Determination and Difference Analysis of DNA Methylation Content Both in Blood and Muscle Tissue of Pigs

2008 ◽  
Vol 7 (8) ◽  
pp. 1010-1015 ◽  
Author(s):  
Qiu-ju LIANG ◽  
Li-na LIU ◽  
Jian PENG ◽  
Zhi-da SUN ◽  
Si-wen JIANG
Keyword(s):  
Dna Methylation ◽  
Muscle Tissue ◽  
Difference Analysis

scholarly journals Integrative methylome and transcriptome analysis of Japanese flounder (Paralichthys olivaceus) skeletal muscle during development

2019 ◽  
Author(s):  
Jingru Zhang ◽  
Shuxian Wu ◽  
Yajuan Huang ◽  
Haishen Wen ◽  
Meizhao Zhang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Dna Methylation ◽  
Axon Guidance ◽  
Muscle Tissue ◽  
Muscle Development ◽  
Adherens Junction ◽  
Japanese Flounder ◽  
Gene Body ◽  
Skeletal Muscle Development ◽  
Genome Wide

AbstractDNA methylation is an important epigenetic modification in vertebrate and is essential for epigenetic gene regulation in skeletal muscle development. We showed the genome-wide DNA methylation profile in skeletal muscle tissue of larval 7dph (JP1), juvenile 90dph (JP2), adult female 24 months (JP3) and adult male 24 months (JP4) Japanese flounder. The distribution and levels of methylated DNA within genomic features (1stexons, gene body, introns, TSS200, TSS1500 and intergenic) show different developmental landscapes. We also successfully identified differentially methylated regions (DMRs) and different methylated genes (DMGs) through a comparative analysis, indicating that DMR in gene body, intron and intergenic regions were more compared to other regions of all DNA elements. A gene ontology analysis indicated that the DMGs were mainly related to regulation of skeletal muscle fiber development process, Axon guidance, Adherens junction, and some ATPase activity. Methylome and transcriptome clearly revealed a exhibit a negative correlation. And integration analysis revealed a total of 425, 398 and 429 negatively correlated genes with methylation in the JP2_VS_JP1, JP3_VS_JP1 and JP4_VS_JP1 comparison groups, respectively. And these genes were functionally associated with pathways including Adherens junction, Axon guidance, Focal adhesion, cell junctions, Actin cytoskeleton and Wnt signaling pathways. In addition, we validated the MethylRAD results by bisulfite sequencing PCR (BSP) in some of the differentially methylated skeletal muscle growth-related genes (Myod1, Six1 and Ctnnb1). In this study, we have generated the genome-wide profile of methylome and transcriptome in Japanese flounder for the first time, and our results bring new insights into the epigenetic regulation of developmental processes in Japanese flounder. This study contributes to the knowledge on epigenetics in vertebrates.Author summaryEpigenetic mechanisms like DNA methylation have recently reported as vital regulators of some species skeletal muscle development through the control of genes related to growth. To date, although genome-wide DNA methylation profiles of many organisms have been reported and the Japanese flounder reference genome and whole transcriptome data are publically available, the methylation pattern of Japanese flounder skeletal muscle tissue remains minimally studied and the global DNA methylation data are yet to be known. Here we investigated the genome-wide DNA methylation patterns in Japanese flounder, throughout its development. These findings help to enrich research in molecular and developmental biology in vertebrates.

scholarly journals DNA methylation across the genome in aged human skeletal muscle tissue and stem cells: The role of HOX genes and physical activity

2019 ◽  
Author(s):  
DC Turner ◽  
PP Gorski ◽  
MF Maasar ◽  
RA Seaborne ◽  
P Baumert ◽  
...  
Keyword(s):  
Physical Activity ◽  
Skeletal Muscle ◽  
Dna Methylation ◽  
Stem Cells ◽  
Axon Guidance ◽  
Muscle Tissue ◽  
Focal Adhesion ◽  
Human Skeletal Muscle ◽  
Hox Genes ◽  
Muscle Stem Cells

AbstractSkeletal muscle tissue demonstrates global hypermethylation with aging. However, methylome changes across the time-course of differentiation in aged human muscle derived stem cells, and larger coverage arrays in aged muscle tissue have not been undertaken. Using 850K DNA methylation arrays we compared the methylomes of young (27 ± 4.4 years) and aged (83 ± 4 years) human skeletal muscle and that of young/aged muscle stem cells over several time points of differentiation (0, 72 hours, 7, 10 days). Aged muscle tissue was hypermethylated compared with young tissue, enriched for; ‘pathways-in-cancer’ (including; focal adhesion, MAPK signaling, PI3K-Akt-mTOR signaling, p53 signaling, Jak-STAT signaling, TGF-beta and notch signaling), ‘rap1-signaling’, ‘axon-guidance’ and ‘hippo-signalling’. Aged muscle stem cells also demonstrated a hypermethylated profile in pathways; ‘axon-guidance’, ‘adherens-junction’ and ‘calcium-signaling’, particularly at later timepoints of myotube formation, corresponding with reduced morphological differentiation and reductions in MyoD/Myogenin gene expression compared with young cells. While young cells showed little alteration in DNA methylation during differentiation, aged cells demonstrated extensive and significantly altered DNA methylation, particularly at 7 days of differentiation and most notably in the ‘focal adhesion’ and ‘PI3K-AKT signalling’ pathways. While the methylomes were vastly different between muscle tissue and isolated muscle stem cells, we identified a small number of CpG sites showing a hypermethylated state with age, in both muscle and tissue and stem cells (on genes KIF15, DYRK2, FHL2, MRPS33, ABCA17P). Most notably, differential methylation analysis of chromosomal regions identified three locations containing enrichment of 6-8 CpGs in the HOX family of genes altered with age. With HOXD10, HOXD9, HOXD8, HOXA3, HOXC9, HOXB1, HOXB3, HOXC-AS2 and HOXC10 all hypermethylated in aged tissue. In aged cells the same HOX genes (and additionally HOXC-AS3) displayed the most variable methylation at 7 days of differentiation versus young cells, with HOXD8, HOXC9, HOXB1 and HOXC-AS3 hypermethylated and HOXC10 and HOXC-AS2 hypomethylated. We also determined that there was an inverse relationship between DNA methylation and gene expression for HOXB1, HOXA3 and HOXC-AS3. Finally, increased physical activity in young adults was associated with oppositely regulating HOXB1 and HOXA3 methylation compared with age. Overall, we demonstrate that a considerable number of HOX genes are differentially epigenetically regulated in aged human skeletal muscle and muscle stem cells and increased physical activity may help prevent age-related epigenetic changes in these HOX genes.

scholarly journals DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
D. C. Turner ◽  
P. P. Gorski ◽  
M. F. Maasar ◽  
R. A. Seaborne ◽  
P. Baumert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Physical Activity ◽  
Skeletal Muscle ◽  
Dna Methylation ◽  
Axon Guidance ◽  
Muscle Tissue ◽  
Focal Adhesion ◽  
Human Skeletal Muscle ◽  
Hox Genes ◽  
Skeletal Muscle Tissue

Abstract Skeletal muscle tissue demonstrates global hypermethylation with age. However, methylome changes across the time-course of differentiation in aged human muscle derived cells, and larger coverage arrays in aged muscle tissue have not been undertaken. Using 850K DNA methylation arrays we compared the methylomes of young (27 ± 4.4 years) and aged (83 ± 4 years) human skeletal muscle and that of young/aged heterogenous muscle-derived human primary cells (HDMCs) over several time points of differentiation (0, 72 h, 7, 10 days). Aged muscle tissue was hypermethylated compared with young tissue, enriched for; pathways-in-cancer (including; focal adhesion, MAPK signaling, PI3K-Akt-mTOR signaling, p53 signaling, Jak-STAT signaling, TGF-beta and notch signaling), rap1-signaling, axon-guidance and hippo-signalling. Aged cells also demonstrated a hypermethylated profile in pathways; axon-guidance, adherens-junction and calcium-signaling, particularly at later timepoints of myotube formation, corresponding with reduced morphological differentiation and reductions in MyoD/Myogenin gene expression compared with young cells. While young cells showed little alterations in DNA methylation during differentiation, aged cells demonstrated extensive and significantly altered DNA methylation, particularly at 7 days of differentiation and most notably in focal adhesion and PI3K-AKT signalling pathways. While the methylomes were vastly different between muscle tissue and HDMCs, we identified a small number of CpG sites showing a hypermethylated state with age, in both muscle tissue and cells on genes KIF15, DYRK2, FHL2, MRPS33, ABCA17P. Most notably, differential methylation analysis of chromosomal regions identified three locations containing enrichment of 6–8 CpGs in the HOX family of genes altered with age. With HOXD10, HOXD9, HOXD8, HOXA3, HOXC9, HOXB1, HOXB3, HOXC-AS2 and HOXC10 all hypermethylated in aged tissue. In aged cells the same HOX genes (and additionally HOXC-AS3) displayed the most variable methylation at 7 days of differentiation versus young cells, with HOXD8, HOXC9, HOXB1 and HOXC-AS3 hypermethylated and HOXC10 and HOXC-AS2 hypomethylated. We also determined that there was an inverse relationship between DNA methylation and gene expression for HOXB1, HOXA3 and HOXC-AS3. Finally, increased physical activity in young adults was associated with oppositely regulating HOXB1 and HOXA3 methylation compared with age. Overall, we demonstrate that a considerable number of HOX genes are differentially epigenetically regulated in aged human skeletal muscle and HDMCs and increased physical activity may help prevent age-related epigenetic changes in these HOX genes.

scholarly journals Blood and skeletal muscle ageing determined by epigenetic clocks and their associations with physical activity and functioning

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Elina Sillanpää ◽  
Aino Heikkinen ◽  
Anna Kankaanpää ◽  
Aini Paavilainen ◽  
Urho M. Kujala ◽  
...  
Keyword(s):  
Physical Activity ◽  
Dna Methylation ◽  
Body Composition ◽  
Physical Function ◽  
Muscle Tissue ◽  
Vastus Lateralis ◽  
Monozygotic Twin ◽  
Chronological Age ◽  
Epigenetic Clock ◽  
Biological Ageing

AbstractThe aim of this study was to investigate the correspondence of different biological ageing estimates (i.e. epigenetic age) in blood and muscle tissue and their associations with physical activity (PA), physical function and body composition. Two independent cohorts (N = 139 and N = 47) were included, whose age span covered adulthood (23–69 years). Whole blood and m. vastus lateralis samples were collected, and DNA methylation was analysed. Four different DNA methylation age (DNAmAge) estimates were calculated using genome-wide methylation data and publicly available online tools. A novel muscle-specific methylation age was estimated using the R-package ‘MEAT’. PA was measured with questionnaires and accelerometers. Several tests were conducted to estimate cardiorespiratory fitness and muscle strength. Body composition was estimated by dual-energy X-ray absorptiometry. DNAmAge estimates from blood and muscle were highly correlated with chronological age, but different age acceleration estimates were weakly associated with each other. The monozygotic twin within-pair similarity of ageing pace was higher in blood (r = 0.617–0.824) than in muscle (r = 0.523–0.585). Associations of age acceleration estimates with PA, physical function and body composition were weak in both tissues and mostly explained by smoking and sex. The muscle-specific epigenetic clock MEAT was developed to predict chronological age, which may explain why it did not associate with functional phenotypes. The Horvath’s clock and GrimAge were weakly associated with PA and related phenotypes, suggesting that higher PA would be linked to accelerated biological ageing in muscle. This may, however, be more reflective of the low capacity of epigenetic clock algorithms to measure functional muscle ageing than of actual age acceleration. Based on our results, the investigated epigenetic clocks have rather low value in estimating muscle ageing with respect to the physiological adaptations that typically occur due to ageing or PA. Thus, further development of methods is needed to gain insight into muscle tissue-specific ageing and the underlying biological pathways.

scholarly journals Blood and skeletal muscle ageing determined by epigenetic clocks and their associations with physical activity and functioning

2021 ◽  
Author(s):  
Elina Sillanpää ◽  
Aino Heikkinen ◽  
Anna Kankaanpää ◽  
Aini Paavilainen ◽  
Urho M. Kujala ◽  
...  
Keyword(s):  
Physical Activity ◽  
Dna Methylation ◽  
Body Composition ◽  
Physical Function ◽  
Muscle Tissue ◽  
Vastus Lateralis ◽  
Monozygotic Twin ◽  
Chronological Age ◽  
Epigenetic Clock ◽  
Biological Ageing

AbstractThe aim of this study was to investigate the correspondence of different biological ageing estimates (i.e. epigenetic age) in blood and muscle tissue and their associations with physical activity (PA), physical function and body composition.Two independent cohorts were included, whose age span covered adulthood (23–69 years). Whole blood and m. vastus lateralis samples were collected, and DNA methylation analysed. Four different DNA methylation age (DNAmAge) estimates were calculated using genome-wide methylation data and publicly available online tools. A novel muscle-specific methylation age was estimated using the R-package ‘MEAT’. PA was measured with questionnaires and accelerometers. Several tests were conducted to estimate cardiorespiratory fitness and muscle strength. Body composition was estimated by dual-energy X-ray absorptiometry.DNAmAge estimates from blood and muscle were highly correlated with chronological age, but different age acceleration estimates were weakly associated with each other. The monozygotic twin within-pair similarity of ageing pace was higher in blood (r=0.617–0.824) than in muscle (r=0.523–0.585). Associations of age acceleration estimates with PA, physical function and body composition were weak in both tissues and mostly explained by smoking and sex. The muscle-specific epigenetic clock MEAT was developed to predict chronological age, which may explain why it did not associate with functional phenotypes. The Horvath’s clock and GrimAge were weakly associated with PA and related phenotypes, suggesting that higher PA would be linked to accelerated biological ageing in muscle. This may, however, be more reflective of the low capacity of epigenetic clock algorithms to measure functional muscle ageing than of actual age acceleration.Based our results, the investigated epigenetic clocks have rather low value in estimating muscle ageing with respect to the physiological adaptations that typically occur due to ageing or PA. Thus, further development of methods is needed to gain further insight into muscle tissue-specific ageing and the underlying biological pathways.

scholarly journals PSI-11 Anti-inflammatory treatment modifies epigenetics changes to muscle tissue caused by altered nutrient demand in early lactation dairy cows

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 244-245
Author(s):  
Carrie E Cromer ◽  
Caroline M Ylioja ◽  
Miriam Garcia ◽  
Laman K Mamedova ◽  
Barry J Bradford
Keyword(s):  
Dna Methylation ◽  
Milk Yield ◽  
Muscle Tissue ◽  
Enzyme Linked Immunosorbent Assay ◽  
Early Lactation ◽  
Short Term Treatment ◽  
Global Methylation ◽  
Nutrient Demand ◽  
Milking Frequency ◽  
Anti Inflammatory

Abstract Short-term treatment with non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to alter whole-lactation milk yield; perhaps because epigenetic modifications are responsible for long-term effects, although mechanisms are unclear. Altered nutrient demand due to fasting or exercise in other species has been shown to affect DNA methylation in muscle tissue. Our objective was to determine if NSAID treatment or alterations to nutrient demand have epigenetic effects on muscle tissue in early lactation. In this study, 33 multiparous Holstein cows were enrolled at parturition and randomly assigned to milking frequency (MF; 1× or 3×/day), and either sodium salicylate (SS; 2.3 g/L administered via drinking water) or control (CTL; molasses carrier alone) treatment in a 2×2 factorial design, beginning ~24 h postpartum. Milking frequency treatments were designed to alter nutrient demand, and 3× milked increased milk yield by 24%. After 5 days of treatment, tissue biopsies were collected from the Longissimus dorsi muscle and snap-frozen. DNA was isolated and global methylation (GM) was assessed with a 5-methylcytosine enzyme-linked immunosorbent assay. An interaction between MF and SS treatment was detected (P = 0.02), with GM of muscle tissue decreased by more frequent milking only in the CTL cows (4.9 and 1.4 ± 1.0% of DNA methylated for 1× and 3×, respectively; P < 0.001). No effect of MF was detected in SS-treated cows (2.9 and 2.4 ± 1.0% of DNA methylated for 1× and 3×, respectively; P > 0.1). Observed changes to DNA methylation in muscle tissue due to altered nutrient supply are consistent with results reported after fasting and exercise. Additionally, increased demand for milk component precursors in 3×-milked cows may alter the availability of methyl donors for DNA methylation. Our data support a link between SS and epigenetic changes, but further research is needed to determine how SS may have altered the muscle DNA methylation response to nutrient demand.

scholarly journals Genome-wide DNA Methylation Profiles and Their Relationships with mRNA and the microRNA Transcriptome in Bovine Muscle Tissue (Bos taurine)

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Yong-Zhen Huang ◽  
Jia-Jie Sun ◽  
Liang-Zhi Zhang ◽  
Cong-Jun Li ◽  
James E. Womack ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Muscle Tissue ◽  
Bovine Muscle ◽  
Genome Wide

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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