scholarly journals Application of the LUminometric Methylatoion Assay for plant ecological researches: the study of global DNA methylation in leaves of Elodea canadensis under laboratory conditions and in leaves of fen orchid from wild populations

Plant Omics ◽  
2020 ◽  
pp. 30-36
Author(s):  
Natalja Škute ◽  
Marina Savicka ◽  
Aleksandrs Petjukevičs ◽  
Nadežda Harlamova
Keyword(s):  
Dna Methylation ◽  
Environmental Factors ◽  
Methylation Level ◽  
Aquatic Macrophyte ◽  
Elodea Canadensis ◽  
Global Dna Methylation ◽  
Dna Amount ◽  
Methylation Assay ◽  
Liparis Loeselii ◽  
Plant Ecological

The epigenetic changes in the genome of plants are one of the important regulatory mechanisms in response to the environmental factors. The LUminometric Methylation Assay (LUMA) requires a relatively small DNA amount, a short processing time and is easily adapted for species with a non-resolved genome. The LUMA has not been previously used for ecological research of plants. In this research, LUMA was used for the first time to investigate the changes of global DNA methylation under different environmental factors in the leaves of different plants. The influence of salinity on global DNA methylation was studied on aquatic macrophyte Elodea canadensis Michx, which grew in aquatic tanks under different NaCl concentrations. After the third week of growth, the HpaII/MspI ratio was measured by LUMA and global DNA methylation percentages were calculated. The results showed salt stress-induced changes in the global DNA methylation level in E.canadensis leaves, compared to control. The response was salt dose-dependent. The changes of global DNA methylation in wildlife plant populations were analogically assessed on fen orchid Liparis loeselii (L.) Rich. It was shown that global DNA methylation level was higher in leaves of these plants in Engure Lake, where there are temporary changes in water regime, compared to leaves of plants from other places. It was assumed that global GC-DNA methylation plays an essential role in the survival of this plant. Therefore, we show the possibilities of using the LUMA method for epigenetic study of different plants ecological researches.

scholarly journals Disentangling age-dependent DNA methylation: deterministic, stochastic, and nonlinear

2020 ◽  
Author(s):  
O. Vershinina ◽  
M. Ivanchenko ◽  
M.G. Bacalini ◽  
A. Zaikin ◽  
C. Franceschi
Keyword(s):  
Dna Methylation ◽  
Environmental Factors ◽  
Methylation Level ◽  
Signal To Noise Ratio ◽  
Cross Sectional ◽  
Ample Evidence ◽  
Systematic Assessment ◽  
Relative Contribution ◽  
Age Dependent ◽  
The Individual

ABSTRACTDNA methylation variability arises due to concurrent genetic and environmental influences. Each of them is a mixture of regular and noisy sources, whose relative contribution has not been satisfactorily understood yet. We conduct a systematic assessment of the age-dependent methylation by the signal-to-noise ratio and identify a wealth of “deterministic” CpG probes (about 90%), whose methylation variability likely originates due to genetic and general environmental factors. The remaining 10% of “stochastic” CpG probes are arguably governed by the biological noise or incidental environmental factors. Investigating the mathematical functional relationship between methylation levels and variability, we find that in about 90% of the age-associated differentially methylated positions, the variability changes as the square of the methylation level, whereas in the most of the remaining cases the dependence is linear. Furthermore, we demonstrate that the methylation level itself in more than 15% cases varies nonlinearly with age (according to the power law), in contrast to the previously assumed linear changes. Our findings present ample evidence of the ubiquity of strong DNA methylation regulation, resulting in the individual age-dependent and nonlinear methylation trajectories, whose divergence explains the cross-sectional variability. It may also serve a basis for constructing novel nonlinear epigenetic clocks.

scholarly journals Repeats as global DNA methylation marker in bovine preimplantation embryos

2017 ◽  
Vol 62 (No. 2) ◽  
pp. 43-50 ◽  
Author(s):  
W. Li ◽  
A. Van Soom ◽  
L. Peelman
Keyword(s):  
Dna Methylation ◽  
Mutation Rate ◽  
Methylation Level ◽  
Methylation Status ◽  
Repetitive Sequences ◽  
Cell Types ◽  
Blastocyst Stage ◽  
Repeat Sequence ◽  
Preimplantation Embryos ◽  
Global Dna Methylation

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.

scholarly journals 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

2019 ◽  
Vol 8 (1) ◽  
pp. 87 ◽  
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.

scholarly journals Sperm global DNA methylation level: association with semen parameters and genome integrity

Andrology ◽  
2015 ◽  
Vol 3 (2) ◽  
pp. 235-240 ◽  
Author(s):  
D. Montjean ◽  
A. Zini ◽  
C. Ravel ◽  
S. Belloc ◽  
A. Dalleac ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Semen Parameters ◽  
Genome Integrity ◽  
Global Dna Methylation

scholarly journals Influence of maternal age on intracytoplasmic sperm injection outcome and global deoxyribonucleic acid methylation in women undergoing intracytoplasmic sperm injection cycle

2021 ◽  
Vol 10 (6) ◽  
pp. 2185
Author(s):  
Mohammed M. Laqqan ◽  
Maged M. Yassin
Keyword(s):  
Dna Methylation ◽  
Intracytoplasmic Sperm Injection ◽  
Methylation Level ◽  
Maternal Age ◽  
Deoxyribonucleic Acid ◽  
Global Dna Methylation ◽  
Age Group ◽  
Icsi Cycle ◽  
Injection Cycle ◽  
Positive Significant Correlation

Background: Intracytoplasmic sperm injection needs sufficient oocytes of high quality in order to increase the rate of fertilization and pregnancy. This study was designed to investigate the influence of maternal age on the ICSI outcomes in women undergoing to first ICSI cycle and to evaluate the influence of maternal age on global DNA methylation.Methods: A total of 242 females were included in this study with a mean age of 30.5±7.3 years. The participants were divided into three groups depending on women's age≤25, N=70; 26-35, N=102 and>35, N=70). The genomic DNA was isolated from the blood samples, then the global DNA methylation was evaluated using ELISA.Results: A significant reduction has been found in the level of anti-Müllerian hormone (AMH), total number of the collected oocyte, mature oocytes, fertilized oocytes and number of embryos transferred in the older females compared to the younger group (p<0.001). While a significant increase has been found in global DNA methylation level in the older females compared to the younger group (p<0.001). A positive significant correlation has been found between global DNA methylation level and maternal age (p<0.001). In contrast, a negative significant correlation has been shown between AMH level, mature oocytes and maternal age (p<0.001).Conclusions: Maternal age has a significant influence on the number of mature oocytes, number of embryos transferred and global DNA methylation. The pregnancy chance is more in the age group less than 35 years.

Lead (Pb) exposure reduces global DNA methylation level by non-competitive inhibition and alteration of dnmt expression

Metallomics ◽  
2017 ◽  
Vol 9 (2) ◽  
pp. 149-160 ◽  
Author(s):  
Oscar F. Sanchez ◽  
Jinyoung Lee ◽  
Nathaphon Yu King Hing ◽  
Seong-Eun Kim ◽  
Jennifer L. Freeman ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Competitive Inhibition ◽  
Global Dna Methylation ◽  
Pb Exposure
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