- Cadmium-induced genome-wide DNA methylation changes in growth and oxidative metabolism in Drosophila melanogaster. - DNA methylation is an important mechanism for the regulation of gene expression.. - In this study we examined the effects of Cd exposure on global DNA methylation in a living organism by whole-genome bisulfite sequencing (WGBS) using Drosophila melanogaster as model.. - A total of 39 genes were demethylated in the Cd treatment group but not in the control group, whereas 24 showed increased methylation in the former relative to the latter. - Conclusions: DNA methylation actively regulates the physiological response to heavy metal stress in Drosophila in part via activation of apoptosis.. - Although global DNA methylation level is lower overall in the genome of Drosophila as compared to mammals, there are also fewer methylases. - Although it is presumed that DNA methylation is in- volved in the response to Cd stress in Drosophila, there have been no detailed surveys of DNA methylation. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - To address these points, in this study we used whole-genome bisulfite sequencing (WGBS) to evaluate genome-wide DNA methylation changes in D. - Our results provide evidence for the broad involvement of DNA methylation in the response to heavy metal stress in animals.. - DNA methylation state of the Drosophila genome. - poly-A contamination, and contamination by adaptor sequences), at least 98% of the reads were retained and were taken as the high-quality (HQ) clean reads. - The average number of methylated cytosines detected in the Cd treatment and control groups was about 0.1% of all cytosines in the Drosophila genome. - There were 12,397 methylated cytosines for CG, 9880 for CHG, and 30,678 for CHH (where H represents A, C, or T) in the treatment group (Fig. - 0.05, Fisher’s exact test) than in the control group and 37,246, respectively, Fig. - We analyzed the relationship between the type of methy- lation and surrounding sequences by identifying the fea- tures of the 9-mer sequence around the methylation site (Fig. - In the CG and CHG environment, sequences around methylation were slightly different. - “AAAA” being the preferred sequences of the treatment group and “TTT” and “AATT” being those of the control group. - Thus, there doesn’t seem to be any significantly enriched motifs in any of the treatments.. - DNA methylation levels in different genomic regions DNA methylation levels generally show a varied distribu- tion across different functional regions of the genome. - We examined the distribution of DNA methylation sites and found that the methylation levels in the promoter, 5′ un- translated region (UTR), exon, intron, and 3′ UTR were similar between Cd treatment and control groups (Fig. - We used the sliding window method to examine DNA methylation levels in these five gene components. - Methylation levels were simi- larly distributed in the treatment and control groups (Fig. - Compared to other genetic components, changes in methylation level were observed in the promoter region, but the overall methylation level was high. - there was little change in the exon and intron, which showed a stable distribution of methylation marks.. - In the treatment group, 30 DMRs in 24 genes were hypermethylated and 41 DMRs in 39 genes were demethylated relative to the control group. - A box plot analysis of the DMRs showed that the methylation level was slightly lower in the treatment as compared to the control group (Fig. - Add- itionally, more DMRs were demethylated than were meth- ylated, and methylation sites of the CHH type were mostly demethylated (Fig. - 1 Distribution of mC in CG, CHG, and CHH in the (a) treatment group, (b) control group and (c) all six different samples. - This was true for both hyper- and demethylation, suggesting that DNA methylation broadly affects gene regulation in intricately connected bio- logical processes. - In the cell component and mo- lecular function categories, organelle and catalytic activity were significantly enriched. - Thus, genes regulated by DNA methylation are not limited to those directly involved in the response to Cd toxicity. - Cd exposure altered a variety of pathways in the KEGG enrichment analysis. - Thus, the results of the KEGG analysis demonstrate that multiple cellular mechanisms are. - activated in the response to Cd exposure and that DNA methylation is actively involved in their regulation.. - The GO and KEGG enrichment analyses of DMRs provided insight into the processes affected by DNA methylation in D. - To identify the specific genes in- volved in these processes, we compared the complete gene sequences of these DMRs—that is, DMGs—with Drosophila digital expression library (DGE) data ob- tained under the same Cd treatment conditions as those of the present study. - indicating that changes in DNA methylation state regulate gene expression but are not the main regulatory process in Drosophila. - In most of the 37 DMRs, methylation levels were negatively correlated with gene expression level, that is, methylation repressed gene expression, which in turn activated expression. - An analysis of the 37 overlapping genes showed that 27 of these had critical functions (Fig. - Of these genes, Mekk1 has been linked to the response to Cd toxicity through positive regulation of the mitogen-activated protein kinase (MAPK) cascade, whereas Cdc42 is closely related to cell cycle arrest and apoptosis.. - The expression levels of these genes were up- regulated (except for dx, which was downregulated) in response to Cd stress through DNA methylation.. - DNA methylation is an epigenetic regulatory mechanism that controls gene expression through modification of cytosine bases that alters chromatin structure and stabil- ity and DNA–protein interactions [21, 22]. - There is in- creasing evidence that DNA methylation is a mechanism in animals that allows adaptation to environmental stress or trauma [23] through controlled changes in gene ex- pression levels [24–27].. - In this study, we determined that Cd ion stress altered DNA methylation patterns in the Drosophila genome by WGBS. - Although the DNA methylation rate in the gen- ome was very low. - Our results provide new evidence for the biological importance of DNA methylation and insight into how gene expression is regulated by epigenetic modifica- tions under conditions of stress.. - 4 DNA methylation levels in different functional regions of Cd treatment and control groups. - The coordinates are compressed according to the size of the region, while the x-axis represents the positions of different regions, and the y-axis represents the level of methylation. - In this study, we carried out a functional enrichment analysis of GO terms and KEGG pathways for all DMRs [31, 32] and found that DNA methylation during Cd stress affects genes that are involved in basic physiological functions.. - Similar results were obtained by KEGG pathway analysis, which identified pathways associated with the phago- some, Hippo and Notch signaling, and phototransduc- tion as those affected by changes in DNA methylation as a result of Cd stress. - these processes and pathways are implicated in the regulation of immunity, somite devel- opment, ocular development, neurogenesis, and embryo- genesis. - Thus, DNA methylation can directly affect biological mechanisms such as development and im- munity to counteract Cd toxicity, which has not yet been demonstrated. - We examined genes showing the greatest differences in expression due to changes in DNA methylation [36] and identified 27 including AGO3, Myo81F, and Cdc42 from the set of 37 DMGs overlapping with the DGEs. - This expression profile is consistent with the mechanism of stress resistance and demonstrates that it is not possible to predict changes in the regulation of gene expression based solely on changes in DNA methy- lation levels.. - 5 Methylation levels of DMRs in the Cd treatment and control groups. - the black line in the box represents the median distribution (50% quartile). - On the other hand, alphaTub84B and Act79B are involved in regulation of the actin cytoskel- eton and mitotic spindle. - In conclusion, the results of this study demonstrate that changes in DNA methylation in Drosophila caused by exposure to Cd activate genes involved in apoptosis and other basic cellular processes. - Bars represent the number of the DMRs in enriched GO terms. - The cytosine methylation sequencing linker was then ligated to both ends of the DNA fragments, which were treated with the EZ DNA Methylation-Gold kit (Zymo Research, Irvine, CA, USA) and bisulfite and PCR amplified. - At the same time, the Q20, Q30, and GC contents of the data were calculated using internal scripts.. - The methylation status of all cytosine positions in the reads was inferred from the mapping results. - Identical reads that were aligned to the same location in the Dros- ophila genome were considered as replicate reads. - The depth of methylation and transcripts per million were used in the calculation and log2 analysis was used to standardize the data. - The results of the methylated ex- tract were converted to bigWig format so that they could be viewed using the IGV browser. - The unconverted so- dium bisulfite was determined as the percentage of se- quenced cytosines that were sequenced at the reference position in the phage genome.. - The ge- nomes of the treatment and control groups were first scanned using the sliding window method with a window size of 1000 bp and step size of 100 bp. - We compared the chromosomal location information of the DMR with the standard gene file of the D. - The promoter region contained a 2-kb region upstream of the transcription start site.. - Gene names and annotations appearing in the lists of DMGs as well as DEGs. - These funding bodies had no role in the design of the study. - or in the writing of the manuscript.. - Amount and metal composition of midgut gland metallothionein in shore crabs (Carcinus maenas) after exposure to cadmium in the food. - Cell damage and apoptosis in the hepatopancreas of Eriocheir sinensis induced by cadmium. - Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium. - prevention: a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. - Effect of low-dose cadmium exposure on DNA methylation in the endangered European eel.. - Inducible protein traps with dominant phenotypes for functional analysis of the Drosophila genome. - Investigating the role of DNA methylation as an epigenetic mechanism in the pacific oyster (Crassostrea gigas). - DNA methylation in insects. - Epigenetic regulation of motor neuron cell death through DNA methylation. - The early-life social environment and DNA methylation. - Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response. - Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. - methyltransferase inhibitor in the snail Lymnaea stagnalis. - Involvement of DNA methylation in the control of cell growth during heat stress in tobacco BY-2 cells. - Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis. - A global DNA methylation and gene expression analysis of early human B-cell development reveals a. - Genome-wide DNA methylation profile analysis identifies differentially methylated loci associated with ankylosis spondylitis. - Comprehensive DNA methylation and gene expression profiling in differentiating human adipocytes. - Recent progress towards understanding the role of DNA methylation in human placental development. - Effects of dppa3 on DNA methylation dynamics during primordial germ cell development in mice. - Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts.. - DNA methylation-associated repression of cancer-germline genes in human embryonic and adult stem cells. - Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity protein, Par6. - Adaptor functions of Cdc42, Ste50, and Sho1 in the yeast osmoregulatory HOG MAPK pathway. - Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. - Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome. - Differentially DNA methylation changes induced in vitro by traffic-derived nanoparticulate matter.
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