scholarly journals DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 190
Author(s):  
Michael Ackah ◽  
Liangliang Guo ◽  
Shaocong Li ◽  
Xin Jin ◽  
Charles Asakiya ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Drought Stress ◽  
Methylation Status ◽  
Enrichment Analysis ◽  
Plant Genome ◽  
Pcr Analysis ◽  
Kegg Pathways ◽  
Wide Range ◽  
And Control

Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments.

scholarly journals Polyamine Metabolism and Gene Methylation in Conjunction with One-Carbon Metabolism

2018 ◽  
Vol 19 (10) ◽  
pp. 3106 ◽  
Author(s):  
Kuniyasu Soda
Keyword(s):  
Dna Methylation ◽  
Carbon Metabolism ◽  
Methylation Status ◽  
Significant Risk ◽  
Significant Risk Factor ◽  
Dna Methyltransferases ◽  
Polyamine Metabolism ◽  
Methyl Group ◽  
Wide Range ◽  
One Carbon Metabolism

Recent investigations have revealed that changes in DNA methylation status play an important role in aging-associated pathologies and lifespan. The methylation of DNA is regulated by DNA methyltransferases (DNMT1, DNMT3a, and DNMT3b) in the presence of S-adenosylmethionine (SAM), which serves as a methyl group donor. Increased availability of SAM enhances DNMT activity, while its metabolites, S-adenosyl-l-homocysteine (SAH) and decarboxylated S-adenosylmethionine (dcSAM), act to inhibit DNMT activity. SAH, which is converted from SAM by adding a methyl group to cytosine residues in DNA, is an intermediate precursor of homocysteine. dcSAM, converted from SAM by the enzymatic activity of adenosylmethionine decarboxylase, provides an aminopropyl group to synthesize the polyamines spermine and spermidine. Increased homocysteine levels are a significant risk factor for the development of a wide range of conditions, including cardiovascular diseases. However, successful homocysteine-lowering treatment by vitamins (B6, B12, and folate) failed to improve these conditions. Long-term increased polyamine intake elevated blood spermine levels and inhibited aging-associated pathologies in mice and humans. Spermine reversed changes (increased dcSAM, decreased DNMT activity, aberrant DNA methylation, and proinflammatory status) induced by the inhibition of ornithine decarboxylase. The relation between polyamine metabolism, one-carbon metabolism, DNA methylation, and the biological mechanism of spermine-induced lifespan extension is discussed.

scholarly journals Investigating skewness to understand gene expression heterogeneity in large patient cohorts

2019 ◽  
Vol 20 (S24) ◽  
Author(s):  
Benjamin V. Church ◽  
Henry T. Williams ◽  
Jessica C. Mar
Keyword(s):  
Dna Methylation ◽  
Methylation Status ◽  
Microarray Technology ◽  
Statistical Measure ◽  
Large Patient ◽  
Technology Platforms ◽  
Gene Expression Heterogeneity ◽  
Cancer Genome Atlas ◽  
Or Genes ◽  
And Control

Abstract Background Skewness is an under-utilized statistical measure that captures the degree of asymmetry in the distribution of any dataset. This study applied a new metric based on skewness to identify regulators or genes that have outlier expression in large patient cohorts. Results We investigated whether specific patterns of skewed expression were related to the enrichment of biological pathways or genomic properties like DNA methylation status. Our study used publicly available datasets that were generated using both RNA-sequencing and microarray technology platforms. For comparison, the datasets selected for this study also included different samples derived from control donors and cancer patients. When comparing the shift in expression skewness between cancer and control datasets, we observed an enrichment of pathways related to the immune function that reflects an increase towards positive skewness in the cancer relative to control datasets. A significant correlation was also detected between expression skewness and the top 500 genes corresponding to the most significant differential DNA methylation occurring in the promotor regions for four Cancer Genome Atlas cancer cohorts. Conclusions Our results indicate that expression skewness can reveal new insights into transcription based on outlier and asymmetrical behaviour in large patient cohorts.

scholarly journals Combination Analysis of NR3C1, MTHFR and IGFBP3 Gene Polymorphisms and DNA Methylation With Steroid-induced Osteonecrosis of the Femoral Head Risk in Chinese Han Population 

2020 ◽  
Author(s):  
Ronglan Huang ◽  
Qinghao Zhan ◽  
Wenbin Hu ◽  
Renmin Yang ◽  
Nan Cheng ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Femoral Head ◽  
Methylation Level ◽  
Gene Polymorphisms ◽  
Methylation Status ◽  
Chinese Han Population ◽  
Control Group ◽  
Chinese Han ◽  
Han Population ◽  
Wide Range

Abstract Background: Although the precise etiology of osteonecrosis of the femoral head (ONFH) has yet to be fully elucidated, it is known that nuclear receptor subfamily3, group C, member 1 (NR3C1), 5, 10-methylenetetrahydrofolate reductase (MTHFR) and insulin-like growth factor-binding protein 3 (IGFBP3) are related to the pathophysiology of steroid-induced osteonecrosis of the femoral head (SONFH). The expression of NR3C1, MTHFR and IGFBP3 are regulated by epigenetics and genetic profiles. Objective: The primary objective of this study was to investigated the association between NR3C1, MTHFR and IGFBP3 gene polymorphisms and DNA methylation status and SONFH.Methods: This case-control study included 79 patients with SONFH and 114 patients who took steroids but did not develop SONFH. We evaluated 5 single-nucleotide polymorphisms (SNPs) out of 3 genes in Chinese Han population. These SNPs were genotyped by improved multiplex ligation detection reaction (iMLDR). Methyltarget was used to test the methylation level of positive sites, the interaction between SNPs and DNA methylation level was analyzed using eQTLD technique.Results: We identified rs3110697 in the IGFBP3 gene that was potentially associated with a reduced risk of SONFH in the genotype (P=0.008; odds ratio [OR]: 0.741; 95% confidence intervals [CI]: 0.456–1.205) and in the recessive model (P=0.003; OR: NA; 95% CI: NA–NA). Furthermore, CpG sites with significant differences in methylation levels were screened as follows: IGFBP3_2-143, MTHFR_1-36, MTHFR_1-77, MTHFR_1-139, MTHFR_2-42, NR3C1_2-163, NR3C1_4-47, and the differences were statistically significant compared with the control group (p<0.05). A total of 10 pairs of linear regression tests of SNP and methylation sites were statistically significant (p<0.05).Conclusions: SONFH is a polygenic disorder in which a wide range of interactions between SNPs and DNA methylation levels may dominate the course of the disease.

scholarly journals Unraveling microRNA Mediated Gene Regulation in Centella asiatica (L.) Urb. by High-throughput Sequencing based Small-RNA Profiling.

2022 ◽  
Author(s):  
Gouri Priya Ranjith ◽  
Jisha Satheesan ◽  
K K Sabu
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
Centella Asiatica ◽  
Plant Secondary Metabolite ◽  
Pcr Analysis ◽  
Shoot Cultures ◽  
Regulatory Pathways ◽  
Mrna Targets ◽  
Computational Screening ◽  
Wide Range

Abstract Centella asiatica is a widely spread herb mostly found in the tropics having extensive medicinal values. Here, we report for the first time, transcriptome-wide characterization of miRNA profile from the leaves of C. asiatica using high-throughput Illumina sequencing. We identified 227 conserved and 109 putative novel miRNAs. Computational screening revealed potential mRNA targets for both the conserved and novel miRNAs encoding diverse transcription factors and enzymes involved in plant development, disease resistance, metabolic and signaling pathways. Gene ontology annotation and KEGG analysis revealed the miRNA targets to be involved in a wide range of metabolomic and regulatory pathways. The differential expression of the miRNA encoding genes in diverse tissues was determined by real-time PCR analysis. We also found that gene expression levels of miR156, 159 and 1171 was reduced in salicylic acid treated axenic shoot cultures of C. asiatica compared to its control. Furthermore, RLM-RACE experiments mapped miRNA-mediated cleavage at two of the mRNA targets. The present study represents the large-scale identification of microRNAs from C. asiatica and contributes to the base for the up-coming studies on miRNA-mediated gene regulation of plant secondary metabolite pathways in particular.

scholarly journals Unraveling MicroRNA Mediated Gene Regulation in Centella Asiatica (L.) Urb. by High-Throughput Sequencing based Small-RNA Profiling.

2021 ◽  
Author(s):  
Gouri Priya Ranjith ◽  
Jisha Satheesan ◽  
K K Sabu
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
Centella Asiatica ◽  
Plant Secondary Metabolite ◽  
Pcr Analysis ◽  
Shoot Cultures ◽  
Regulatory Pathways ◽  
Mrna Targets ◽  
Computational Screening ◽  
Wide Range

Abstract Centella asiatica is a widely spread herb mostly found in the tropics having extensive medicinal values. Here, we report for the first time, transcriptome-wide characterization of miRNA profile from the leaves of C. asiatica using high-throughput Illumina sequencing. We identified 227 conserved and 109 putative novel miRNAs. Computational screening revealed potential mRNA targets for both the conserved and novel miRNAs encoding diverse transcription factors and enzymes involved in plant development, disease resistance, metabolic and signaling pathways. Gene ontology annotation and KEGG analysis revealed the miRNA targets to be involved in a wide range of metabolomic and regulatory pathways. The differential expression of the miRNA encoding genes in diverse tissues was determined by real-time PCR analysis. We also found that gene expression levels of miR156, 159 and 1171 was reduced in salicylic acid treated axenic shoot cultures of C. asiatica compared to its control. Furthermore, RLM-RACE experiments mapped miRNA-mediated cleavage at two of the mRNA targets. The present study represents the large-scale identification of microRNAs from C. asiatica and contributes to the base for the up-coming studies on miRNA-mediated gene regulation of plant secondary metabolite pathways in particular.

167 EFFECT OF DNA METHYLATION INHIBITOR ON HETEROCHROMATIN IN BOVINE EMBRYOS DERIVED FROM HEAT-SHOCKED OOCYTES

2016 ◽  
Vol 28 (2) ◽  
pp. 213
Author(s):  
T. D. Araujo ◽  
J. Jasmin ◽  
C. C. R. Quintao ◽  
E. D. Souza ◽  
J. H. M. Viana ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Shock ◽  
In Vitro Maturation ◽  
Methylation Status ◽  
Control Groups ◽  
Methylation Inhibitor ◽  
Response To Stress ◽  
Dna Methylation Inhibitor ◽  
And Control

The cell response to stress involves epigenetic modifications in order to regulate the gene expression, which is dependent of chromatin structure and DNA methylation status. On the other hand, changes on DNA methylation can have an effect on chromatin organisation (Espada and Esteller 2010 Semin. Cell. Dev. Biol. 21, 238–246). In this study we evaluated the effect of 5-aza-2′-deoxycytidine (5-aza; Sigma, St. Louis, MO, USA), a DNA methylation inhibitor, on heterochromatin 1 β formation of bovine pre-implantation embryos derived from oocytes that did or did not undergo heat shock during in vitro maturation (IVM). Oocytes were IVM under 38.5°C for 24 h (non-heat-shock: NHS group) or under 41.5°C for 12 h followed by 38.5°C for 12 h (heat-shock: HS group). Oocytes were IVF for 20 h and the denuded presumptive zygotes from NHS or HS groups were cultured with 0 (nontreated controls) or 10 nM of 5-aza for 24 h or 48 h in CR2aa plus 2.5% FCS at 38.5°C with 5% CO2, 5% O2 and 90% N2. Embryos with 4–7 cells at 44 h post-insemination (hpi) and embryos with 8–16 cells at 68 hpi were fixed in 4% paraformaldehyde and stained with anti-mouse HP1β first antibody, then immunofluorescence was evaluated by confocal microscopy (Leica TCS SP5II) and images were processed by ImageJ 1.49 (NIH, Bethesda, MD, USA). Fluorescence of nuclei and of background area (fluorescence/unit area) were measured and then the corrected relative fluorescence per nucleus was calculated. We analysed 129 and 149 nuclei at 44 hpi from 29 and 34 embryos as well as 268 and 182 nuclei at 68 hpi from 37 and 22 embryos of the NHS and HS groups, respectively, obtained from 3 replicates. Data underwent log-transformation and was analysed by ANOVA, and means compared by Student-Newman-Keuls. Embryos with 8–16 cells derived from NHS oocytes and treated with 5-aza for 24 h or for 48 h had nuclei with lower HP1 fluorescence than their respective NHS (nontreated) control (P < 0.01). In contrast, 8–16-cells embryos derived from HS and treated with 5-aza displayed nuclei with the same HP1 fluorescence of their respective HS control (P > 0.05). When embryos derived from HS and NHS (nontreated) control groups were compared, higher HP1 fluorescence was found in those with 4–7 cells of HS group (P < 0.05); however, embryos with 8–16 cells displayed similar HP1 fluorescence between both NHS and HS control groups (P > 0.05). There was no difference on HP1 fluorescence between nuclei of embryos with 4–7 cells treated with 5-aza for 24 h and control (nontreated) in both HS and NHS groups. These data suggest that embryos derived from heat-shocked oocytes can accumulate more heterochromatin at earlier stages than those from non-heat-shocked oocytes and that the effect of DNA methylation inhibition by 5-aza on embryo heterochromatin can vary accordingly to the exposure of the oocyte to heat shock during in vitro maturation. Financial support from CNPq, Fapemig, and CAPES is acknowledged.

Association of exposure to deoxynivalenol with DNA methylation in white blood cells in children in China

2021 ◽  
pp. 1-14
Author(s):  
P. Cao ◽  
X.D. Wang ◽  
J.F. Sun ◽  
J. Liang ◽  
P.P. Zhou ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Cells ◽  
Chronic Exposure ◽  
Methylation Status ◽  
White Blood Cells ◽  
Dietary Exposure ◽  
Health Concern ◽  
Kegg Pathways ◽  
Differentially Methylated Genes ◽  
Great Public Health

Deoxynivalenol (DON) is a mycotoxin that commonly contaminates cereals worldwide. Dietary exposure to DON is a subject of great public health concern, but studies on the health effects of chronic exposure to DON are not available. In this study, we investigated the connection between DNA methylation levels and DON exposure in children. The DNA methylation status of white blood cells from 32 children aged 2~15 years old in Henan, China, was profiled. A total of 378 differentially methylated CpGs were identified between the high and low DON exposure groups, and 8 KEGG pathways were found to be significantly enriched among the differentially methylated genes. In addition, the quantitative methylation of EIF2AK4, EMID2 and GNASAS was analysed using the Sequenom MassARRAY platform. The results showed that the methylation level of EIF2AK4 was significantly different between the two groups, and the methylation levels were associated with exposure to DON. Conclusively, our study found that chronic exposure to DON during childhood could affect DNA methylation levels.

scholarly journals Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation

2003 ◽  
Vol 23 (15) ◽  
pp. 5293-5300 ◽  
Author(s):  
Robert A. Waterland ◽  
Randy L. Jirtle
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Transposable Element ◽  
Methylation Status ◽  
Dietary Supplementation ◽  
Vitamin B ◽  
Transposable Element Insertion ◽  
Insertion Sites ◽  
Nutritional Effects ◽  
Epigenetic Gene Regulation

ABSTRACT Early nutrition affects adult metabolism in humans and other mammals, potentially via persistent alterations in DNA methylation. With viable yellow agouti (Avy ) mice, which harbor a transposable element in the agouti gene, we tested the hypothesis that the metastable methylation status of specific transposable element insertion sites renders them epigenetically labile to early methyl donor nutrition. Our results show that dietary methyl supplementation of a/a dams with extra folic acid, vitamin B12, choline, and betaine alter the phenotype of their Avy/a offspring via increased CpG methylation at the Avy locus and that the epigenetic metastability which confers this lability is due to the Avy transposable element. These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans.

scholarly journals The effect of DNA methylation on bumblebee colony development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
María I. Pozo ◽  
Benjamin J. Hunt ◽  
Gaby Van Kemenade ◽  
Jose M. Guerra-Sanz ◽  
Felix Wäckers ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Status ◽  
Developmental Rate ◽  
Colony Development ◽  
Control Group ◽  
Parental Line ◽  
Caste Determination ◽  
Genome Bisulfite Sequencing ◽  
Neuron Function ◽  
And Control

Abstract Background Although around 1% of cytosines in bees’ genomes are known to be methylated, less is known about methylation’s effect on bee behavior and fitness. Chemically altered DNA methylation levels have shown clear changes in the dominance and reproductive behavior of workers in queen-less colonies, but the global effect of DNA methylation on caste determination and colony development remains unclear, mainly because of difficulties in controlling for genetic differences among experimental subjects in the parental line. Here, we investigated the effect of the methylation altering agent decitabine on the developmental rate of full bumblebee colonies. Whole genome bisulfite sequencing was used to assess differences in methylation status. Results Our results showed fewer methylated loci in the control group. A total of 22 CpG loci were identified as significantly differentially methylated between treated and control workers with a change in methylation levels of 10% or more. Loci that were methylated differentially between groups participated in pathways including neuron function, oocyte regulation and metabolic processes. Treated colonies tended to develop faster, and therefore more workers were found at a given developmental stage. However, male production followed the opposite trend and it tended to be higher in control colonies. Conclusion Overall, our results indicate that altered methylation patterns resulted in an improved cooperation between workers, while there were no signs of abnormal worker dominance or caste determination.

scholarly journals Transcriptome and Methylome Changes in Two Contrasting Mungbean Genotypes in Response to Drought Stress

2021 ◽  
Author(s):  
Peilei Zhao ◽  
Bao Ma ◽  
Chunmei Cai ◽  
Jihua Xu
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Drought Stress ◽  
Stress Responses ◽  
Methylation Status ◽  
Physiological Parameters ◽  
Gene Body ◽  
Sequence Context ◽  
Transcriptomic Data ◽  
Growth Distribution

Abstract Background: Due to drought stress, the growth, distribution, and production of mungbean is severely restricted. Previous study combining physiological and transcriptomic data indicated different genotypes of mungbean exhibited variable responses when exposed to drought stress. Aside from the genetic variation, the modifications of environmentally induced epigenetics alterations on mungbean drought-stress responses were still elusive. Results: In this study, firstly, we compared the drought tolerance capacity at seedling stages by detecting physiological parameters in two contrasting genotypes wild mungbean 61 and cultivar 70 in response to drought stress. We found that wild mungbean 61 showed lower level of MDA and higher levels of SOD, POD, and CAT, suggesting wild mungbean 61 exhibited stronger drought resistances. Transcriptomic analysis indicated totally 2659 differentially expressed genes (DEGs) were detected when 61 compared with 70 (C61 vs C70), and the number increased to 3121 in the comparison of drought-treated 70 compared with drought-treated 61 (D70 vs D61). In addition, when drought-treated 61 and 70 were compared with their controls, the DEGs were 1117 and 185 respectively, with more down-regulated DEGs than up-regulated in D61 vs C61, which was opposite in D70 vs C70. Interestingly, corresponding to this, after drought stress, more hypermethylated differentially methylated regions (DMRs) in 61 were detected and more hypomethylated DMRs in 70 were detected. Further analysis suggested that the main variations between 61 and 70 existed in CHH methylation in promoter. Moreover, the preference of methylation status alterations in D60 vs C60 and D70 vs C70 also fell in CHH sequence context. Further analysis of the correlation between DMRs and DEGs indicated in both D61 vs C61 and D70 vs C70, the DMRs in gene body was significantly negatively correlated with DEGs. Conclusion: The physiological parameters in this research suggested that wild mungbean 61 was more resistant to drought stress, with more hypermethylated DMRs and less hypomethylated DMRs after drought stress, corresponding to more down-regulated DEGs than up-regulated DEGs. Among the three DNA methylation contexts CG, CHG, and CHH, asymmetric CHH contexts were more dynamic and prone to be altered by drought stress and genotypic variations.

Sign in / Sign up

Export Citation Format

Share Document