scholarly journals Epigenetic, transcriptional and phenotypic responses in two generations of Daphnia magna exposed to the DNA methylation inhibitor 5-azacytidine

2019 ◽  
Vol 5 (3) ◽  
Author(s):  
Leif Christopher Lindeman ◽  
Jens Thaulow ◽  
You Song ◽  
Jorke H Kamstra ◽  
Li Xie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Modifications ◽  
Environmental Stressors ◽  
Global Dna Methylation ◽  
Two Generations ◽  
Methylation Inhibitor ◽  
Dna Methylation Inhibitor ◽  
Offspring Generation ◽  
Phenotypic Responses

Abstract The water flea Daphnia magna is a keystone species in freshwater ecosystems and has been widely used as a model organism in environmental ecotoxicology. This aquatic crustacean is sensitive to environmental stressors and displays considerable plasticity in adapting to changing environmental conditions. Part of this plasticity may be due to epigenetic regulation of gene expression, including changes to DNA methylation and histone modifications. Because of the generally hypomethylated genome of this species, we hypothesized that the histone code may have an essential role in the epigenetic control and that histone modifications might be an early marker for stress. This study aims to characterize the epigenetic, transcriptional and phenotypic responses and their causal linkages in directly exposed adult (F0) Daphnia and peritoneal exposed neonates (F1) after a chronic (7-day) exposure to a sublethal concentration (10 mg/l) of 5-azacytidine, a well-studied vertebrate DNA methylation inhibitor. Exposure of the F0 generation significantly reduced the cumulative fecundity, accompanied with differential expression of genes in the one-carbon-cycle metabolic pathway. In the epigenome of the F0 generation, a decrease in global DNA methylation, but no significant changes on H3K4me3 or H3K27me3, were observed. In the F1 offspring generation, changes in gene expression, a significant reduction in global DNA methylation and changes in histone modifications were identified. The results indicate that exposure during adulthood may result in more pronounced effects on early development in the offspring generation, though interpretation of the data should be carefully done since both the exposure regime and developmental period is different in the two generations examined. The obtained results improve our understanding of crustacean epigenetics and the tools developed may promote use of epigenetic markers in hazard assessment of environmental stressors.

Differences in global DNA methylation of testicular seminoma are not associated with changes in histone modifications, clinical prognosis, BRAF mutations or gene expression

2016 ◽  
Vol 209 (11) ◽  
pp. 506-514 ◽  
Author(s):  
Louise Holm Pedersen ◽  
John E. Nielsen ◽  
Gedske Daugaard ◽  
Thomas v.O. Hansen ◽  
Ewa Rajpert-De Meyts ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Modifications ◽  
Global Dna Methylation ◽  
Braf Mutations ◽  
Testicular Seminoma ◽  
Clinical Prognosis ◽  
Or Gene

scholarly journals Analysis of Gene Expression Patterns of Epigenetic Enzymes Dnmt3a, Tet1 and Ogt in Murine Chondrogenic Models

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2678
Author(s):  
Judit Vágó ◽  
Katalin Kiss ◽  
Edina Karanyicz ◽  
Roland Takács ◽  
Csaba Matta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
In Situ Hybridization ◽  
Marker Genes ◽  
Specific Gene ◽  
Cartilage Formation ◽  
Methylation Inhibitor ◽  
Dna Methylation Inhibitor

We investigated the gene expression pattern of selected enzymes involved in DNA methylation and the effects of the DNA methylation inhibitor 5-azacytidine during in vitro and in vivo cartilage formation. Based on the data of a PCR array performed on chondrifying BMP2-overexpressing C3H10T1/2 cells, the relative expressions of Tet1 (tet methylcytosine dioxygenase 1), Dnmt3a (DNA methyltransferase 3), and Ogt (O-linked N-acetylglucosamine transferase) were further examined with RT-qPCR in murine cell line-based and primary chondrifying micromass cultures. We found very strong but gradually decreasing expression of Tet1 throughout the entire course of in vitro cartilage differentiation along with strong signals in the cartilaginous embryonic skeleton using specific RNA probes for in situ hybridization on frozen sections of 15-day-old mouse embryos. Dnmt3a and Ogt expressions did not show significant changes with RT-qPCR and gave weak in situ hybridization signals. The DNA methylation inhibitor 5-azacytidine reduced cartilage-specific gene expression and cartilage formation when applied during the early stages of chondrogenesis. In contrast, it had a stimulatory effect when added to differentiated chondrocytes, and quantitative methylation-specific PCR proved that the DNA methylation pattern of key chondrogenic marker genes was altered by the treatment. Our results indicate that the DNA demethylation inducing Tet1 plays a significant role during chondrogenesis, and inhibition of DNA methylation exerts distinct effects in different phases of in vitro cartilage formation.

Is Cladribine, a Treatment for Chronic Lymphocytic Leukemia, a DNA Methylation Inhibitor?.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4770-4770
Author(s):  
Margaret K. Yu ◽  
Mark Wade ◽  
Brent C. Moore ◽  
Frank A. Fitzpatrick
Keyword(s):  
Dna Methylation ◽  
Chronic Lymphocytic Leukemia ◽  
Genomic Dna ◽  
Inhibitory Effect ◽  
Lymphocytic Leukemia ◽  
Leukemia Cells ◽  
Global Dna Methylation ◽  
Methylation Inhibitor ◽  
Dna Methylation Inhibitor ◽  
Ht 29

Abstract Chronic lymphocytic leukemia is a heterogenous B lymphocyte disorder with a variable natural history. Like other Malignancies, key regulatory genes like the tumor suppressor, p16, and the mismatch repair gene, hMLH1, are frequently silenced by DNA methylation in patients with chronic lymphocytic leukemia (CLL). Although focal hypermethylation is found, global genomic DNA is hypomethylated compared to genomic DNA from healthy volunteers. Inhibition of DNA methylation may help CLL cells regain normal cellular function. Few studies have been done evaluating DNA methylation of CLL cells likely in part due to the difficulty in establishing a CLL cell line without altering DNA methylation. In addition, the primary cells do not divide in vitro, making the assessment of effect of a DNA methylation inhibitor very difficult. Of the ten samples tested from patients with CLL, we have not found p16 or hMLH1 expression by western blotting. Since 2-Chlorodeoxyadenosine (Cladribine) is already used clinically for treatment of CLL and may deplete available methyl donors, we asked if Cladribine is effective because of its inhibitory effect on DNA methylation in leukemia cells. To further evaluate the role of DNA methylation in CLL, we assessed the effect of 5-aza-2′-deoxycitidine (Decitabine), a DNA methyltransferase inhibitor compared to Cladribine in HT-29 cells. HT-29 cells do not express p16 and MAGE because of DNA methylation of the promoters. Assessment of global DNA methylation is done using reversed-phase high-performance liquid chromatography. Our results reveal that daily doses of 300nM Cladribine modestly inhibited global DNA methylation by 20+/−14% at 72 hours (n=3), while daily doses of 500nM Decitabine inhibited global DNA methylation by 75+/−9% at 72 hours (n=3). This results in re-expression of MAGE-1, a gene silenced by DNA methylation in all somatic tissues and p16, only in the Decitabine treated cells. We also evaluated the Cdx-2 promoter, an intestinal restricted gene silenced by DNA methylation in HT-29 cells. Decreased methylation of two regions of the Cdx-2 promoter was seen in the cells treated with Decitabine compared to the control cells. Cladribine treated cells had no effect on the Cdx-2, and may actually increase DNA methylation (result of 20 sequences). These results could be explained by the marked growth inhibitory effect of Cladribine at 300nM. We chose to evaluate Cladribine at 300nM because this plasma concentration is obtainable in patients treated with 0.1mg/kg of Cladribine, a dose frequently used in treatment of hairy cell leukemia. Cells with decreased DNA methylation after treatment with Cladribine may have died at the 72 hour time point.

scholarly journals Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

2016 ◽  
Vol 311 (6) ◽  
pp. L1245-L1258 ◽  
Author(s):  
Isaac K. Sundar ◽  
Irfan Rahman
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoke ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Chromatin Modification ◽  
Gene Expression Patterns ◽  
Validation Data ◽  
Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

scholarly journals Zebularine: A Novel DNA Methylation Inhibitor that Forms a Covalent Complex with DNA Methyltransferases

2002 ◽  
Vol 321 (4) ◽  
pp. 591-599 ◽  
Author(s):  
L. Zhou ◽  
X. Cheng ◽  
B.A. Connolly ◽  
M.J. Dickman ◽  
P.J. Hurd ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferases ◽  
Methylation Inhibitor ◽  
Dna Methylation Inhibitor ◽  
Covalent Complex

scholarly journals The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e30515 ◽  
Author(s):  
Andriy Bilichak ◽  
Yaroslav Ilnystkyy ◽  
Jens Hollunder ◽  
Igor Kovalchuk
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Histone Modifications
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