Repeats as global DNA methylation marker in bovine preimplantation embryos

DNA methylation undergoes dynamic changes and is a crucial part of the epigenetic regulation during mammalian early development. To determine the DNA methylation levels in bovine embryos, we applied a bisulfite sequencing based method aimed at repetitive sequences including three retrotransposons (L1_BT, BovB, and ERV1-1-I_BT) and Satellite I. A more accurate estimate of the global DNA methylation level compared to previous methods using only one repeat sequence, like Alu, could be made by calculation of the weighted arithmetic mean of multiple repetitive sequences, considering the copy number of each repetitive sequence. Satellite I and L1_BT showed significant methylation reduction at the blastocyst stage, while BovB and ERV1-1-I_BT showed no difference. The mean methylation level of the repetitive sequences during preimplantation development was the lowest at the blastocyst stage. No methylation difference was found between embryos cultured in 5% and 20% O<sub>2</sub>. Because mutations of CpGs negatively influence the calculation accuracy, we checked the mutation rate of the sequenced CpG sites. Satellite I and L1_BT showed a relatively low mutation rate (1.92 and 3.72% respectively) while that of ERV1-1-I_BT and BovB was higher (11.95 and 24% respectively). Therefore we suggest using a combination of repeats with low mutation rate, taking into account the proportion of each sequence, as a relatively quick marker for the global DNA methylation status of preimplantation stages and possibly also for other cell types.

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Global DNA Methylation Profiles of Buffalo (Bubalus Bubalis) Preimplantation Embryos Produced by Handmade Cloning and in Vitro Fertilization

10.21203/rs.3.rs-550977/v1 ◽

2021 ◽

Author(s):

Shivani Malpotra ◽

Pallavi Goel ◽

Songyukta Shyam ◽

Manoj Kumar Singh ◽

Prabhat Palta

Keyword(s):

Dna Methylation ◽

Developmental Stages ◽

Methylation Status ◽

Cpg Islands ◽

Live Birth Rate ◽

Preimplantation Embryos ◽

Global Dna Methylation ◽

Vitro Fertilization ◽

Low Efficiency

Abstract Somatic cell nuclear transfer technique (SCNT) has proved to be an outstanding method of multiplication of elite animals but accompanied with low efficiency and live birth rate of cloned animals. Epigenetic alterations of DNA has been one of the culprits behind this issue. Cloned embryos are found to deviate slightly from regular pattern of demethylation and re-methylation at the time of nuclear reprogramming and embryonic development when compared with embryos produced by in vitro fertilization (IVF). Thus, the present study was aimed at evaluating global DNA methylation profiles of cloned embryos at 2-cell, 8-cell and blastocyst stages and compare it with corresponding stages of embryos produced by IVF by using MeDIP-Sequencing on Illumina-based platform. We found out that cloned embryos exhibited significantly different DNA methylation pattern as compared to IVF embryos with respect to distribution of differentially methylated regions in different components of genome, CpG islands distribution and methylation status, gene ontological profiles and pathways affected throughout the developmental stages. The data generated from MeDIP-Seq was validated at blastocyst stage cloned and IVF embryos by bisulfite-sequencing PCR on five randomly selected gene regions.

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DNA Methylation Status of the Interspersed Repetitive Sequences for LINE-1, Alu, HERV-E, and HERV-K in Trabeculectomy Specimens from Glaucoma Eyes

Journal of Ophthalmology ◽

10.1155/2018/9171536 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10

Author(s):

Sunee Chansangpetch ◽

Sasiprapa Prombhul ◽

Visanee Tantisevi ◽

Pimpayao Sodsai ◽

Anita Manassakorn ◽

...

Keyword(s):

Dna Methylation ◽

Methylation Level ◽

Restriction Analysis ◽

Methylation Status ◽

Repetitive Sequences ◽

Secondary Glaucoma ◽

Angle Closure ◽

Dna Hypomethylation ◽

Global Methylation ◽

Normal Controls

Background/Aims. Epigenetic mechanisms via DNA methylation may be related to glaucoma pathogenesis. This study aimed to determine the global DNA methylation level of the trabeculectomy specimens among patients with different types of glaucoma and normal subjects. Methods. Trabeculectomy sections from 16 primary open-angle glaucoma (POAG), 12 primary angle-closure glaucoma (PACG), 16 secondary glaucoma patients, and 10 normal controls were assessed for DNA methylation using combined-bisulfite restriction analysis. The percentage of global methylation level of the interspersed repetitive sequences for LINE-1, Alu, HERV-E, and HERV-K were compared between the 4 groups. Results. There were no significant differences in the methylation for LINE-1 and HERV-E between patients and normal controls. For the Alu marker, the methylation was significantly lower in all types of glaucoma patients compared to controls (POAG 52.19% versus control 52.83%, p=0.021; PACG 51.50% versus control, p=0.005; secondary glaucoma 51.95% versus control, p=0.014), whereas the methylation level of HERV-K was statistically higher in POAG patients compared to controls (POAG 49.22% versus control 48.09%, p=0.017). Conclusions. The trabeculectomy sections had relative DNA hypomethylation of Alu in all glaucoma subtypes and relative DNA hypermethylation of HERV-K in POAG patients. These methylation changes may lead to the fibrotic phenotype in the trabecular meshwork.

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Potential effect of tobacco cigarettes smoking on global DNA methylation status and protamines transcripts in human spermatozoa

Middle East Fertility Society Journal ◽

10.1186/s43043-021-00066-3 ◽

2021 ◽

Vol 26 (1) ◽

Author(s):

Mohammed M. Laqqan ◽

Maged M. Yassin

Keyword(s):

Dna Methylation ◽

Cigarette Smoking ◽

Dna Fragmentation ◽

Methylation Status ◽

Human Spermatozoa ◽

Global Dna Methylation ◽

Transcription Level ◽

Heavy Smokers ◽

Protamine 1 ◽

Protamine 2

Abstract Background Epigenetics refers to an alteration in gene expression without alteration in the sequence of DNA and this process may be affected by environmental factors and lifestyle like cigarette smoking. This study was designed to evaluate the potential effect of cigarette smoking on the global DNA methylation status and the transcription level of protamine 1 and protamine 2 in human spermatozoa. A total of 188 semen samples were collected from men with a mean age of 34.9 ± 5.8 years old (98 heavy smokers and 90 non-smokers). The DNA and RNA were isolated from purified spermatozoa, then the status of global DNA methylation and the transcription level of protamine 1 and protamine 2 were evaluated using ELISA and qPCR, respectively. The chromatin non-condensation and DNA fragmentation in human spermatozoa were evaluated using chromomycin A3 staining and TUNEL assay, respectively. Results A significant increase has been found in the status of global DNA methylation in spermatozoa of heavy smokers compared to non-smokers (7.69 ± 0.69 ng/μl vs. 4.90 ± 0.40 ng/μl, P < 0.001). Additionally, a significant reduction has been found in transcription level of protamine 1 (25.49 ± 0.31 vs. 23.94 ± 0.40, P < 0.001) and protamine 2 (28.27 ± 0.39 vs. 23.45 ± 0.30, P < 0.001) in heavy smokers. A downregulation has been found in the transcription level of protamine 1 and protamine 2 with a fold change of 0.497 and 0.047, respectively. A significant increase has been shown in the level of DNA fragmentation and chromatin non-condensation in heavy smokers compared to non-smokers (P < 0.001). On the other hand, a significant positive correlation has been found between sperm chromatin non-condensation, sperm DNA fragmentation, transcription level of protamine 1, transcription level of protamine 2, and global DNA methylation status (r = 0.304, P < 0.001; r = 0.399, P < 0.001; r = 0.216, P = 0.003; r = 0.494, P < 0.001, respectively). Conclusion Tobacco cigarette smoking has a potential influence on the global DNA methylation and the transcription level of protamine genes in human spermatozoa, and consequently, affect negatively on the semen parameters.

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Overexpression of CDKN2B (p15INK4B) and altered global DNA methylation status in mesenchymal stem cells of high-risk myelodysplastic syndromes

Leukemia ◽

10.1038/leu.2014.197 ◽

2014 ◽

Vol 28 (11) ◽

pp. 2241-2244 ◽

Cited By ~ 8

Author(s):

A Poloni ◽

G Maurizi ◽

D Mattiucci ◽

S Amatori ◽

B Fogliardi ◽

...

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Mesenchymal Stem Cells ◽

High Risk ◽

Myelodysplastic Syndromes ◽

Methylation Status ◽

Global Dna Methylation

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Differential DNA methylation reprogramming of various repetitive sequences in mouse preimplantation embryos

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2004.09.023 ◽

2004 ◽

Vol 324 (1) ◽

pp. 58-63 ◽

Cited By ~ 39

Author(s):

Seok-Ho Kim ◽

Yong-Kook Kang ◽

Deog-Bon Koo ◽

Man-Jong Kang ◽

Seung-Ju Moon ◽

...

Keyword(s):

Dna Methylation ◽

Repetitive Sequences ◽

Preimplantation Embryos

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Using a medium-throughput comet assay to evaluate the global DNA methylation status of single cells

Frontiers in Genetics ◽

10.3389/fgene.2014.00215 ◽

2014 ◽

Vol 5 ◽

Cited By ~ 15

Author(s):

AngÃ©lique Lewies ◽

Etresia Van Dyk ◽

Johannes F. Wentzel ◽

Pieter J. Pretorius

Keyword(s):

Dna Methylation ◽

Comet Assay ◽

Single Cells ◽

Methylation Status ◽

Global Dna Methylation

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Global DNA methylation level in females with idiopathic scoliosis

Studies in Health Technology and Informatics - Research into Spinal Deformities 9 ◽

10.3233/shti210478 ◽

2021 ◽

Author(s):

P Janusz ◽

M Chmielewska ◽

M Andrusiewicz ◽

T Kotwicki ◽

M Kotwicka

Keyword(s):

Dna Methylation ◽

Idiopathic Scoliosis ◽

Methylation Level ◽

Global Dna Methylation

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DNA methylation of insulin-like growth factor 2 and H19 cluster in cord blood and prenatal air pollution exposure to fine particulate matter

Environmental Health ◽

10.1186/s12940-020-00677-9 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Congrong Wang ◽

Michelle Plusquin ◽

Akram Ghantous ◽

Zdenko Herceg ◽

Rossella Alfano ◽

...

Keyword(s):

Dna Methylation ◽

Particulate Matter ◽

Growth Factor ◽

Cord Blood ◽

Gene Cluster ◽

Methylation Level ◽

Fine Particulate Matter ◽

Methylation Status ◽

Insulin Like Growth Factor ◽

Fine Particulate

Abstract Background The IGF2 (insulin-like growth factor 2) and H19 gene cluster plays an important role during pregnancy as it promotes both foetal and placental growth. We investigated the association between cord blood DNA methylation status of the IGF2/H19 gene cluster and maternal fine particulate matter exposure during fetal life. To the best of our knowledge, this is the first study investigating the association between prenatal PM2.5 exposure and newborn DNA methylation of the IGF2/H19. Methods Cord blood DNA methylation status of IGF2/H19 cluster was measured in 189 mother-newborn pairs from the ENVIRONAGE birth cohort (Flanders, Belgium). We assessed the sex-specific association between residential PM2.5 exposure during pregnancy and the methylation level of CpG loci mapping to the IGF2/H19 cluster, and identified prenatal vulnerability by investigating susceptible time windows of exposure. We also addressed the biological functionality of DNA methylation level in the gene cluster. Results Prenatal PM2.5 exposure was found to have genetic region-specific significant association with IGF2 and H19 during specific gestational weeks. The association was found to be sex-specific in both gene regions. Functionality of the DNA methylation was annotated by the association to fetal growth and cellular pathways. Conclusions The results of our study provided evidence that prenatal PM2.5 exposure is associated with DNA methylation in newborns’ IGF2/H19. The consequences within the context of fetal development of future phenotyping should be addressed.

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Altered Adipose Tissue DNA Methylation Status in Metabolic Syndrome: Relationships Between Global DNA Methylation and Specific Methylation at Adipogenic, Lipid Metabolism and Inflammatory Candidate Genes and Metabolic Variables

Journal of Clinical Medicine ◽

10.3390/jcm8010087 ◽

2019 ◽

Vol 8 (1) ◽

pp. 87 ◽

Cited By ~ 23

Author(s):

Daniel Castellano-Castillo ◽

Isabel Moreno-Indias ◽

Lidia Sanchez-Alcoholado ◽

Bruno Ramos-Molina ◽

Juan Alcaide-Torres ◽

...

Keyword(s):

Metabolic Syndrome ◽

Dna Methylation ◽

Adipose Tissue ◽

Lipid Metabolism ◽

Environmental Factors ◽

Metabolic Diseases ◽

Methylation Status ◽

Serum Triglyceride ◽

Positive Association ◽

Global Dna Methylation

Metabolic syndrome (MetS) has been postulated to increase the risk for type 2 diabetes, cardiovascular disease and cancer. Adipose tissue (AT) plays an important role in metabolic homeostasis, and AT dysfunction has an active role in metabolic diseases. MetS is closely related to lifestyle and environmental factors. Epigenetics has emerged as an interesting landscape to evaluate the possible interconnection between AT and metabolic disease, since it can be modulated by environmental factors and metabolic status. The aim of this study was to determine whether MetS has an impact on the global DNA methylation pattern and the DNA methylation of several genes related to adipogenesis (PPARG, PPARA), lipid metabolism (RXRA, SREBF2, SREBF1, SCD, LPL, LXRb), and inflammation (LRP1 C3, LEP and TNF) in visceral adipose tissue. LPL and TNF DNA methylation values were significantly different in the control-case comparisons, with higher and lower methylation respectively in the MetS group. Negative correlations were found between global DNA methylation (measured by LINE-1 methylation levels) and the metabolic deterioration and glucose levels. There were associations among variables of MetS, BMI, and HOMA-IR with DNA methylation at several CpG positions for the studied genes. In particular, there was a strong positive association between serum triglyceride levels (TG) with PPARA and LPL methylation levels. TNF methylation was negatively associated with the metabolic worsening and could be an important factor in preventing MetS occurrence according to logistic regression analysis. Therefore, global DNA methylation and methylation at specific genes related to adipogenesis, lipid metabolism and inflammation are related to the etiology of MetS and might explain in part some of the features associated to metabolic disorders.

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