scholarly journals Comparison of DNA Methylation in Schwann Cells before and after Peripheral Nerve Injury in Rats

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Xian-Hu Zhou ◽  
Wei Lin ◽  
Yi-Ming Ren ◽  
Shen Liu ◽  
Bao-You Fan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Peripheral Nerve ◽  
Schwann Cells ◽  
Expression Patterns ◽  
Analysis Data ◽  
Differentially Methylated Genes ◽  
Before And After ◽  
Intergenic Regions ◽  
The Difference ◽  
Nerve System

This study aims to find the difference of genomewide DNA methylation in Schwann cells (SCs) before and after peripheral nerve system (PNS) injury by Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq) and seek meaningful differentially methylated genes related to repairment of injured PNS. SCs harvested from sciatic nerve were named as activated Schwann cells (ASCs), and the ones harvested from brachial plexus were named as normal Schwann cells (NSCs). Genomic DNA of ASCs and NSCs were isolated and MeDIP-Seq was conducted. Differentially methylated genes and regions were discovered and analyzed by bioinformatic methods. MeDIP-Seq analysis showed methylation differences were identified between ASCs and NSCs. The distribution of differentially methylated regions (DMRs) peaks in different components of genome was mainly located in distal intergenic regions. GO and KEGG analysis of these methylated genes were also conducted. The expression patterns of hypermethylated genes (Dgcr8, Zeb2, Dixdc1, Sox2, and Shh) and hypomethylated genes (Gpr126, Birc2) detected by qRT-PCR were opposite to the MeDIP analysis data with significance (p< 0.05), which proved MeDIP analysis data were real and believable. Our data serve as a basis for understanding the injury-induced epigenetic changes in SCs and the foundation for further studies on repair of PNS injury.

scholarly journals Maternal and Post-weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts

2019 ◽  
Vol 20 (13) ◽  
pp. 3229 ◽  
Author(s):  
Moody ◽  
Wang ◽  
Jung ◽  
Chen ◽  
Pan
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Metabolic Pathways ◽  
Expression Patterns ◽  
Sprague Dawley ◽  
High Fat ◽  
Differentially Methylated Genes ◽  
High Fat Diets ◽  
Diet Intake ◽  
Fat Diets

Calorie-dense high-fat diets (HF) are associated with detrimental health outcomes, including obesity, cardiovascular disease, and diabetes. Both pre- and post-natal HF diets have been hypothesized to negatively impact long-term metabolic health via epigenetic mechanisms. To understand how the timing of HF diet intake impacts DNA methylation and metabolism, male Sprague–Dawley rats were exposed to either maternal HF (MHF) or post-weaning HF diet (PHF). At post-natal week 12, PHF rats had similar body weights but greater hepatic lipid accumulation compared to the MHF rats. Genome-wide DNA methylation was evaluated, and analysis revealed 1744 differentially methylation regions (DMRs) between the groups with the majority of the DMR located outside of gene-coding regions. Within differentially methylated genes (DMGs), intragenic DNA methylation closer to the transcription start site was associated with lower gene expression, whereas DNA methylation further downstream was positively correlated with gene expression. The insulin and phosphatidylinositol (PI) signaling pathways were enriched with 25 DMRs that were associated with 20 DMGs, including PI3 kinase (Pi3k), pyruvate kinase (Pklr), and phosphodiesterase 3 (Pde3). Together, these results suggest that the timing of HF diet intake determines DNA methylation and gene expression patterns in hepatic metabolic pathways that target specific genomic contexts.

scholarly journals Altered DNA Methylation of Long Noncoding RNA uc.167 Inhibits Cell Differentiation in Heart Development

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Anwen Yin ◽  
Mengwen Feng ◽  
Zijie Cheng ◽  
Qijun Zhang ◽  
Hua Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heart Development ◽  
Noncoding Rna ◽  
Biological Process ◽  
Methylation Status ◽  
P19 Cells ◽  
Methylated Dna ◽  
Differentially Methylated Genes ◽  
Intergenic Regions ◽  
Pathway Analyses

In previous studies, we have demonstrated the function of uc.167 in the heart development. DNA methylation plays a crucial role in regulating the expression of developmental genes during embryonic development. In this study, the methylomic landscape was investigated in order to identify the DNA methylation alterations. Methylated DNA immunoprecipitation (MeDIP) was performed to examine the differences in methylation status of overexpressed uc.167 in P19 cells. GO and KEGG pathway analyses of differentially methylated genes were also conducted. We found that the distribution of differentially methylated regions (DMRs) peaks in different components of genome was mainly located in intergenic regions and intron. The biological process associated with uc.167 was focal adhesion and Rap1 signaling pathway. MEF2C was significantly decreased in uc.167 overexpressed group, suggesting that uc.167 may influence the P19 differentiation through MEF2C reduction. Taken together, our findings revealed that the effect of uc.167 on P19 differentiation may be attributed to the altered methylation of specific genes.

scholarly journals Detecting multiple differentially methylated CpG sites and regions related to dimensional psychopathology in youths

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Leticia M. Spindola ◽  
Marcos L. Santoro ◽  
Pedro M. Pan ◽  
Vanessa K. Ota ◽  
Gabriela Xavier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Peripheral Blood ◽  
Child Behavior Checklist ◽  
Differentially Expressed ◽  
Mrna Levels ◽  
Independent Population ◽  
Differentially Methylated Genes ◽  
Before And After ◽  
Using Data

Abstract Background Psychiatric symptomatology during late childhood and early adolescence tends to persist later in life. In the present longitudinal study, we aimed to identify changes in genome-wide DNA methylation patterns that were associated with the emergence of psychopathology in youths from the Brazilian High-Risk Cohort (HRC) for psychiatric disorders. Moreover, for the differentially methylated genes, we verified whether differences in DNA methylation corresponded to differences in mRNA transcript levels by analyzing the gene expression levels in the blood and by correlating the variation of DNA methylation values with the variation of mRNA levels of the same individuals. Finally, we examined whether the variations in DNA methylation and mRNA levels were correlated with psychopathology measurements over time. Methods We selected 24 youths from the HRC who presented with an increase in dimensional psychopathology at a 3-year follow-up as measured by the Child Behavior Checklist (CBCL). The DNA methylation and gene expression data were compared in peripheral blood samples (n = 48) obtained from the 24 youths before and after developing psychopathology. We implemented a methodological framework to reduce the effect of chronological age on DNA methylation using an independent population of 140 youths and the effect of puberty using data from the literature. Results We identified 663 differentially methylated positions (DMPs) and 90 differentially methylated regions (DMRs) associated with the emergence of psychopathology. We observed that 15 DMPs were mapped to genes that were differentially expressed in the blood; among these, we found a correlation between the DNA methylation and mRNA levels of RB1CC1 and a correlation between the CBCL and mRNA levels of KMT2E. Of the DMRs, three genes were differentially expressed: ASCL2, which is involved in neurogenesis; HLA-E, which is mapped to the MHC loci; and RPS6KB1, the gene expression of which was correlated with an increase in the CBCL between the time points. Conclusions We observed that changes in DNA methylation and, consequently, in gene expression in the peripheral blood occurred concurrently with the emergence of dimensional psychopathology in youths. Therefore, epigenomic modulations might be involved in the regulation of an individual’s development of psychopathology.

scholarly journals Obestatin signaling controls Schwann cells and axonal transport to counteract neuromuscular synaptic loss in skeletal muscle

2020 ◽  
Author(s):  
Jesus P Camiña ◽  
Agustín Sánchez-Temprano ◽  
Saúl Leal-López ◽  
Jessica González-Sánchez ◽  
Carlos S. Mosteiro ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Peripheral Nerve ◽  
Schwann Cells ◽  
Nerve Injury ◽  
Nerve Repair ◽  
Axon Growth ◽  
Neuromuscular Synapses ◽  
Axonal Regrowth ◽  
Peripheral Nerve System ◽  
Nerve System

Abstract Background. Injuries to the peripheral nerve system are common conditions, with broad spectrum of symptoms depending on the impaired nerves and severity of damage. Although peripheral nervous system retains a remarkable ability for regeneration, it is estimated that less than ten percent of patients fully recover function after nerve injury and the available treatments remain suboptimal. Here, we identify a role for the obestatin/GPR39 system in the regulation of the Schwann cell plasticity as well as in the preservation of neuromuscular synapses in the course of nerve repair. Methods. Utilizing a compression model of sciatic nerve injury, axonotmesis, we assessed the obestatin-related regenerative response in the peripheral nerve system. The role of the obestatin/GPR39 system was further evaluated on immortalized rat Schwann cells, IFRS1, and the model of neuronal differentiation, PC12 cells. The interactions between SCs and neurons was evaluated using a co-culture system that combine the SC cell line IFRS1 and the NGF-primed PC12. Results. Obestatin signaling directs proliferation and migration of Schwann cells that sustain axonal regrowth and later remyelinate regenerated axons. We provide evidence supporting the preservation of skeletal muscle by the maintenance of neuromuscular synapses through the axonal regulation of calpain-calpastatin proteolytic system. This encompasses the control of skeletal muscle homeostasis by regulation of the ubiquitin proteasome system and the autophagy machinery. Conclusions. These results provide important insights into how the obestatin/GPR39 system promotes nerve repair through integration of multiple molecular cues of neuron-Schwann cells crosstalk aimed to promote axon growth and guide axons back to their targets.

scholarly journals Methylome and Transcriptome Analyses of Soybean Response to Bean Pyralid Larvae

2021 ◽  
Author(s):  
Wei-Ying Zeng ◽  
Yu -Rong Tan ◽  
Sheng-Feng Long ◽  
Zu-Dong Sun ◽  
Zhen-Guang Lai ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Protein Biosynthesis ◽  
Cell Structure ◽  
Expression Patterns ◽  
Primary Metabolism ◽  
Gene Expressions ◽  
Global Methylation ◽  
Lectin Domain ◽  
Differentially Methylated Genes ◽  
Soybean Resistance

Abstract Background: Bean pyralid is an important leaf-feeding insect which affects soybean production. DNA methylation can control the networks of gene expressions, and it plays an important role in the growth, development, and responses to biotic stress. However, the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far. Results: Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analysed the highly resistant material (Gantai-2-2) and highly susceptible material (Wan82-178), under the conditions of 0 h and 48 h feeding by bean pyralid larvae, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2,194, 6,872, 39,704, and 40,018 differentially methylated regions (DMRs), as well as 497, 1,594, 9,596, and 9,554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0, and HSK48/HRK48 comparisons, respectively. We found that 265 differentially expressed genes (DEGs) were negatively correlated with the DMGs, there were 34, 49, 141, and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0, and HSK48/HRK48 comparisons, respectively. The MapMan cluster analysis results indicated that negatively correlated genes in the pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Finally, the PS-PCR and qRT-PCR were used to validate the expression patterns of several genes and the results showed an excellent agreement with deep sequencing. Conclusions: Through the analysis of global methylation and transcription, we speculated that the expression levels of CRK40; CRK62; STK; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; SPATULA; bHLH25; bHLH79; GATA26, were regulated by methylation, and they may potentially play important roles in the soybean responses to bean pyralid larvae. Our results laid a foundation for revealing the occurrence mechanism of soybean response to bean pyralid at the level of DNA methylation.

scholarly journals Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0241515
Author(s):  
Ying Shi ◽  
Weihua Gong ◽  
Xiangrong Gong ◽  
Ping Wang ◽  
Xin Zhao
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Drug Resistance ◽  
Chemotherapy Resistance ◽  
Cancer Drug ◽  
Genome Wide ◽  
Differentially Methylated Genes ◽  
Breast Cells ◽  
The Difference ◽  
Dna Methylation Analysis

Breast cancer (BC) is the most frequently diagnosed tumor in women worldwide. Although the combination of surgery and Taxol chemotherapy can achieve a certain therapeutic effect, patients often develop drug-resistance, resulting in a poor prognosis. Therefore, it is significative to seek the molecular mechanism of chemotherapy resistance. Recent studies have found that abnormal epigenetic regulation in breast cells changes the expression of key genes, which can lead to the occurrence, development, and maintenance of cancer, even related to the development of drug-resistance. Therefore, in this study, we performed methylated DNA immunoprecipitation-sequencing (MeDIP-seq) to reveal the difference in methylation between breast cancer drug-resistant cells and sensitive cells. A total of 55076 differentially methylated genes (DMGs) were detected, including 21061 hypermethylated DMGs and 34015 hypomethylated DMGs. Moreover, Gene Ontology (GO) analysis and KEGG pathway analysis reveal the function and pathway of screening genes. These results indicate that DNA methylation may be involved in regulating the occurrence and development of breast cancer.

scholarly journals Schwann cells regulate sensory neuron gene expression before and after peripheral nerve injury

Glia ◽  
2018 ◽  
Vol 66 (8) ◽  
pp. 1577-1590 ◽  
Author(s):  
Gunnar Poplawski ◽  
Tetsuhiro Ishikawa ◽  
Coralie Brifault ◽  
Corinne Lee-Kubli ◽  
Robert Regestam ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Nerve ◽  
Schwann Cells ◽  
Nerve Injury ◽  
Sensory Neuron ◽  
Peripheral Nerve Injury ◽  
Before And After

scholarly journals Genome-wide DNA Methylation and Gene Expression Patterns of Androgenetic Haploid Tiger Pufferfish (Takifugu Rubripes) Provide Insights into Haploid Syndrome

2021 ◽  
Author(s):  
He Zhou ◽  
Qian Wang ◽  
Zi-Yu Zhou ◽  
Xin Li ◽  
Yu-Qing Sun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Abnormal Development ◽  
Takifugu Rubripes ◽  
Ploidy Levels ◽  
Genome Wide ◽  
Differentially Methylated Genes ◽  
Tiger Pufferfish

Abstract Androgenesis is an important chromosome set manipulation technique used in sex control in aquaculture. Haploid embryos exhibit haploid syndrome and show abnormalities and even die during early embryonic development. In this study, we used whole genome bisulfite sequencing (WGBS) to investigate the genome-wide DNA methylation profiles in haploid females (1n-X) and males (1n-Y), and diploid females (2n-XX) and males (2n-XY) of tiger pufferfish (Takifugu rubripes), an economically important fish in China. A total of 96.32 Gb clean data was produced. Analysis of differentially methylated regions (DMRs) showed that haploids had more hyper-methylated regions than diploids, which may be related to abnormal development and early embryonic death in haploids. There were 7,838 hyper-methylated differentially methylated genes (DMGs) and 4,755 hypo-methylated DMGs in haploid vs. diploid comparisons in both females and males. These DMGs were mainly related to genomic stability maintenance and cell cycle regulation. slf1, actr8, gas2, and pbrm1 genes were detected to validate the methylation sequencing. After combining the methylation data with the corresponding transcriptome data, we identified several genes, including guca2a, myoc, fezf2, rprml, telo2, s100a1, and marveld1, which exhibited differential expression levels modulated by DNA methylation. In conclusion, our study revealed different methylation and expression profiles between haploid and diploid T. rubripes for the first time. Several DMGs were identified between different ploidy levels, which may be related to haploid syndrome formation. The results expand the understanding of the effects of ploidy on the early development of teleosts and provide knowledge about target genes and networks to improve the survival rate of haploids.

scholarly journals Effectiveness of Kaempferia Galanga Linn Rhizome's Extract Towards the Healing of Minor Recurrent Aphthous Stomatitis in RSGMP USU's Patients

2017 ◽  
Vol 1 ◽  
Author(s):  
Laurenzia Veronica Tambunan ◽  
Wilda Hafny Lubis
Keyword(s):  
Experimental Research ◽  
Alternative Therapy ◽  
Analysis Data ◽  
Recurrent Aphthous Stomatitis ◽  
Aphthous Stomatitis ◽  
Purposive Sampling ◽  
Kaempferia Galanga ◽  
Before And After ◽  
The Difference

<p class="AbstractContent"><strong>Objective:</strong> The aim of this study was to determine the effect of Kaempferiae galanga L extract on the healing speed of minor RAS ulcer through its decrease in size and the scale of soreness.</p><p class="AbstractContent"><strong>Methods:</strong> This is an experimental research using one group pretest-posttest design. The sample chosen in this research is nonprobability sampling which is a purposive sampling which consists of 16 patients who has minor RAS and who pays a visit to RSGMP USU. The data is collected by doing an early examination of RAS about its location, size and the scale of soreness which later will be controlled for the first three days. Analysis data is done by using ANOVA Repeated to determine the difference between the observation of RAS before and after treatment.</p><p class="AbstractContent"><strong>Results:</strong> The results of this research showed that it is statistically significant on its decreasing size of ulcer (p&lt;0,05), on the first day, second day and third day of control. The scale of soreness shows a significant result as well (p&lt;0,05) on the first day, second day and third day of control.</p><p class="AbstractContent"><strong>Conclusion</strong>: The overall results shows there is a decrease in the size of the ulcer and its soreness which concludes, the gel of its extract can be used as an alternative therapy for the treatment of minor RAS.</p>

Tem analysis of multiple-energy arsenic implanted and Rta'd silicon

1987 ◽  
Vol 45 ◽  
pp. 246-247
Author(s):  
R.A. Herring
Keyword(s):  
Device Fabrication ◽  
High Concentration ◽  
Tem Analysis ◽  
Defect Clusters ◽  
High Fluences ◽  
Small Defect ◽  
Before And After ◽  
The Matrix ◽  
The Difference ◽  
Factor Type

Rapid thermal annealing (RTA) of ion-implanted Si is important for device fabrication. The defect structures of 2.5, 4.0, and 6.0 MeV As-implanted silicon irradiated to fluences of 2E14, 4E14, and 6E14, respectively, have been analyzed by electron diffraction both before and after RTA at 1100°C for 10 seconds. At such high fluences and energies the implanted As ions change the Si from crystalline to amorphous. Three distinct amorphous regions emerge due to the three implantation energies used (Fig. 1). The amorphous regions are separated from each other by crystalline Si (marked L1, L2, and L3 in Fig. 1) which contains a high concentration of small defect clusters. The small defect clusters were similar to what had been determined earlier as being amorphous zones since their contrast was principally of the structure-factor type that arises due to the difference in extinction distance between the matrix and damage regions.

Sign in / Sign up

Export Citation Format

Share Document