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Tan Z, Jiang H. Molecular and Cellular Mechanisms of Intramuscular Fat Development and Growth in Cattle. Int J Mol Sci 2024; 25:2520. [PMID: 38473768 DOI: 10.3390/ijms25052520] [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: 01/23/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Intramuscular fat, also referred to as marbling fat, is the white fat deposited within skeletal muscle tissue. The content of intramuscular fat in the skeletal muscle, particularly the longissimus dorsi muscle, of cattle is a critical determinant of beef quality and value. In this review, we summarize the process of intramuscular fat development and growth, the factors that affect this process, and the molecular and epigenetic mechanisms that mediate this process in cattle. Compared to other species, cattle have a remarkable ability to accumulate intramuscular fat, partly attributed to the abundance of sources of fatty acids for synthesizing triglycerides. Compared to other adipose depots such as subcutaneous fat, intramuscular fat develops later and grows more slowly. The commitment and differentiation of adipose precursor cells into adipocytes as well as the maturation of adipocytes are crucial steps in intramuscular fat development and growth in cattle. Each of these steps is controlled by various factors, underscoring the complexity of the regulatory network governing adipogenesis in the skeletal muscle. These factors include genetics, epigenetics, nutrition (including maternal nutrition), rumen microbiome, vitamins, hormones, weaning age, slaughter age, slaughter weight, and stress. Many of these factors seem to affect intramuscular fat deposition through the transcriptional or epigenetic regulation of genes directly involved in the development and growth of intramuscular fat. A better understanding of the molecular and cellular mechanisms by which intramuscular fat develops and grows in cattle will help us develop more effective strategies to optimize intramuscular fat deposition in cattle, thereby maximizing the quality and value of beef meat.
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Affiliation(s)
- Zhendong Tan
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Honglin Jiang
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Yang C, Gao Z, Wang Y, Zhang Q, Bai M, Yang H, Guo J, Zhang Y. Genome-wide DNA methylation analysis reveals layer-specific methylation patterns in deer antler tissue. Gene 2023; 884:147744. [PMID: 37640118 DOI: 10.1016/j.gene.2023.147744] [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: 05/21/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
This paper explored using of deer antlers as a model for studying rapid growth and cartilage formation in mammals. The genes and regulatory mechanisms involved in antler chondrogenesis are poorly understood, however, previous research has suggested that DNA methylation played a key role in antler regeneration. By using fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP), this study measured DNA methylation levels in cartilage (CA) and reserve mesenchyme (RM) cells and tissues. Results showed that RM cells (RMCs) DNA methylation levels were significantly lower than those of CA, suggesting that DNA demethylation may be involved in antler fast cartilage differentiation. The study also identified 20 methylated fragments specific to RMCs or CA using the methylation-sensitive amplified polymorphism (MSAP) technique and confirmed these findings using southern blot analysis. The data provide the first experimental evidence of a link between epigenetic regulation and rapid cartilage differentiation in antlers.
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Affiliation(s)
- Chun Yang
- College of Basic Medicine, Beihua University, Jilin, PR China.
| | - Zizheng Gao
- College of Basic Medicine, Beihua University, Jilin, PR China
| | - Yukun Wang
- School of Stomatology, Beihua University, Jilin, PR China
| | - Qi Zhang
- School of Public Health, Beihua University, Jilin, PR China
| | - Muran Bai
- School of Stomatology, Beihua University, Jilin, PR China
| | - Huiran Yang
- School of Public Health, Beihua University, Jilin, PR China
| | - Junqi Guo
- The Third Clinical Medicine Affiliated to Changchun University of Chinese Medicine, Changchun, PR China.
| | - Yan Zhang
- School of Public Health, Beihua University, Jilin, PR China.
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Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023; 23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Peter M van Bodegom
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
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Vrablik M, Dlouha D, Todorovova V, Stefler D, Hubacek JA. Genetics of Cardiovascular Disease: How Far Are We from Personalized CVD Risk Prediction and Management? Int J Mol Sci 2021; 22:ijms22084182. [PMID: 33920733 PMCID: PMC8074003 DOI: 10.3390/ijms22084182] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
Despite the rapid progress in diagnosis and treatment of cardiovascular disease (CVD), this disease remains a major cause of mortality and morbidity. Recent progress over the last two decades in the field of molecular genetics, especially with new tools such as genome-wide association studies, has helped to identify new genes and their variants, which can be used for calculations of risk, prediction of treatment efficacy, or detection of subjects prone to drug side effects. Although the use of genetic risk scores further improves CVD prediction, the significance is not unambiguous, and some subjects at risk remain undetected. Further research directions should focus on the “second level” of genetic information, namely, regulatory molecules (miRNAs) and epigenetic changes, predominantly DNA methylation and gene-environment interactions.
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Affiliation(s)
- Michal Vrablik
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
- Correspondence: ; Tel.: +420-224-962-122
| | - Dana Dlouha
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
| | - Veronika Todorovova
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
| | - Denes Stefler
- Department of Epidemiology and Public Health, Institute of Epidemiology and Health Care, University College London, London WC1E 7HB, UK;
| | - Jaroslav A. Hubacek
- 3rd Department of Internal Medicine, General University Hospital and 1st Faculty of Medicine, Charles University, 11636 Prague, Czech Republic; (V.T.); (J.A.H.)
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
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Perini F, Cendron F, Rovelli G, Castellini C, Cassandro M, Lasagna E. Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review. Animals (Basel) 2020; 11:ani11010046. [PMID: 33383690 PMCID: PMC7823582 DOI: 10.3390/ani11010046] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary New genomic tools have been used as an instrument in order to assess the molecular pathway involved in heat stress resistance. Local chicken breeds have a better attitude to face heat stress. This review aims to summarize studies linked to chickens, heat stress, and heat shock protein. Abstract Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field.
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Affiliation(s)
- Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia (PG), Italy; (F.P.); (G.R.); (C.C.); (E.L.)
| | - Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro (PD), Italy;
- Correspondence:
| | - Giacomo Rovelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia (PG), Italy; (F.P.); (G.R.); (C.C.); (E.L.)
| | - Cesare Castellini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia (PG), Italy; (F.P.); (G.R.); (C.C.); (E.L.)
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro (PD), Italy;
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia (PG), Italy; (F.P.); (G.R.); (C.C.); (E.L.)
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Zheng M, Xiao S, Guo T, Rao L, Li L, Zhang Z, Huang L. DNA methylomic homogeneity and heterogeneity in muscles and testes throughout pig adulthood. Aging (Albany NY) 2020; 12:25412-25431. [PMID: 33231562 PMCID: PMC7803572 DOI: 10.18632/aging.104143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/09/2020] [Indexed: 01/24/2023]
Abstract
DNA methylome pattern is significantly different among tissues, ages, breeds, and genders. We assessed 20 methylome and transcriptome data in longissimus dorsi (LD) or testicles from Bamaxiang (BMX) and Large White pigs (LW) by deep sequencing technology. We identified ~55.7M CpGs and 5.30M, 0.20M, 1.20M, and 0.16M differential CpGs (P<0.01) between tissues, ages, breeds, and genders, respectively. Interestingly, 7.54% of differentially methylated regions (DMRs) are co-localized with promoters, which potentially regulate gene expression. RNA-seq analysis revealed that 23.42% CpGs are significantly correlated with gene expression (mean |r|=0.58, P<0.01), most of which are enriched in tissue-specific functions. Specially, we also found that the methylation levels in promoters of 655 genes were strongly associated with their expression levels (mean |r|=0.66, P<0.01). In addition, differentially methylated CpGs (DMCpGs) between breeds in HOXC gene cluster imply important regulatory roles in myocytes hypertrophy and intermuscular fat (IMF) deposition. Dramatically, higher similarity of methylation pattern was observed within pedigree than across pedigrees, which indicates the existence of heritable methylation regions. In summary, a part of CpGs in promoter can change its methylation pattern and play a marked regulatory function in different physiological or natural environments.
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Affiliation(s)
- Min Zheng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tianfu Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lin Rao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Longyun Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Lv Y, Zheng X, Shi M, Wang Z, Cui L. Different EPHX1 methylation levels in promoter area between carbamazepine-resistant epilepsy group and carbamazepine-sensitive epilepsy group in Chinese population. BMC Neurol 2019; 19:114. [PMID: 31164100 PMCID: PMC6549255 DOI: 10.1186/s12883-019-1308-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/18/2019] [Indexed: 12/13/2022] Open
Abstract
Background Epigenetics underlying refractory epilepsy is poorly understood. DNA methylation may affect gene expression in epilepsy patients without affecting DNA sequences. Herein, we investigated the association between Carbamazepine-resistant (CBZ-resistant) epilepsy and EPHX1 methylation in a northern Han Chinese population, and conducted an analysis of clinical risk factors for CBZ-resistant epilepsy. Methods Seventy-five northern Han Chinese patients participated in this research. 25 cases were CBZ-resistant epilepsy, 25 cases were CBZ-sensitive epilepsy and the remaining 25 cases were controls. Using a CpG searcher was to make a prediction of CpG islands; bisulfite sequencing PCR (BSP) was applied to test the methylation of EPHX1. We then did statistical analysis between clinical parameters and EPHX1 methylation. Results There was no difference between CBZ-resistant patients, CBZ-sensitive patients and healthy controls in matched age and gender. However, a significant difference of methylation levels located in NC_000001.11 (225,806,929.....225807108) of the EPHX1 promoter was found in CBZ-resistant patients, which was much higher than CBZ-sensitive and controls. Additionally, there was a significant positive correlation between seizure frequency, disease course and EPHX1 methylation in CBZ-resistant group. Conclusion Methylation levels in EPHX1 promoter associated with CBZ-resistant epilepsy significantly. EPHX1 methylation may be the potential marker for CBZ resistance prior to the CBZ therapy and potential target for treatments.
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Affiliation(s)
- Yudan Lv
- Department of Neurology, The First hospital of Jilin University, 71-Xinmin Street, Changchun, People's Republic of China
| | - Xiangyu Zheng
- Department of Neurology, The First hospital of Jilin University, 71-Xinmin Street, Changchun, People's Republic of China
| | - Mingchao Shi
- Department of Neurology, The First hospital of Jilin University, 71-Xinmin Street, Changchun, People's Republic of China
| | - Zan Wang
- Department of Neurology, The First hospital of Jilin University, 71-Xinmin Street, Changchun, People's Republic of China
| | - Li Cui
- Department of Neurology, The First hospital of Jilin University, 71-Xinmin Street, Changchun, People's Republic of China.
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Zhang X, Nie Y, Cai S, Ding S, Fu B, Wei H, Chen L, Liu X, Liu M, Yuan R, Qiu B, He Z, Cong P, Chen Y, Mo D. Earlier demethylation of myogenic genes contributes to embryonic precocious terminal differentiation of myoblasts in miniature pigs. FASEB J 2019; 33:9638-9655. [PMID: 31145867 DOI: 10.1096/fj.201900388r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we performed whole-genome bisulfite sequencing of longissimus dorsi muscle from Landrace and Wuzhishan (WZS) miniature pigs during 18, 21, and 28 d postcoitum. It was uncovered that in regulatory regions only around transcription start sites (TSSs), gene expression and methylation showed negative correlation, whereas in gene bodies, positive correlation occurred. Furthermore, earlier myogenic gene demethylation around TSSs and earlier hypermethylation of myogenic genes in gene bodies were considered to trigger their earlier expression in miniature pigs. Furthermore, by analyzing the methylation pattern of the myogenic differentiation 1(MyoD) promoter and distal enhancer, we found that earlier demethylation of the MyoD distal enhancer in WZSs contributes to its earlier expression. Moreover, DNA demethylase Tet1 was found to be involved in the demethylation of the myogenin promoter and promoted immortalized mouse myoblast cell line (C2C12) and porcine embryonic myogenic cell differentiation. This study reveals that earlier demethylation of myogenic genes contributes to precocious terminal differentiation of myoblasts in miniature pigs.-Zhang, X., Nie, Y., Cai, S., Ding, S., Fu, B., Wei, H., Chen, L., Liu, X., Liu, M., Yuan, R., Qiu, B., He, Z., Cong, P., Chen, Y., Mo, D. Earlier demethylation of myogenic genes contributes to embryonic precocious terminal differentiation of myoblasts in miniature pigs.
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Affiliation(s)
- Xumeng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Shenzhen Kingsino Technology Company Limited, Shenzhen, China
| | - Yaping Nie
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shufang Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Suying Ding
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bingqiang Fu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hong Wei
- Shenzhen Kingsino Technology Company Limited, Shenzhen, China
| | - Luxi Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Minggui Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Renqiang Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Boqin Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Park H, Seo KS, Lee M, Seo S. Identification of meat quality-related differentially methylated regions in the DNA of the longissimus dorsi muscle in pig. Anim Biotechnol 2019; 31:189-194. [PMID: 31060422 DOI: 10.1080/10495398.2019.1604378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The objective of this study was to investigate the association of DNA methylation with postmortem energy metabolism and the pH of the porcine longissimus dorsi muscle (LDM). Analysis of the DNA methylome of eight LDM samples (four pairs of the highest and lowest pH among littermates) identified a total of 3468 differentially methylated regions (DMRs) between high and low pH samples (p ≤ 0.001). Of DMRs, 45.3% co-mapped with quantitative trait loci known to be associated with meat pH and postmortem metabolism. Among the DMRs, 203 hyper-methylated regions (HR) and 190 hypo-methylated regions (HO) were identified for the high pH group compared to the low pH. Furthermore, 44 and 21 protein-coding genes contained HR and HO in their gene body, respectively. It was revealed that ENO1, GYS2, SDHC and DERA, which encode core enzymes in postmortem energy metabolism, contained HR or HO in their gene body.
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Affiliation(s)
- Hyesun Park
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Kang-Seok Seo
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Suncheon National University, Suncheon, Republic of Korea
| | - Mingyung Lee
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
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Chen X, Shen LH, Gui LX, Yang F, Li J, Cao SZ, Zuo ZC, Ma XP, Deng JL, Ren ZH, Chen ZX, Yu SM. Genome-wide DNA methylation profile of prepubertal porcine testis. Reprod Fertil Dev 2018; 30:349-358. [PMID: 28727982 DOI: 10.1071/rd17067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
The biological structure and function of the mammalian testis undergo important developmental changes during prepuberty and DNA methylation is dynamically regulated during testis development. In this study, we generated the first genome-wide DNA methylation profile of prepubertal porcine testis using methyl-DNA immunoprecipitation (MeDIP) combined with high-throughput sequencing (MeDIP-seq). Over 190 million high-quality reads were generated, containing 43642 CpG islands. There was an overall downtrend of methylation during development, which was clear in promoter regions but less so in gene-body regions. We also identified thousands of differentially methylated regions (DMRs) among the three prepubertal time points (1 month, T1; 2 months, T2; 3 months, T3), the majority of which showed decreasing methylation levels over time. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that many genes in the DMRs were linked with cell proliferation and some important pathways in porcine testis development. Our data suggest that DNA methylation plays an important role in prepubertal development of porcine testis, with an obvious downtrend of methylation levels from T1 to T3. Overall, our study provides a foundation for future studies and gives new insights into mammalian testis development.
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Affiliation(s)
- Xi Chen
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Liu-Hong Shen
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Li-Xuan Gui
- OnMath Science and Technology Limited Company, No. 500 Tianfu Road, Chengdu, Sichuan, 611130, China
| | - Fang Yang
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jie Li
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Sui-Zhong Cao
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhi-Cai Zuo
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Xiao-Ping Ma
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Jun-Liang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhi-Hua Ren
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Zhong-Xu Chen
- OnMath Science and Technology Limited Company, No. 500 Tianfu Road, Chengdu, Sichuan, 611130, China
| | - Shu-Min Yu
- College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
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Yang SX, Guo C, Zhao XT, Sun JT, Hong XY. Divergent methylation pattern in adult stage between two forms of Tetranychus urticae (Acari: Tetranychidae). INSECT SCIENCE 2018; 25:667-678. [PMID: 28217963 DOI: 10.1111/1744-7917.12444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
The two-spotted spider mite, Tetranychus urticae Koch has two forms: green form and red form. Understanding the molecular basis of how these two forms established without divergent genetic background is an intriguing area. As a well-known epigenetic process, DNA methylation has particularly important roles in gene regulation and developmental variation across diverse organisms that do not alter genetic background. Here, to investigate whether DNA methylation could be associated with different phenotypic consequences in the two forms of T. urticae, we surveyed the genome-wide cytosine methylation status and expression level of DNA methyltransferase 3 (Tudnmt3) throughout their entire life cycle. Methylation-sensitive amplification polymorphism (MSAP) analyses of 585 loci revealed variable methylation patterns in the different developmental stages. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between female adults of the two forms. The gene expression of Tudnmt3 was detected in all examined developmental stages, which was significantly different in the adult stage of the two forms. Together, our results reveal the epigenetic distance between the two forms of T. urticae, suggesting that DNA methylation might be implicated in different developmental demands, and contribute to different phenotypes in the adult stage of these two forms.
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Affiliation(s)
- Si-Xia Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Chao Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiu-Ting Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
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Vinoth A, Thirunalasundari T, Shanmugam M, Uthrakumar A, Suji S, Rajkumar U. Evaluation of DNA methylation and mRNA expression of heat shock proteins in thermal manipulated chicken. Cell Stress Chaperones 2018; 23:235-252. [PMID: 28842808 PMCID: PMC5823805 DOI: 10.1007/s12192-017-0837-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 07/29/2017] [Accepted: 08/02/2017] [Indexed: 01/20/2023] Open
Abstract
Thermal manipulation during embryogenesis has been demonstrated to enhance the thermotolerance capacity of broilers through epigenetic modifications. Heat shock proteins (HSPs) are induced in response to stress for guarding cells against damage. The present study investigates the effect of thermal conditioning during embryogenesis and thermal challenge at 42 days of age on HSP gene and protein expression, DNA methylation and in vitro luciferase assay in brain tissue of Naked Neck (NN) and Punjab Broiler-2 (PB-2) chicken. On the 15th day of incubation, fertile eggs from two breeds, NN and PB-2, were randomly divided in to two groups: control (C)-eggs were incubated under standard incubation conditions, and thermal conditioning (TC)-eggs were exposed to higher incubation temperature (40.5°C) for 3 h on the 15th, 16th, and 17th days of incubation. The chicks obtained from each group were further subdivided and reared under different environmental conditions from the 15th to the 42nd day as normal [N; 25 ± 1 °C, 70% relative humidity (RH)] and heat exposed (HE; 35 ± 1 °C, 50% RH) resulting in four treatment groups (CN, CHE, TCN, and TCHE). The results revealed that HSP promoter activity was stronger in CHE, which had lesser methylation and higher gene expression. The activity of promoter region was lesser in TCHE birds that were thermally manipulated at the embryonic stage, thus reflecting their stress-free condition. This was confirmed by the lower level of mRNA expression of all the HSP genes. In conclusion, thermal conditioning during embryogenesis has a positive impact and improves chicken thermotolerance capacity in postnatal life.
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Affiliation(s)
- A Vinoth
- Department of Industrial Biotechnology, Bharathidhasan University, Tiruchirappalli, Tamilnadu, 620 024, India
| | - T Thirunalasundari
- Department of Industrial Biotechnology, Bharathidhasan University, Tiruchirappalli, Tamilnadu, 620 024, India
| | - M Shanmugam
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad, Telangana, 500 030, India
| | - A Uthrakumar
- Tamilnadu Veterinary and Animal Sciences University, Chennai, Tamilnadu, India
| | - S Suji
- M.S. Swaminathan Research Institute, Taramani, Chennai, Tamilnadu, India
| | - U Rajkumar
- ICAR-Directorate of Poultry Research, Rajendranagar, Hyderabad, Telangana, 500 030, India.
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13
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Kim W, Park H, Seo KS, Seo S. Characterization and functional inferences of a genome-wide DNA methylation profile in the loin ( longissimus dorsi) muscle of swine. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:3-12. [PMID: 28728396 PMCID: PMC5756920 DOI: 10.5713/ajas.16.0793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/07/2017] [Accepted: 05/01/2017] [Indexed: 12/28/2022]
Abstract
Objective DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates). The reference pig genome was annotated with 78.5% of the raw reads. A total of 33,506 putative methylated regions (PMR) were identified from methylated regions that overlapped at least two samples. Results Of these, only 3.1% were commonly observed in all eight samples. DNA methylation patterns between two littermates were as diverse as between unrelated individuals (p = 0.47), indicating that maternal genetic effects have little influence on the variation in DNA methylation of porcine LDM. The highest density of PMR was observed on chromosome 10. A major proportion (47.7%) of PMR was present in the repeat regions, followed by introns (21.5%). The highest conservation of PMR was found in CpG islands (12.1%). These results show an important role for DNA methylation in species- and tissue-specific regulation of gene expression. PMR were also significantly related to muscular cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism. Conclusion This study indicated the biased distribution and functional role of DNA methylation in gene expression of porcine LDM. DNA methylation was related to cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism (e.g., insulin signaling pathways). Nutritional and environmental management may have a significant impact on the variation in DNA methylation of porcine LDM.
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Affiliation(s)
- Woonsu Kim
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hyesun Park
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Kang-Seok Seo
- Department of Animal Science & Technology, College of Life Science and Natural Resources, Suncheon National University, Suncheon 57922, Korea
| | - Seongwon Seo
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon 34134, Korea
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Niknazar S, Nahavandi A, Peyvandi AA, Peyvandi H, Zare Mehrjerdi F, Karimi M. Effect of Maternal Stress Prior to Conception on Hippocampal BDNF Signaling in Rat Offspring. Mol Neurobiol 2016; 54:6436-6445. [DOI: 10.1007/s12035-016-0143-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/19/2016] [Indexed: 02/06/2023]
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15
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Yang C, Lu X, Sun H, Chu WH, Li C. Analysis of Genomewide DNA Methylation Reveals Differences in DNA Methylation Levels between Dormant and Naturally as well as Artificially Potentiated Pedicle Periosteum of Sika Deer (Cervus nippon). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:375-383. [PMID: 27554771 DOI: 10.1002/jez.b.22695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/19/2016] [Accepted: 07/23/2016] [Indexed: 11/10/2022]
Abstract
Deer antlers are the only mammalian appendages that can fully regenerate each year from the permanent bony protuberances of the frontal bones, called pedicles. Pedicle periosteum (PP) is the key tissue for antler regeneration and the source of antler stem cells. The distal one third of the PP has acquired the ability to regenerate antlers and is termed the potentiated PP (PPP), whereas the proximal two thirds of the PP requires further interactions within its niche to launch antler regeneration and is termed the dormant PP (DPP). However, the molecular mechanisms underlying the process of potentiation from the DPP to the PPP are unknown. In this study, we used the fluorescence-labeled methylation-sensitive amplified polymorphism method to assess the levels of DNA methylation in both cells and tissues of the PPP and the DPP. The results showed that the levels of DNA methylation were significantly lower in the PPP compared to the DPP (P < 0.05). Therefore, DNA demethylation may be involved in the process of this potentiation. This involvement was further confirmed by functional testing by artificially creating a potentiated PP (aPPP) from DPP tissue. Moreover, we identified 15 methylated fragments by the methylation sensitive amplified polymorphism method that are either unique to the PPP or the DPP, which were further confirmed by Southern blot analysis. Taken together, our data suggest that DNA demethylation is involved in the process of PP potentiation, which is a prerequisite step for the initiation of antler regeneration. These findings provide the first experimental evidence to link epigenetic regulation and mammalian appendage regeneration.
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Affiliation(s)
- Chun Yang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, People's Republic of China.,State key Laboratory for Molecular Biology of Special Economic Animals, Changchun, People's Republic of China
| | - Xiao Lu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, People's Republic of China.,State key Laboratory for Molecular Biology of Special Economic Animals, Changchun, People's Republic of China
| | - Hongmei Sun
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, People's Republic of China.,State key Laboratory for Molecular Biology of Special Economic Animals, Changchun, People's Republic of China
| | - Wen Hui Chu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, People's Republic of China.,State key Laboratory for Molecular Biology of Special Economic Animals, Changchun, People's Republic of China
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, People's Republic of China. .,State key Laboratory for Molecular Biology of Special Economic Animals, Changchun, People's Republic of China.
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16
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Yang Y, Zhou R, Mu Y, Hou X, Tang Z, Li K. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep 2016; 6:30160. [PMID: 27444743 PMCID: PMC4957084 DOI: 10.1038/srep30160] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5' and 3' flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals.
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Affiliation(s)
- Yalan Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Rong Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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17
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Schomberg DT, Tellez A, Meudt JJ, Brady DA, Dillon KN, Arowolo FK, Wicks J, Rousselle SD, Shanmuganayagam D. Miniature Swine for Preclinical Modeling of Complexities of Human Disease for Translational Scientific Discovery and Accelerated Development of Therapies and Medical Devices. Toxicol Pathol 2016; 44:299-314. [DOI: 10.1177/0192623315618292] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Noncommunicable diseases, including cardiovascular disease, diabetes, chronic respiratory disease, and cancer, are the leading cause of death in the world. The cost, both monetary and time, of developing therapies to prevent, treat, or manage these diseases has become unsustainable. A contributing factor is inefficient and ineffective preclinical research, in which the animal models utilized do not replicate the complex physiology that influences disease. An ideal preclinical animal model is one that responds similarly to intrinsic and extrinsic influences, providing high translatability and concordance of preclinical findings to humans. The overwhelming genetic, anatomical, physiological, and pathophysiological similarities to humans make miniature swine an ideal model for preclinical studies of human disease. Additionally, recent development of precision gene-editing tools for creation of novel genetic swine models allows the modeling of highly complex pathophysiology and comorbidities. As such, the utilization of swine models in early research allows for the evaluation of novel drug and technology efficacy while encouraging redesign and refinement before committing to clinical testing. This review highlights the appropriateness of the miniature swine for modeling complex physiologic systems, presenting it as a highly translational preclinical platform to validate efficacy and safety of therapies and devices.
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Affiliation(s)
- Dominic T. Schomberg
- Biomedical & Genomic Research Group, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | | | - Jennifer J. Meudt
- Biomedical & Genomic Research Group, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | | | | | - Folagbayi K. Arowolo
- Biomedical & Genomic Research Group, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Joan Wicks
- Alizée Pathology, LLC, Thurmont, Maryland, USA
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18
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Jiang Q, Li Q, Yu H, Kong L. Inheritance and Variation of Genomic DNA Methylation in Diploid and Triploid Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:124-132. [PMID: 26585587 DOI: 10.1007/s10126-015-9674-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
DNA methylation is an important epigenetic mechanism that could be responsive to environmental changes indicating a potential role in natural selection and adaption. In order to evaluate an evolutionary role of DNA methylation, it is essential to first gain a better insight into inheritability. To address this question, this study investigated DNA methylation variation from parents to offspring in the Pacific oyster Crassostrea gigas using fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP) analysis. Most of parental methylated loci were stably transmitted to offspring segregating following Medelian expectation. However, methylated loci deviated more often than non-methylated loci and offspring showed a few de novo methylated loci indicating DNA methylation changes from parents to offspring. Interestingly, some male-specific methylated loci were found in this study which might help to explore sex determination in oyster. Despite environmental stimuli, genomic stresses such as polyploidization also can induce methylation changes. This study also compared global DNA methylation level and individual methylated loci between diploid and triploid oysters. Results showed no difference in global methylation state but a few ploidy-specific loci were detected. DNA methylation variation during polyploidization was less than autonomous methylation variation from parents to offspring.
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Affiliation(s)
- Qun Jiang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Hong Yu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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19
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Schook LB, Collares TV, Darfour-Oduro KA, De AK, Rund LA, Schachtschneider KM, Seixas FK. Unraveling the swine genome: implications for human health. Annu Rev Anim Biosci 2016; 3:219-44. [PMID: 25689318 DOI: 10.1146/annurev-animal-022114-110815] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pig was first used in biomedical research in ancient Greece and over the past few decades has quickly grown into an important biomedical research tool. Pigs have genetic and physiological traits similar to humans, which make them one of the most useful and versatile animal models. Owing to these similarities, data generated from porcine models are more likely to lead to viable human treatments than those from murine work. In addition, the similarity in size and physiology to humans allows pigs to be used for many experimental approaches not feasible in mice. Research areas that employ pigs range from neonatal development to translational models for cancer therapy. Increasing numbers of porcine models are being developed since the release of the swine genome sequence, and the development of additional porcine genomic and epigenetic resources will further their use in biomedical research.
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Affiliation(s)
- Lawrence B Schook
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801; , , , ,
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20
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Chen XL, Wang FM, Li JJ, He XY, Liu XY, Ma LB. The effect of two nucleoside antitumor drugs on the proliferation and DNA methylation of human gastric cancer cells. Oncol Lett 2015; 10:1919-1923. [PMID: 26622775 DOI: 10.3892/ol.2015.3427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 06/02/2015] [Indexed: 11/06/2022] Open
Abstract
Fluorouracil (5-Fu) and 5-azacitidine (5-aza) are two types of nucleoside analog, which have been widely applied in the treatment of several types of cancer. However, the effect of these two types of drug on the proliferation and DNA methylation of cancer cells has not been compared in a single study. In the present study, in vitro cultured human gastric cancer cells (hGCCs) were treated with various concentrations of 5-Fu and 5-aza, and cell counting, MTT assay and methyl-sensitive amplified polymorphism were used to evaluate the resulting levels of proliferation and DNA methylation of hGCCs. The results revealed that the two drugs were able to inhibit the proliferation of hGCCs, but that the effect of 5-aza was weaker than that of 5-Fu. However, 5-aza decreased the level of DNA methylation in hGCCs, whereas 5-Fu did not alter DNA methylation. These results indicated that 5-Fu was able to more efficiently inhibit the proliferation of hGCCs than 5-aza, and that this difference may be due to differences in the anticancer mechanism of these two types of drug.
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Affiliation(s)
- Xiu-Li Chen
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia 014010, P.R. China ; Faculty of Biological Science and Technology, Baotou Teachers College, Baotou, Inner Mongolia 014030, P.R. China
| | - Feng-Mei Wang
- School of Farm and Garden Engineering, Baotou Light Industry Vocational Technical College, Baotou, Inner Mongolia 014030, P.R. China
| | - Jia-Jia Li
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia 014010, P.R. China
| | - Xiao-Ying He
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia 014010, P.R. China
| | - Xi-Yu Liu
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia 014010, P.R. China
| | - Li-Bing Ma
- School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia 014010, P.R. China
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21
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Xu Y, Liu L, Pan B, Zhu J, Nan C, Huang X, Tian J. DNA methylation regulates mouse cardiac myofibril gene expression during heart development. J Biomed Sci 2015; 22:88. [PMID: 26475623 PMCID: PMC4609054 DOI: 10.1186/s12929-015-0203-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/09/2015] [Indexed: 12/31/2022] Open
Abstract
Background It is well known that epigenetic modifications play an important role in controlling the regulation of gene expression during the development. Our previous studies have demonstrated that the expression of fetal troponin I gene (also called slow skeletal troponin I, ssTnI) is predominated in the fetal stage, reduced after birth and disappeared in the adulthood. The mechanism underlying the developmentally related ssTnI gene regulation is not clear. In this study, we have explored the epigenetic role of DNA methylation in the regulation of ssTnI expression in the heart during the development. Results The DNA methylation levels of CpG island and CpG dinucleotides region were detected using methylation specific PCR (MSP) and bisulfite sequence PCR (BSP) in 2000 bp upstream and 100 bp upstream of ssTnI gene promoter. Real time RT-PCR and Western blot were used to detect ssTnI mRNA and protein expression levels. We found that DNA methylation levels of the CpG dinucleotides region in ssTnI gene promoter were increased with the development, corresponding to a decreased expression of ssTnI gene in mouse heart. However the DNA methylation levels of CpG islands in this gene were not changed during the development. Application of a methylation inhibitor, 5-Azacytidine, in cultured myocardial cells partially prevented the decline of ssTnI expression. Conclusion Our results indicate that DNA methylation, as an epigenetic intervention, plays a role in the regulation of the fetal TnI gene expression in the heat during the development.
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Affiliation(s)
- Yang Xu
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Road, Yu Zhong District, Chongqing, 400014, P.R. of China
| | - Lingjuan Liu
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Road, Yu Zhong District, Chongqing, 400014, P.R. of China.,Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, P.R. of China
| | - Bo Pan
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Road, Yu Zhong District, Chongqing, 400014, P.R. of China
| | - Jing Zhu
- Ministry of Education Key Laboratory of Child Development and Disorders; Key Laboratory of Pediatrics in Chongqing, CSTC2009CA5002; Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, P.R. of China
| | - Changlong Nan
- Department of Biomedical Science, Charlie E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Xupei Huang
- Department of Biomedical Science, Charlie E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA.
| | - Jie Tian
- Department of Cardiology, Heart Centre, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Road, Yu Zhong District, Chongqing, 400014, P.R. of China.
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22
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Schachtschneider KM, Madsen O, Park C, Rund LA, Groenen MAM, Schook LB. Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model. BMC Genomics 2015; 16:743. [PMID: 26438392 PMCID: PMC4594891 DOI: 10.1186/s12864-015-1938-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/19/2015] [Indexed: 12/13/2022] Open
Abstract
Background Pigs (Sus scrofa) provide relevant biomedical models to dissect complex diseases due to their anatomical, genetic, and physiological similarities with humans. Aberrant DNA methylation has been linked to many of these diseases and is associated with gene expression; however, the functional similarities and differences between porcine and human DNA methylation patterns are largely unknown. Methods DNA and RNA was isolated from eight tissue samples (fat, heart, kidney, liver, lung, lymph node, muscle, and spleen) from the adult female Duroc utilized for the pig genome sequencing project. Reduced representation bisulfite sequencing (RRBS) and RNA-seq were performed on an Illumina HiSeq2000. RRBS reads were aligned using BSseeker2, and only sites with a minimum depth of 10 reads were used for methylation analysis. RNA-seq reads were aligned using Tophat, and expression analysis was performed using Cufflinks. In addition, SNP calling was performed using GATK for targeted control and whole genome sequencing reads for CpG site validation and allelic expression analysis, respectively. Results Analysis on the influence of DNA variation in methylation calling revealed a reduced effectiveness of WGS datasets in covering CpG rich regions, as well as the usefulness of a targeted control library for SNP detection. Analysis of over 500,000 CpG sites demonstrated genome wide methylation patterns similar to those observed in humans, including reduced methylation within CpG islands and at transcription start sites (TSS), X chromosome inactivation, and anticorrelation of TSS CpG methylation with gene expression. In addition, a positive correlation between TSS CpG density and expression, and a negative correlation between TSS TpG density and expression were demonstrated. Low but non-random non-CpG methylation (<1%) was also detected in all non-neuronal somatic tissues, with differences in tissue clustering observed based on CpG and non-CpG methylation patterns. Finally, allele specific expression analysis revealed enrichment of genes involved in metabolic and regulatory processes. Discussion These results provide transcriptional and DNA methylation datasets for the biomedical community that are directly relatable to current genomic resources. In addition, the correlation between TSS CpG density and expression suggests increased mutation rates at CpG sites play a significant role in adaptive evolution by reducing CpG density at TSS over time, resulting in higher methylation levels in these regions and more permanent changes to lower gene expression. This is proposed to occur predominantly through deamination of 5-methylcytosine to thymidine, resulting in the replacement of CpG with TpG sites in these regions, as indicated by the increased TSS TpG density observed in non-expressed genes, resulting in a negative correlation between expression and TSS TpG density. Conclusions This study provides baseline methylation and gene transcription profiles for a healthy adult pig, reports similar patterns to those observed in humans, and supports future porcine studies related to human disease and development. Additionally, the observed reduced CpG and increased TpG density at TSS of lowly expressed genes suggests DNA methylation plays a significant role in adaptive evolution through more permanent changes to lower gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1938-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyle M Schachtschneider
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA. .,Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands.
| | - Ole Madsen
- Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands.
| | - Chankyu Park
- Department of Animal Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea.
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA.
| | - Martien A M Groenen
- Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands.
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA. .,Institute for Genomic Biology, University of Illinois, Urbana, IL, USA. .,, 1201 W Gregory Drive #382 ERML, Urbana, IL, 61801, USA.
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23
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Liu S, Sun K, Jiang T, Feng J. Natural epigenetic variation in bats and its role in evolution. ACTA ACUST UNITED AC 2015; 218:100-6. [PMID: 25568456 DOI: 10.1242/jeb.107243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When facing the challenges of environmental change, such as habitat fragmentation, organisms have to adjust their phenotype to adapt to various environmental stresses. Recent studies show that epigenetic modifications could mediate environmentally induced phenotypic variation, and this epigenetic variance could be inherited by future generations, indicating that epigenetic processes have potential evolutionary effects. Bats living in diverse environments show geographic variations in phenotype, and the females usually have natal philopatry, presenting an opportunity to explore how environments shape epigenetic marks on the genome and the evolutionary potential of epigenetic variance in bat populations for adaptation. We have explored the natural epigenetic diversity and structure of female populations of the great roundleaf bat (Hipposideros armiger), the least horseshoe bat (Rhinolophus pusillus) and the eastern bent-winged bat (Miniopterus fuliginosus) using a methylation-sensitive amplified polymorphism technique. We have also estimated the effects of genetic variance and ecological variables on epigenetic diversification. All three bat species have a low level of genomic DNA methylation and extensive epigenetic diversity that exceeds the corresponding genetic variance. DNA sequence divergence, epigenetic drift and environmental variables contribute to the epigenetic diversities of each species. Environment-induced epigenetic variation may be inherited as a result of both mitosis and meiosis, and their potential roles in evolution for bat populations are also discussed in this review.
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Affiliation(s)
- Sen Liu
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, Henan, China
| | - Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China
| | - Tinglei Jiang
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China
| | - Jiang Feng
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China
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Comparison of the Adulthood Chronic Stress Effect on Hippocampal BDNF Signaling in Male and Female Rats. Mol Neurobiol 2015; 53:4026-4033. [PMID: 26189832 DOI: 10.1007/s12035-015-9345-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
Abstract
Studies show that gender plays an important role in stress-related disorders, and women are more vulnerable to its effect. The present study was undertaken to investigate differences in the change in expression of brain-derived neurotrophic factor (BDNF), and its tyrosine intracellular kinase-activating receptor (TrkB) genes in the male and female rats' hippocampus (HPC) under chronic mild repeated stress (CMRS) conditions. In this experiment, male and female Wistar rats were randomly divided into two groups: the CMRS and the control group. To induce stress, a repeated forced swimming paradigm was employed daily for adult male and female rats for 21 days. At the end of the stress phase, elevated plus maze (EPM) was used for measuring the stress behavioral effects. Serum corticosterone level was measured by ELISA. BDNF and TrkB gene methylation and protein expression in the HPC were detected using real-time PCR and Western blotting. Chronic stress in the adolescence had more effects on anxiety-like behavior and serum corticosterone concentration in female rats than males. Furthermore, stressed female rats had higher methylation levels and following reduced protein expression of BDNF but not TrkB compared to stressed male rats. These findings suggest that in exposure to a stressor, sex differences in BDNF methylation may be root cause of decreased BDNF levels in females and may underlie susceptibility to pathology development.
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Analysis of DNA methylation in tissues and development stages of pearl oyster Pinctada fucata. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0246-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Zhao Y, Chen M, Storey KB, Sun L, Yang H. DNA methylation levels analysis in four tissues of sea cucumber Apostichopus japonicus based on fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) during aestivation. Comp Biochem Physiol B Biochem Mol Biol 2014; 181:26-32. [PMID: 25461675 DOI: 10.1016/j.cbpb.2014.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/04/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
DNA methylation plays an important role in regulating transcriptional change in response to environmental stimuli. In the present study, DNA methylation levels of tissues of the sea cucumber Apostichopus japonicus were analyzed by the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique over three stages of the aestivation cycle. Overall, a total of 26,963 fragments were amplified including 9112 methylated fragments among four sea cucumber tissues using 18 pairs of selective primers. Results indicated an average DNA methylation level of 33.79% for A. japonicus. The incidence of DNA methylation was different across tissue types in the non-aestivation stage: intestine (30.16%), respiratory tree (27.61%), muscle (27.94%) and body wall (56.25%). Our results show that hypermethylation accompanied deep-aestivation in A. japonicus, which suggests that DNA methylation may have an important role in regulating global transcriptional suppression during aestivation. Further analysis indicated that the main DNA modification sites were focused on intestine and respiratory tree tissues and that full-methylation but not hemi-methylation levels exhibited significant increases in the deep-aestivation stage.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Muyan Chen
- Fisheries College, Ocean University of China, Qingdao 266003, PR China.
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada, K1S 5B6
| | - Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Hongsheng Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China.
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Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS, Han K, Yi JM, Cha HJ, Cho BW, Bhak J, Kim HS. Genome-wide analysis of DNA methylation patterns in horse. BMC Genomics 2014; 15:598. [PMID: 25027854 PMCID: PMC4117963 DOI: 10.1186/1471-2164-15-598] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 07/07/2014] [Indexed: 12/23/2022] Open
Abstract
Background DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density. Conclusions We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-598) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jong Bhak
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
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Rico L, Ogaya R, Barbeta A, Peñuelas J. Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:419-27. [PMID: 23889779 DOI: 10.1111/plb.12049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/11/2013] [Indexed: 05/22/2023]
Abstract
Rapid genetic changes in plants have been reported in response to current climate change. We assessed the capacity of trees in a natural forest to produce rapid acclimation responses based on epigenetic modifications. We analysed natural populations of Quercus ilex, the dominant tree species of Mediterranean forests, using the methylation-sensitive amplified polymorphism (MSAP) technique to assess patterns and levels of methylation in individuals from unstressed forest plots and from plots experimentally exposed to drought for 12 years at levels projected for the coming decades. The percentage of hypermethylated loci increased, and the percentage of fully methylated loci clearly decreased in plants exposed to drought. Multivariate analyses exploring the status of methylation at MSAP loci also showed clear differentiation depending on stress. The PCA scores for the MSAP profiles clearly separated the genetic from the epigenetic structure, and also significantly separated the samples within each group in response to drought. Changes in DNA methylation highlight the large capacity of plants to rapidly acclimate to changing environmental conditions, including trees with long life spans, and our results demonstrate those changes. These changes, although unable to prevent the decreased growth and higher mortality associated with this experimental drought, occurred together with a dampening in such decreases as the long-term treatment progressed.
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Affiliation(s)
- L Rico
- CSIC, Global Ecology Unit CREAF-CEAB-UAB, Catalonia, Spain; CREAF, Cerdanyola del Vallès, Catalonia, Spain
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Zhang Y, Guo J, Gao Y, Niu S, Yang C, Bai C, Yu X, Zhao Z. Genome-wide methylation changes are associated with muscle fiber density and drip loss in male three-yellow chickens. Mol Biol Rep 2014; 41:3509-16. [DOI: 10.1007/s11033-014-3214-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/28/2014] [Indexed: 11/28/2022]
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Sun Y, Hou R, Fu X, Sun C, Wang S, Wang C, Li N, Zhang L, Bao Z. Genome-wide analysis of DNA methylation in five tissues of Zhikong scallop, Chlamys farreri. PLoS One 2014; 9:e86232. [PMID: 24454962 PMCID: PMC3891877 DOI: 10.1371/journal.pone.0086232] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 12/10/2013] [Indexed: 01/22/2023] Open
Abstract
DNA methylation plays a vital role in tissue development and differentiation in eukaryotes. Epigenetic studies have been seldom conducted in the extremely diverse and evolutionarily highly successful bilaterian lineage Mollusca. In the present study, we conducted the genome-wide profiling of DNA methylation for five tissues of a bivalve mollusc, Chlamys farreri using the methylation-sensitive amplification polymorphism (MSAP) technique. The methylation levels were quite similar among tissues, ranging from 20.9% to 21.7%. CG methylation was the dominant type (14.9%-16.5%) in the C. farreri genome, but CHG methylation also accounted for a substantial fraction of total methylation (5.1%-6.3%). Relatively high methylation diversity was observed within tissues. Methylation differentiation between tissues was evaluated and 460 tissue-specific epiloci were identified. Kidney differs from the other tissues in DNA methylation profiles. Our study presents the first look at the tissue-specific DNA methylation patterns in a bivalve mollusc and represents an initial step towards understanding of epigenetic regulatory mechanism underlying tissue development and differentiation in bivalves.
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Affiliation(s)
- Yan Sun
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Rui Hou
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Changsen Sun
- School of Life Science, Taizhou University, Taizhou, China
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chen Wang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ning Li
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Fulneček J, Kovařík A. How to interpret methylation sensitive amplified polymorphism (MSAP) profiles? BMC Genet 2014; 15:2. [PMID: 24393618 PMCID: PMC3890580 DOI: 10.1186/1471-2156-15-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 12/10/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND DNA methylation plays a key role in development, contributes to genome stability, and may also respond to external factors supporting adaptation and evolution. To connect different types of stimuli with particular biological processes, identifying genome regions with altered 5-methylcytosine distribution at a genome-wide scale is important. Many researchers are using the simple, reliable, and relatively inexpensive Methylation Sensitive Amplified Polymorphism (MSAP) method that is particularly useful in studies of epigenetic variation. However, electrophoretic patterns produced by the method are rather difficult to interpret, particularly when MspI and HpaII isoschizomers are used because these enzymes are methylation-sensitive, and any C within the CCGG recognition motif can be methylated in plant DNA. RESULTS Here, we evaluate MSAP patterns with respect to current knowledge of the enzyme activities and the level and distribution of 5-methylcytosine in plant and vertebrate genomes. We discuss potential caveats related to complex MSAP patterns and provide clues regarding how to interpret them. We further show that addition of combined HpaII + MspI digestion would assist in the interpretation of the most controversial MSAP pattern represented by the signal in the HpaII but not in the MspI profile. CONCLUSIONS We recommend modification of the MSAP protocol that definitely discerns between putative hemimethylated mCCGG and internal CmCGG sites. We believe that our view and the simple improvement will assist in correct MSAP data interpretation.
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Affiliation(s)
- Jaroslav Fulneček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, Brno CZ-612 65, Czech Republic
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Zhou X, Chen J, Shike Liang M, Wang F. Differential DNA methylation between two wing phenotypes adults ofSogatella furcifera. Genesis 2013; 51:819-26. [DOI: 10.1002/dvg.22722] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Xiaosui Zhou
- State Key Laboratory for Biocontrol and Institute of Entomology; Sun Yat-sen University; Guangzhou Guangdong People's Republic of China
| | - Jialin Chen
- State Key Laboratory for Biocontrol and Institute of Entomology; Sun Yat-sen University; Guangzhou Guangdong People's Republic of China
| | - Meizhang Shike Liang
- State Key Laboratory for Biocontrol and Institute of Entomology; Sun Yat-sen University; Guangzhou Guangdong People's Republic of China
| | - Fanghai Wang
- State Key Laboratory for Biocontrol and Institute of Entomology; Sun Yat-sen University; Guangzhou Guangdong People's Republic of China
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Bang WY, Kim SW, Kwon SG, Hwang JH, Kim TW, Ko MS, Cho IC, Joo YK, Cho KK, Jeong JY, Kim CW. Swine liver methylomes of Berkshire, Duroc and Landrace breeds by MeDIPS. Anim Genet 2013; 44:463-6. [PMID: 23441856 DOI: 10.1111/age.12030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2013] [Indexed: 01/21/2023]
Abstract
Using a methyl-DNA immunoprecipitation technique in combination with next-generation deep sequencing, we conducted comprehensive DNA methylation profiling of liver genomes from three pig breeds: Berkshire, Duroc and Landrace. The profiles revealed that the distribution patterns of methylation signals along the genome are conserved among the three pig breeds. Specifically, many signals in coding genes were found in introns, and most signals in the repetitive elements were identified in non-long terminal repeat (LTR) retrotransposons such as long and short interspersed repetitive elements, implying a significant association with alternative splicing and expression of retrotransposable elements respectively. Differentially methylated regions among the three pig breeds were identified in the non-LTR retrotransposons, suggesting that they may lead to differential retrotransposable element activity. Altogether, this study provides advanced swine methylome data and valuable resources for understanding the function of DNA methylation in the evolutionary divergence of different pig breeds.
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Affiliation(s)
- Woo Young Bang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, Korea
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Snell-Rood EC, Troth A, Moczek AP. DNA methylation as a mechanism of nutritional plasticity: limited support from horned beetles. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:22-34. [PMID: 22951993 PMCID: PMC3708545 DOI: 10.1002/jez.b.22479] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 06/01/2012] [Accepted: 07/23/2012] [Indexed: 01/30/2023]
Abstract
Epigenetic changes to DNA, potentially heritable alterations above the sequence level, such as DNA methylation, are thought to underlie many instances of adaptive phenotypic plasticity. Our understanding of the links between epigenetic variation and adaptive phenotypic plasticity in natural populations is limited. If DNA methylation underlies adaptive responses to different nutritional environments, methylation patterns should be correlated with differences in performance across nutritional environments, and respond to changes in the environment. Additionally, genotypes that can cope with a broader range of nutritional environments are expected to have greater flexibility in methylation patterns. We tested these predictions using horned beetles (genus Onthophagus), which can cope with a wide range of variation in larval nutrition. We surveyed levels of methylation across several methylated loci in lab-reared beetles originating from natural populations using a methylation-specific amplified fragment length polymorphism (AFLP) analysis. For less than half the of the loci investigated, methylation level was correlated with performance, measured as adult body size attained on a given diet, in different nutritional environments, with an overall greater effect in males (the more nutritionally plastic sex) than females. Methylation levels at most sites were influenced more by genotype (iso-female line) than by environment (dung type). Only 1 site (of 12) showed a significant genotype-by-environment interaction. Taken together, our results provide modest support for the hypothesis that DNA methylation underlies nutritional plasticity, as only 8-16% of methylated sites conformed to all of our predictions.
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Fu C, Li L, Wu W, Li M, Yu X, Yu L. Assessment of genetic and epigenetic variation during long-term Taxus cell culture. PLANT CELL REPORTS 2012; 31:1321-1331. [PMID: 22562779 DOI: 10.1007/s00299-012-1251-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/15/2012] [Accepted: 03/17/2012] [Indexed: 05/31/2023]
Abstract
UNLABELLED Gradual loss of secondary metabolite production is a common obstacle in the development of a large-scale plant cell production system. In this study, cell morphology, paclitaxel (Taxol®) biosynthetic ability, and genetic and epigenetic variations in the long-term culture of Taxus media cv Hicksii cells were assessed over a 5-year period to evaluate the mechanisms of the loss of secondary metabolites biosynthesis capacity in Taxus cell. The results revealed that morphological variations, gradual loss of paclitaxel yield and decreased transcriptional level of paclitaxel biosynthesis key genes occurred during long-term subculture. Genetic and epigenetic variations in these cultures were also studied at different times during culture using amplified fragment-length polymorphism (AFLP), methylation-sensitive amplified polymorphism (MSAP), and high-performance liquid chromatography (HPLC) analyses. A total of 32 primer combinations were used in AFLP amplification, and none of the AFLP loci were found to be polymorphic, thus no major genetic rearrangements were detected in any of the tested samples. However, results from both MSAP and HPLC indicated that there was a higher level of DNA methylation in the low-paclitaxel yielding cell line after long-term culture. Based on these results, we proposed that accumulation of paclitaxel in Taxus cell cultures might be regulated by DNA methylation. To our knowledge, this is the first report of increased methylation with the prolongation of culture time in Taxus cell culture. It provides substantial clues for exploring the gradual loss of the taxol biosynthesis capacity of Taxus cell lines during long-term subculture. KEY MESSAGE DNA methylation maybe involved in the regulation of paclitaxel biosynthesis in Taxus cell culture.
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Affiliation(s)
- Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, 430074 Wuhan, China
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