scholarly journals Exploration of the Effect on Genome-Wide DNA Methylation by miR-143 Knock-Out in Mice Liver

2021 ◽  
Vol 22 (23) ◽  
pp. 13075
Author(s):  
Xingping Chen ◽  
Junyi Luo ◽  
Jie Liu ◽  
Ting Chen ◽  
Jiajie Sun ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Hepatoma Cell ◽  
Whole Genome ◽  
Phosphoribosyl Pyrophosphate ◽  
Knock Out ◽  
Spermine Synthase ◽  
Mice Liver ◽  
Acyl Coenzyme A

MiR-143 play an important role in hepatocellular carcinoma and liver fibrosis via inhibiting hepatoma cell proliferation. DNA methyltransferase 3 alpha (DNMT3a), as a target of miR-143, regulates the development of primary organic solid tumors through DNA methylation mechanisms. However, the effect of miR-143 on DNA methylation profiles in liver is unclear. In this study, we used Whole-Genome Bisulfite Sequencing (WGBS) to detect the differentially methylated regions (DMRs), and investigated DMR-related genes and their enriched pathways by miR-143. We found that methylated cytosines increased 0.19% in the miR-143 knock-out (KO) liver fed with high-fat diet (HFD), compared with the wild type (WT). Furthermore, compared with the WT group, the CG methylation patterns of the KO group showed lower CG methylation levels in CG islands (CGIs), promoters and hypermethylation in CGI shores, 5′UTRs, exons, introns, 3′UTRs, and repeat regions. A total of 984 DMRs were identified between the WT and KO groups consisting of 559 hypermethylation and 425 hypomethylation DMRs. Furthermore, DMR-related genes were enriched in metabolism pathways such as carbon metabolism (serine hydroxymethyltransferase 2 (Shmt2), acyl-Coenzyme A dehydrogenase medium chain (Acadm)), arginine and proline metabolism (spermine synthase (Sms), proline dehydrogenase (Prodh2)) and purine metabolism (phosphoribosyl pyrophosphate synthetase 2 (Prps2)). In summary, we are the first to report the change in whole-genome methylation levels by miR-143-null through WGBS in mice liver, and provide an experimental basis for clinical diagnosis and treatment in liver diseases, indicating that miR-143 may be a potential therapeutic target and biomarker for liver damage-associated diseases and hepatocellular carcinoma.

scholarly journals The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples

2020 ◽  
Vol 8 (8) ◽  
pp. 1252
Author(s):  
Bart Cuypers ◽  
Franck Dumetz ◽  
Pieter Meysman ◽  
Kris Laukens ◽  
Géraldine De Muylder ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Leishmania Donovani ◽  
Clinical Samples ◽  
Knock Out ◽  
The Status ◽  
Genome Bisulfite Sequencing ◽  
Genomic Scale ◽  
Commercial Kits ◽  
Eukaryotic Organisms

Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we showed that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, whose function is still unclear, and verified its expression at the RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterized their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite the DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites, and 0.0126% at CHH sites at the genomic scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrated that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation) allowed enrichment of parasite vs. host DNA using methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62× up to 263×. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.

scholarly journals Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome

2017 ◽  
Author(s):  
Jacob L. Steenwyk ◽  
James St. Denis ◽  
Jacqueline M. Dresch ◽  
Denis A. Larochelle ◽  
Robert A. Drewell
Keyword(s):  
Dna Methylation ◽  
Dictyostelium Discoideum ◽  
Dna Methyltransferase ◽  
Model Organism ◽  
Epigenetic Mark ◽  
Whole Genome ◽  
Protein Coding ◽  
Genome Bisulfite Sequencing ◽  
Chromatin Structural ◽  
And Function

AbstractDNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the slime mold Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methyl-cytosine in the genome is unclear. Here we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage, replicate sequencing of bisulfite converted gDNA extracted from post-starvation cells. We find an overall very low level of DNA methylation, occurring at only 462 out of the ~7.5 million (0.006%) cytosines in the genome. Despite this sparse profile, significant methylation can be detected at 51 of these sites in replicate experiments, suggesting they are robust targets for DNA methylation. These 5-methyl-cytosines are associated with a broad range of protein-coding genes, tRNA-encoding genes and retrotransposable elements. Our data provides evidence of a minimal, but functional, methylome in Dictyostelium, thereby making Dictyostelium a candidate model organism to further investigate the evolutionary function of DNA methylation.

scholarly journals Whole-genome DNA methylation and hydroxymethylation profiling for HBV-related hepatocellular carcinoma

2016 ◽  
Vol 49 (2) ◽  
pp. 589-602 ◽  
Author(s):  
Chao Ye ◽  
Ran Tao ◽  
Qingyi Cao ◽  
Danhua Zhu ◽  
Yini Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Dna Methylation ◽  
Whole Genome

scholarly journals Dnmt3a is an epigenetic mediator of adipose insulin resistance

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Dongjoo You ◽  
Emma Nilsson ◽  
Danielle E Tenen ◽  
Anna Lyubetskaya ◽  
James C Lo ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Human Subjects ◽  
Human Adipose Tissue ◽  
Gene Profiling ◽  
Knock Out ◽  
Unbiased Gene

Insulin resistance results from an intricate interaction between genetic make-up and environment, and thus may be orchestrated by epigenetic mechanisms like DNA methylation. Here, we demonstrate that DNA methyltransferase 3a (Dnmt3a) is both necessary and sufficient to mediate insulin resistance in cultured mouse and human adipocytes. Furthermore, adipose-specific Dnmt3a knock-out mice are protected from diet-induced insulin resistance and glucose intolerance without accompanying changes in adiposity. Unbiased gene profiling studies revealed Fgf21 as a key negatively regulated Dnmt3a target gene in adipocytes with concordant changes in DNA methylation at the Fgf21 promoter region. Consistent with this, Fgf21 can rescue Dnmt3a-mediated insulin resistance, and DNA methylation at the FGF21 locus was elevated in human subjects with diabetes and correlated negatively with expression of FGF21 in human adipose tissue. Taken together, our data demonstrate that adipose Dnmt3a is a novel epigenetic mediator of insulin resistance in vitro and in vivo.

scholarly journals Effects of Choline on DNA Methylation and Macronutrient Metabolic Gene Expression in in Vitro Models of Hyperglycemia

2016 ◽  
Vol 9 ◽  
pp. NMI.S29465 ◽  
Author(s):  
Xinyin Jiang ◽  
Esther Greenwald ◽  
Chauntelle Jack-Roberts
Keyword(s):  
Dna Methylation ◽  
Glycemic Control ◽  
High Glucose ◽  
Hepg2 Cells ◽  
Dna Methyltransferase ◽  
Phosphoenolpyruvate Carboxykinase ◽  
In Vitro Models ◽  
Culture Models ◽  
Acyl Coenzyme A

Choline is an essential nutrient that plays an important role in lipid metabolism and DNA methylation. Studies in rodents suggest that choline may adversely affect glycemic control, yet studies in humans are lacking. Using the human hepatic and placental cells, HepG2 and BeWo, respectively, we examined the interaction between choline and glucose treatments. In HepG2 cells, choline supplementation (1 mM) increased global DNA methylation and DNA methyltransferase expression in both low-glucose (5 mM) and high-glucose (35 mM) conditions. Choline supplementation increased the expression of peroxisomal acyl-coenzyme A oxidase 1 ( ACOX1), which mediates fatty acid β-oxidation, especially in the high-glucose condition. High-glucose exposure increased the transcription of the gluconeogenic gene phosphoenolpyruvate carboxykinase ( PEPCK), while choline supplementation mitigated such increase. Compared to HepG2 cells, the placenta-derived BeWo cells were relatively unresponsive to either high-glucose or -choline treatment. In conclusion, choline and glucose interacted to affect macronutrient metabolic genes, yet there was no indication that choline may worsen glycemic control in these in vitro human cell culture models.

scholarly journals The absence of C-5 DNA methylation in Leishmania donovani allows DNA enrichment from complex samples

2019 ◽  
Author(s):  
B Cuypers ◽  
F Dumetz ◽  
P Meysman ◽  
K Laukens ◽  
G De Muylder ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Leishmania Donovani ◽  
Clinical Samples ◽  
Knock Out ◽  
Complex Samples ◽  
The Status ◽  
Genome Bisulfite Sequencing ◽  
Commercial Kits ◽  
Eukaryotic Organisms

AbstractCytosine C5 methylation is an important epigenetic control mechanism in a wide array of Eukaryotic organisms and generally carried out by proteins of C-5 DNA methyltransferase family (DNMTs). In several protozoans the status of this mechanism remains elusive, such as in Leishmania, the causative agent of the disease leishmaniasis in humans and a wide array of vertebrate animals. In this work, we show that the Leishmania donovani genome contains a C-5 DNA methyltransferase (DNMT) from the DNMT6 subfamily, of which the function is still unclear, and verified its expression at RNA level. We created viable overexpressor and knock-out lines of this enzyme and characterised their genome-wide methylation patterns using whole-genome bisulfite sequencing, together with promastigote and amastigote control lines. Interestingly, despite DNMT6 presence, we found that methylation levels were equal to or lower than 0.0003% at CpG sites, 0.0005% at CHG sites and 0.0126% at CHH sites at genome scale. As none of the methylated sites were retained after manual verification, we conclude that there is no evidence for DNA methylation in this species. We demonstrate that this difference in DNA methylation between the parasite (no detectable DNA methylation) and the vertebrate host (DNA methylation), allows enrichment of parasite versus host DNA using Methyl-CpG-binding domain columns, readily available in commercial kits. As such, we depleted methylated DNA from mixes of Leishmania promastigote and amastigote DNA with human DNA, resulting in average Leishmania:human enrichments from 62x up to 263x. These results open a promising avenue for unmethylated DNA enrichment as a pre-enrichment step before sequencing Leishmania clinical samples.

scholarly journals SALL3 Interacts with DNMT3A and Shows the Ability To Inhibit CpG Island Methylation in Hepatocellular Carcinoma

2009 ◽  
Vol 29 (7) ◽  
pp. 1944-1958 ◽  
Author(s):  
Yuko Shikauchi ◽  
Akio Saiura ◽  
Takahiko Kubo ◽  
Yasuharu Niwa ◽  
Junji Yamamoto ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Cpg Island ◽  
Functional Characterization ◽  
Direct Interaction ◽  
Aberrant Methylation ◽  
Pwwp Domain ◽  
Cpg Island Methylation

ABSTRACT The mechanisms of aberrant CpG island methylation in oncogenesis are not fully characterized. In particular, little is known about the mechanisms of inhibition of CpG island methylation. Here we show that sal-like 3 (SALL3) is a novel inhibitory factor for DNA methyltransferase 3 alpha (DNMT3A). SALL3 binds to DNMT3A by a direct interaction between the double zinc finger motif of SALL3 and the PWWP domain of DNMT3A. SALL3 expression reduces DNMT3A-mediated CpG island methylation in cell culture and in vitro. CpG island methylation is enhanced in SALL3-depleted cells. Consistently, DNMT3A from SALL3-depleted cells increases methyltransferase activity in vitro. Binding of DNMT3A to chromatin is reduced or increased by SALL3 expression or depletion, respectively, accounting for the mechanism by which SALL3 inhibits DNMT3A-mediated CpG island methylation. We also show that SALL3 is inducible by BMP-4 and silenced by associated DNA methylation in hepatocellular carcinoma (HCC). Our results suggest that silencing of SALL3 results in acceleration of DNA methylation in HCC. This functional characterization of SALL3 sheds light on regulatory mechanisms for DNMT3A and provides new strategies to inhibit aberrant methylation in cancer.

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