do, Yeongju 36052, Korea;
| | - Yong-Soo Park
- Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea
- Correspondence: (Y.-S.P.); (K.H.); Tel.: +82-41-550-1298 (Y.-S.P. & K.H.)
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea; (W.L.); (S.M.)
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan 31116, Korea
- Correspondence: (Y.-S.P.); (K.H.); Tel.: +82-41-550-1298 (Y.-S.P. & K.H.)
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12
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Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HES, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021; 118:e2006474118. [PMID: 33853939 PMCID: PMC8072238 DOI: 10.1073/pnas.2006474118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
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Affiliation(s)
- Pouya Dini
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Theodore Kalbfleisch
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202
| | - José M Uribe-Salazar
- Department of Biochemistry and Molecular Medicine, Genome Center, Medical Investigation of Neurodevelopmental Disorders Institute, University of California, Davis, CA 95616
| | - Mariano Carossino
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, 35516, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Alejandro Esteller-Vico
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Jamie K Norris
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Ernest Bailey
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Peter Daels
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Barry A Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503;
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13
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Wang M, Liang Y, Ibeagha-Awemu EM, Li M, Zhang H, Chen Z, Sun Y, Karrow NA, Yang Z, Mao Y. Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis. Front Genet 2020; 11:550515. [PMID: 33193625 PMCID: PMC7604493 DOI: 10.3389/fgene.2020.550515] [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: 04/09/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) following experimentally induced S. aureus mastitis, and to explore the potential gene regulatory mechanisms affected by DNA methylation during S. aureus mastitis. DNA was extracted from S. aureus-positive (n = 3) and S. aureus-negative (n = 3) mammary gland quarters and subjected to methylation-dependent restriction-site associated DNA sequencing (Methyl-RAD Seq). Results showed that CmCGG/CmCWGG DNA methylation sites were unevenly distributed and concentrated on chromosomes 5, 11, and 19, and within intergenic regions and intron regions of genes. Compared with healthy control quarters, 9,181 significantly differentially methylated (DM) CmCGG sites and 1,790 DM CmCWGG sites were found in the S. aureus-positive quarters (P < 0.05, |log2FC| > 1). Furthermore, 363 CmCGG differently methylated genes (DMGs) and 301 CmCWGG DMGs (adjusted P < 0.05, |log2FC| > 1) were identified. Gene ontology and KEGG enrichment analysis indicated that CmCGG DMGs are involved in immune response pathways, while the CmCWGG DMGs were mainly enriched in gene ontology terms related to metabolism. The mRNAs of 526 differentially methylated CmCGG genes and 124 differentially methylated CmCWGG genes were also significantly differentially expressed (RNA-Seq data) in the same samples, herein denoted differentially methylated and expressed genes (DMEGs) (P < 0.05). Functional enrichment analysis of DMEGs revealed roles related to biological processes, especially the regulation of immune response to diseases. CmCGG DMEGs like IL6R, TNF, BTK, IL1R2, and TNFSF8 enriched in several immune-related GO terms and pathways indicated their important roles in host immune response and their potential as candidate genes for S. aureus mastitis. These results suggest potential regulatory roles for DNA methylation in bovine mammary gland processes during S. aureus mastitis and serves as a reference for future epigenetic regulation and mechanistic studies.
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Affiliation(s)
- Mengqi Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Yan Liang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Mingxun Li
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Huimin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Zhi Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Niel A. Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Zhangping Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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14
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Denham J, McCluskey M, Denham MM, Sellami M, Davie AJ. Epigenetic control of exercise adaptations in the equine athlete: Current evidence and future directions. Equine Vet J 2020; 53:431-450. [PMID: 32671871 DOI: 10.1111/evj.13320] [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: 03/26/2020] [Revised: 06/04/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Horses (Equus ferus caballus) have evolved over the past 300 years in response to man-made selection for particular athletic traits. Some of the selected traits were selected based on the size and horses' muscular power (eg Clydesdales), whereas other breeds were bred for peak running performance (eg Thoroughbred and Arabian). Although the physiological changes and some of the cellular adaptations responsible for athletic potential of horses have been identified, the molecular mechanisms are only just beginning to be comprehensively investigated. The purpose of this review was to outline and discuss the current understanding of the molecular mechanisms underpinning the athletic performance and cardiorespiratory fitness in athletic breeds of horses. A brief review of the biology of epigenetics is provided, including discussion on DNA methylation, histone modifications and small RNAs, followed by a summary and critical review of the current work on the exercise-induced epigenetic and transcriptional changes in horses. Important unanswered questions and currently unexplored areas that deserve attention are highlighted. Finally, a rationale for the analysis of epigenetic modifications in the context with exercise-related traits and ailments associated with athletic breeds of horses is outlined in order to help guide future research.
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Affiliation(s)
- Joshua Denham
- RMIT University, School of Health and Biomedical Sciences, Melbourne, VIC, Australia
| | | | | | - Maha Sellami
- Qatar University, College of Arts and Sciences (CAS), Sport Science Program (SSP), Doha, Qatar
| | - Allan J Davie
- Australian Equine Racing and Research Centre (AERR), Ballina, NSW, Australia
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15
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Abstract
The sequencing and assembly of a reference genome for the horse has been revolutionary for investigation of horse health and performance. Next-generation sequencing (NGS) methods represent a second revolution in equine genomics. Researchers can align and compare DNA and RNA sequencing data to the reference genome to explore variation that may contribute or be attributed to disease. NGS has also facilitated the translation of research discovery to clinically relevant applications. This article discusses the history and development of NGS, details some of the available sequencing platforms, and describes currently available applications in the context of both discovery and clinical settings.
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16
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Zhang J, Luo S, Gu Z, Deng Y, Jiao Y. Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:380-390. [PMID: 32140888 DOI: 10.1007/s10126-020-09957-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from Pinctada fucata martensii. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from P. f. martensii via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of P. f. martensii and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.
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Affiliation(s)
- Jiabin Zhang
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Shaojie Luo
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zefeng Gu
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yuewen Deng
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
- Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province, Zhanjiang, 524088, China
| | - Yu Jiao
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province, Zhanjiang, 524088, China.
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17
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Qian Y, Ji C, Yue S, Zhao M. Exposure of low-dose fipronil enantioselectively induced anxiety-like behavior associated with DNA methylation changes in embryonic and larval zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 249:362-371. [PMID: 30909129 DOI: 10.1016/j.envpol.2019.03.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Fipronil, a broad-spectrum chiral insecticide, has been documented to induce significant neurotoxicity to nontarget aquatic species; however, whether its neurotoxicity behaves enantioselectively and what molecular mechanisms correspond to the neurotoxicity remain unanswered. To date, few investigations have focused on the genomic mechanisms responsible for the enantioselective toxicity of chiral pesticides. The epigenetic modifications, especially DNA methylation, caused by the pesticides are also blind spot of the research works. Video tracking showed that R-fipronil exhibited more intense neurotoxicity, as well as the induction of more severe anxiety-like behavior, such as boosted swimming speed and dysregulated photoperiodic locomotion, to embryonic and larval zebrafish compared with S-fipronil. The MeDIP-Seq analysis, combined with Gene Ontology and KEGG, revealed that R-fipronil disrupted five signaling pathways (MAPK, Calcium signaling, Neuroactive ligand-receptor interaction, Purine metabolism, and Endocytosis) to a greater extent than S-fipronil through the hypermethylation of several important neuro-related genes, whereas no significant alterations of global DNA methylation were observed on the two enantiomers. To summarize, our data indicated that the fipronil-conducted enantioselective neurotoxicity likely applied its enantioselectivity by the dysregulation of DNA methylation. Our study also provided novel epigenetic insights into the study of enantioselective biological effects and the relevant underlying mechanisms of chiral insecticide.
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Affiliation(s)
- Yi Qian
- College of Life Science, Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Chenyang Ji
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Siqing Yue
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.
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18
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Detilleux JC. Bayesian Networks in Equine Genetic Counseling. J Equine Vet Sci 2019. [DOI: 10.1016/j.jevs.2018.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Data on novel DNA methylation changes induced by valproic acid in human hepatocytes. Data Brief 2017; 16:161-171. [PMID: 29201983 PMCID: PMC5702865 DOI: 10.1016/j.dib.2017.11.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022] Open
Abstract
Valproic acid (VPA) is a widely prescribed antiepileptic drug in the world. Despite its pharmacological importance, it may cause liver toxicity and steatosis. However the exact mechanism of the steatosis formation is unknown. The data presented in this DIB publication is used to further investigate the VPA-induced mechanisms of steatosis by analyzing changes in patterns of methylation. Therefore, primary human hepatocytes (PHHs) were exposed to VPA at a concentration which was shown to cause steatosis without inducing overt cytotoxicity. VPA was administered for 5 days daily to PHHs. Furthermore, after 5 days VPA-treatment parts of the PHHs were followed for a 3 days washout. Differentially methylated DNA regions (DMRs) were identified by using the ‘Methylated DNA Immuno-Precipitation - sequencing’ (MeDIP-seq) method. The data presented in this DIB demonstrate induced steatosis pathways by all DMRs during VPA-treatment, covering interesting drug-induced steatosis genes (persistent DMRs upon terminating VPA treatment and the EP300 network). This was illustrated in our associated article (Wolters et al., 2017) [1]. MeDIP-seq raw data are available on ArrayExpress (accession number: E-MTAB-4437).
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Wolters JEJ, van Breda SGJ, Caiment F, Claessen SM, de Kok TMCM, Kleinjans JCS. Nuclear and Mitochondrial DNA Methylation Patterns Induced by Valproic Acid in Human Hepatocytes. Chem Res Toxicol 2017; 30:1847-1854. [PMID: 28853863 PMCID: PMC5645762 DOI: 10.1021/acs.chemrestox.7b00171] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Valproic
acid (VPA) is one of the most widely prescribed antiepileptic
drugs in the world. Despite its pharmacological importance, it may
cause liver toxicity and steatosis through mitochondrial dysfunction.
The aim of this study is to further investigate VPA-induced mechanisms
of steatosis by analyzing changes in patterns of methylation in nuclear
DNA (nDNA) and mitochondrial DNA (mtDNA). Therefore, primary human
hepatocytes (PHHs) were exposed to an incubation concentration of
VPA that was shown to cause steatosis without inducing overt cytotoxicity.
VPA was administered daily for 5 days, and this was followed by a
3 day washout (WO). Methylated DNA regions (DMRs) were identified
by using the methylated DNA immunoprecipitation–sequencing
(MeDIP-seq) method. The nDNA DMRs after VPA treatment could indeed
be classified into oxidative stress- and steatosis-related pathways.
In particular, networks of the steatosis-related gene EP300 provided novel insight into the mechanisms of toxicity induced by
VPA treatment. Furthermore, we suggest that VPA induces a crosstalk
between nDNA hypermethylation and mtDNA hypomethylation that plays
a role in oxidative stress and steatosis development. Although most
VPA-induced methylation patterns appeared reversible upon terminating
VPA treatment, 31 nDNA DMRs (including 5 zinc finger protein genes)
remained persistent after the WO period. Overall, we have shown that
MeDIP-seq analysis is highly informative in disclosing novel mechanisms
of VPA-induced toxicity in PHHs. Our results thus provide a prototype
for the novel generation of interesting methylation biomarkers for
repeated dose liver toxicity in vitro.
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Affiliation(s)
- Jarno E J Wolters
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Sandra M Claessen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University , P.O. Box 616, Maastricht 6200 MD, The Netherlands
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21
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Dou L, Jia X, Wei H, Fan S, Wang H, Guo Y, Duan S, Pang C, Yu S. Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq. PLoS One 2017; 12:e0179141. [PMID: 28715427 PMCID: PMC5513416 DOI: 10.1371/journal.pone.0179141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.
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Affiliation(s)
- Lingling Dou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- Weinan Institute of Agricultural Sciences, Weinan, Shaanxi, P. R. China
| | - Xiaoyun Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Yaning Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Shan Duan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- * E-mail: (CP); (SY)
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, P. R. China
- * E-mail: (CP); (SY)
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Cao Y, Jin HG, Ma HH, Zhao ZH. Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1529-1539. [PMID: 28728367 PMCID: PMC5666187 DOI: 10.5713/ajas.17.0154] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/25/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022]
Abstract
Objective The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.
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Affiliation(s)
- Yang Cao
- College of Animal Science, Jilin University, Changchun 130012, China.,Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Hai-Guo Jin
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Hui-Hai Ma
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Zhi-Hui Zhao
- College of Animal Science, Jilin University, Changchun 130012, China
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Fipronil-induced enantioselective developmental toxicity to zebrafish embryo-larvae involves changes in DNA methylation. Sci Rep 2017; 7:2284. [PMID: 28536466 PMCID: PMC5442102 DOI: 10.1038/s41598-017-02255-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/28/2017] [Indexed: 01/01/2023] Open
Abstract
Enantioselectivity in the aquatic toxicity of chiral pesticides has been widely investigated, while the molecular mechanisms remain unclear. Thus far, few studies has focused on genomic expression related to selective toxicity in chiral pesticide, nor on epigenetic changes, such as DNA methylation. Here, we used fipronil, a broad-spectrum insecticide, as a model chemical to probe its enantioselective toxicity in embryo development. Our results showed that S-(+)-fipronil caused severer developmental toxicity in embryos. The MeDIP-Seq analysis demonstrated that S-(+)-fipronil dysregulated a higher level of genomic DNA methylation than R-(−)-fipronil. Gene Ontology analysis revealed that S-(+)-fipronil caused more differentially methylated genes that are involved in developmental processes. Compared with R-(−)-fipronil, S-(+)-fipronil significantly disrupted 7 signaling pathways (i.e., mitogen-activated protein kinases, tight junctions, focal adhesion, transforming growth factor-β, vascular smooth muscle contraction, and the hedgehog and Wnt signaling pathways) by hyper-methylation of developmentally related genes, which further induced the downregulation of those genes. Together, these data suggest that differences in DNA methylation may partly explain the enantioselectivity of fipronil to zebrafish embryos. The application of epigenetics to investigate the enantioselective toxicity mechanism of chiral chemicals would provide a further understanding of their stereoselectivity biological effects.
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Gim JA, Kim HS. Identification and Expression of Equine MER-Derived miRNAs. Mol Cells 2017; 40:262-270. [PMID: 28320202 PMCID: PMC5424272 DOI: 10.14348/molcells.2017.2295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 11/27/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thorough-bred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miR-NAs that are expressed in several tissues and are thought to have biological functions.
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Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- Genetic Engineering Institute, Pusan National University, Busan 46241,
Korea
- The Genomics Institute, Life Sciences Department, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- Genetic Engineering Institute, Pusan National University, Busan 46241,
Korea
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Harraghy N, Calabrese D, Fisch I, Girod PA, LeFourn V, Regamey A, Mermod N. Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells. Biotechnol J 2015; 10:967-78. [DOI: 10.1002/biot.201400649] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
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