scholarly journals Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1020
Author(s):  
Yujia Yang ◽  
Yingqiu Zheng ◽  
Lina Sun ◽  
Muyan Chen
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Sea Cucumber ◽  
Environmental Changes ◽  
Marine Invertebrates ◽  
Apostichopus Japonicus ◽  
Aquatic Organisms ◽  
Dna Methyltransferases ◽  
Transcriptional Unit ◽  
Differentially Methylated Genes

Organisms respond to severe environmental changes by entering into hypometabolic states, minimizing their metabolic rates, suspending development and reproduction, and surviving critical ecological changes. They come back to an active lifestyle once the environmental conditions are conducive. Marine invertebrates live in the aquatic environment and adapt to environmental changes in their whole life. Sea cucumbers and sponges are only two recently known types of marine organisms that aestivate in response to temperature change. Sea cucumber has become an excellent model organism for studies of environmentally-induced aestivation by marine invertebrates. DNA methylation, the most widely considered epigenetic marks, has been reported to contribute to phenotypic plasticity in response to environmental stress in aquatic organisms. Most of methylation-related enzymes, including DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylases, were up-regulated during aestivation. We conducted high-resolution whole-genome bisulfite sequencing of the intestine from sea cucumber at non-aestivation and deep-aestivation stages. Further DNA methylation profile analysis was also conducted across the distinct genomic features and entire transcriptional units. A different elevation in methylation level at internal exons was observed with clear demarcation of intron/exon boundaries during transcriptional unit scanning. The lowest methylation level occurs in the first exons, followed by the last exons and the internal exons. A significant increase in non-CpG methylation (CHG and CHH) was observed within the intron and mRNA regions in aestivation groups. A total of 1393 genes were annotated within hypermethylated DMRs (differentially methylated regions), and 749 genes were annotated within hypomethylated DMRs. Differentially methylated genes were enriched in the mRNA surveillance pathway, metabolic pathway, and RNA transport. Then, 24 hypermethylated genes and 15 hypomethylated genes were Retrovirus-related Pol polyprotein from transposon (RPPT) genes. This study provides further understanding of epigenetic control on environmental induced hypometabolism in aquatic organisms.

Insights into the DNA methylation of sea cucumber Apostichopus japonicus in response to skin ulceration syndrome infection

2020 ◽  
Vol 104 ◽  
pp. 155-164
Author(s):  
Hongjuan Sun ◽  
Zunchun Zhou ◽  
Ying Dong ◽  
Aifu Yang ◽  
Jingwei Jiang
Keyword(s):  
Dna Methylation ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Skin Ulceration

scholarly journals Characterization of SIRT1/DNMTs Functions and LINE-1 Methylation in Patients with Age-Related Macular Degeneration

2019 ◽  
Vol 8 (2) ◽  
pp. 159 ◽  
Author(s):  
Andrea Maugeri ◽  
Martina Barchitta ◽  
Matteo Fallico ◽  
Niccolò Castellino ◽  
Michele Reibaldi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Macular Degeneration ◽  
Methylation Level ◽  
Surrogate Marker ◽  
Dna Methyltransferases ◽  
Sirtuin 1 ◽  
Age Related Macular Degeneration ◽  
Clinical Biomarkers ◽  
Age Related

Previous studies proposed the application of DNA methylation signatures as clinical biomarkers of age-related macular degeneration (AMD). However, the characterization of Long Interspersed Nuclear Element-1 (LINE-1) methylation levels—a surrogate marker of global DNA methylation—in AMD patients has not been investigated so far. In the present study, we first characterized DNA methyltransferases (DNMTs) and Sirtuin 1 (SIRT1) functions in blood samples of 40 AMD patients and 10 age- and sex-matched controls. Then, we evaluated whether changes in DNMTs functions were associated with different LINE-1 methylation levels in leukocyte DNA. We demonstrated that total DNMTs activity was 48% higher in AMD patients than in controls (p = 0.005). AMD patients also exhibited up-regulation of DNMT1 and DNMT3B expression (FC = 2.6; p = 0.003 and FC = 2.4; p = 0.018, respectively). In line with increased DNMTs functions, the LINE-1 methylation level was higher in AMD patients than in controls (mean = 69.10%; SE = 0.68 vs. mean = 65.73%; SE = 0.59; p = 0.020). All p-values were adjusted by Bonferroni correction. In AMD patients, LINE-1 methylation level was positively associated with total DNMTs activity (r = 0.694; p < 0.001), DNMT1 (r = 0.579; p < 0.001), and DNMT3B (r = 0.521; p = 0.001) expression. Our results encourage further large-size prospective research to understand the relationship between LINE-1 methylation and AMD aetiology, and its usefulness in the clinical setting.

scholarly journals A novel DNA methylation-based model that effectively predicts prognosis in hepatocellular carcinoma

2021 ◽  
Vol 41 (3) ◽  
Author(s):  
Xiang-Yong Hao ◽  
An-Qiang Li ◽  
Hao Shi ◽  
Tian-Kang Guo ◽  
Yan-Fei Shen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Dna Methylation ◽  
Predictive Model ◽  
Risk Score ◽  
Methylation Level ◽  
Pathway Enrichment Analysis ◽  
Validation Group ◽  
Cox Regression Analysis ◽  
Differentially Methylated Genes ◽  
Cox Analysis

Abstract Purpose: To build a novel predictive model for hepatocellular carcinoma (HCC) patients based on DNA methylation data. Methods: Four independent DNA methylation datasets for HCC were used to screen for common differentially methylated genes (CDMGs). Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to explore the biological roles of CDMGs in HCC. Univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox analysis were performed to identify survival-related CDMGs (SR-CDMGs) and to build a predictive model. The importance of this model was assessed using Cox regression analysis, propensity score-matched (PSM) analysis and stratification analysis. A validation group from the Cancer Genome Atlas (TCGA) was constructed to further validate the model. Results: Four SR-CDMGs were identified and used to build the predictive model. The risk score of this model was calculated as follows: risk score = (0.01489826 × methylation level of WDR69) + (0.15868618 × methylation level of HOXB4) + (0.16674959 × methylation level of CDKL2) + (0.16689301 × methylation level of HOXA10). Kaplan–Meier analysis demonstrated that patients in the low-risk group had a significantly longer overall survival (OS; log-rank P-value =0.00071). The Cox model multivariate analysis and PSM analysis identified the risk score as an independent prognostic factor (P&lt;0.05). Stratified analysis results further confirmed this model performed well. By analyzing the validation group, the results of receiver operating characteristic (ROC) curve analysis and survival analysis further validated this model. Conclusion: Our DNA methylation-based prognosis predictive model is effective and reliable in predicting prognosis for patients with HCC.

scholarly journals Transcriptome and DNA Methylome Reveal Insights Into Phytoplasma Infection Responses in Mulberry (Morus multicaulis Perr.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Chaorui Liu ◽  
Xiaonan Dong ◽  
Yuqi Xu ◽  
Qing Dong ◽  
Yuqi Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Differentially Expressed ◽  
Kinase Gene ◽  
Differentially Methylated Genes ◽  
Pathogenesis Related Protein ◽  
Significant Difference ◽  
Average Methylation ◽  
Phytoplasma Infection ◽  
Average Methylation Level

To reveal whether the response of mulberry to phytoplasma infection is associated with genome-wide DNA methylation changes, the methylome and transcriptome patterns of mulberry in response to phytoplasma infection were explored. Though the average methylation level of the infected leaves showed no significant difference from that of healthy leaves, there were 1,253 differentially methylated genes (DMGs) and 1,168 differentially expressed genes (DEGs) in the infected leaves, and 51 genes were found simultaneously to be differently methylated and expressed. It was found that the expression of G-type lectin S-receptor-like serine/threonine protein kinase gene (Mu-GsSRK) was increased, but its methylation level was decreased in the pathogen-infected or salicylic acid (SA)-treated leaves. Overexpression of Mu-GsSRK in Arabidopsis and in the hairy roots of mulberry enhanced transgenic plant resistance to the phytoplasma. Moreover, overexpression of Mu-GsSRK enhanced the expressions of pathogenesis-related protein 1, plant defensin, and cytochrome P450 protein CYP82C2 genes in transgenic plants inoculated with pathogens, which may contribute to the enhanced disease resistance against various pathogens. Finally, the DNA methylation dynamic patterns and functions of the differentially expressed and methylated genes were discussed. The results suggested that DNA methylation has important roles in mulberry responses to phytoplasma infection.

scholarly journals DNA Methyltransferases Contribute to Cold Tolerance in Ticks Dermacentor silvarum and Haemaphysalis longicornis (Acari: Ixodidae)

2021 ◽  
Vol 8 ◽  
Author(s):  
Desmond Onyeka Agwunobi ◽  
Miao Zhang ◽  
Xinyue Shi ◽  
Shiqi Zhang ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cold Tolerance ◽  
Dna Methyltransferase ◽  
Environmental Changes ◽  
Cold Treatment ◽  
Dna Methyltransferases ◽  
Haemaphysalis Longicornis ◽  
Cold Response ◽  
Cytosine Methyltransferase ◽  
Replication Foci

DNA methylation, mediated by DNA methyltransferases (Dnmts), is a typical epigenetic process that plays an important role in affecting organism acclimatization and adaptation to environmental changes. However, information about Dnmts and their associations with the cold tolerance of ticks remains meager. Hence, in the present study, the Dnmts in important vector ticks Dermacentor silvarum and Haemaphysalis longicornis were cloned and identified, and their functions in cold response were further explored. Results showed that the length of DsDnmt and DsDnmt1 in D. silvarum, and HlDnmt1 and HlDnmt in H. longicornis were 1,284, 549, 1,500, and 1,613 bp, respectively. Bioinformatics in protein analysis revealed that they were all unstable hydrophilic proteins and were mainly characterized with Dcm (DNA cytosine methyltransferase domain), Dnmt1-RFD (DNA methyltransferase replication foci domain), zf-CXXC (zinc finger-CXXC domain), and BAH (Bromo adjacent homology domain). The relative expression of these Dnmts was reduced after cold treatment for 3 days (P &lt; 0.05), and increased with the extension of treatment. Western blot revealed that Dnmt1 decreased first and then increased significantly (P &lt; 0.05) in both tick species, whereas other Dnmts fluctuated at varying degrees. RNA interference significantly silenced the genes Dnmts (P &lt; 0.01), and mortality increased significantly (P &lt; 0.05), when exposed to sub-lethal temperature, underscoring the important roles of Dnmts during the cold response of D. silvarum and H. longicornis. The above results lay the foundation for further understanding of the epigenetic regulation of DNA methylation in cold acclimatization and adaptation of ticks.

scholarly journals Methylation dynamics during folliculogenesis and early embryo development in sheep

Reproduction ◽  
2017 ◽  
Vol 153 (5) ◽  
pp. 605-619 ◽  
Author(s):  
Laura Masala ◽  
Giovanni Pietro Burrai ◽  
Emanuela Bellu ◽  
Federica Ariu ◽  
Luisa Bogliolo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Embryo Development ◽  
Environmental Changes ◽  
Temporal Analysis ◽  
Dna Methyltransferases ◽  
Early Embryo ◽  
Developmental Competence ◽  
Oocyte Growth ◽  
Differential Model ◽  
Early Embryo Development

Genome-wide DNA methylation reprogramming occurs during mammalian gametogenesis and early embryogenesis. Post-fertilization demethylation of paternal and maternal genomes is considered to occur by an active and passive mechanism respectively, in most mammals but sheep; in this species no loss of methylation was observed in either pronucleus. Post-fertilization reprogramming relies on methylating and demethylating enzymes and co-factors that are stored during oocyte growth, concurrently with the re-methylation of the oocyte itself. The crucial remodelling of the oocyte epigenetic baggage often overlaps with potential interfering events such as exposure to assisted reproduction technologies or environmental changes. Here, we report a temporal analysis of methylation dynamics during folliculogenesis and early embryo development in sheep. We characterized global DNA methylation and hydroxymethylation by immunofluorescence and relatively quantified the expression of the enzymes and co-factors mainly responsible for their remodelling (DNA methyltransferases (DNMTs), ten-eleven translocation (TET) proteins and methyl-CpG-binding domain (MBD) proteins). Our results illustrate for the first time the patterns of hydroxymethylation during oocyte growth. We observed different patterns of methylation and hydroxymethylation between the two parental pronuclei, suggesting that male pronucleus undergoes active demethylation also in sheep. Finally, we describe gene-specific accumulation dynamics for methylating and demethylating enzymes during oocyte growth and observe patterns of expression associated with developmental competence in a differential model of oocyte potential. Our work contributes to the understanding of the methylation dynamics during folliculogenesis and early embryo development and improves the overall picture of early rearrangements that will originate the embryo epigenome.

scholarly journals Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lingshu Han ◽  
Yi Sun ◽  
Yue Cao ◽  
Pingping Gao ◽  
Zijiao Quan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Body Wall ◽  
Molecular Mechanisms ◽  
Apostichopus Japonicus ◽  
Economic Benefits ◽  
Methylation Pattern ◽  
The Body ◽  
Aquatic Animal ◽  
Sea Cucumbers ◽  
Differentially Methylated Genes

AbstractBreeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene expression and genome-wide comparisons of DNA methylation using the body wall tissue of triploid sea cucumbers using RNA-seq and MethylRAD-seq technologies. We clarified the expression pattern of triploid sea cucumbers and found no dosage effect. DEGs were significantly enriched in the pathways of nucleic acid and protein synthesis, cell growth, cell division, and other pathways. Moreover, we characterized the methylation pattern changes and found 615 differentially methylated genes at CCGG sites and 447 differentially methylated genes at CCWGG sites. Integrative analysis identified 23 genes (such as Guf1, SGT, Col5a1, HAL, HPS1, etc.) that exhibited correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions in the growth of triploid sea cucumbers. Our data provide new insights into the epigenetic and transcriptomic alterations of the body wall tissue of triploid sea cucumbers and preliminarily elucidate the molecular mechanism of their growth, which is of great significance for the breeding of fine varieties of sea cucumbers.

Cytological observations on fertilization and early embryonic development in sea cucumber Apostichopus japonicus

2012 ◽  
Vol 36 (2) ◽  
pp. 272 ◽  
Author(s):  
Jie TAN ◽  
Hui-ling SUN ◽  
Fei GAO ◽  
Jing-ping YAN ◽  
Ying-hui DONG ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Early Embryonic Development
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