Escherichia coli: untreated versus 5-azacytidine-treated expression profiles
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ABSTRACT:
ORGANISM(S): Escherichia coli Escherichia coli O157:H7 str. EDL933 Escherichia coli O157:H7 str. Sakai Escherichia coli CFT073 Escherichia coli str. K-12 substr. MG1655
PROVIDER: GSE73707 | GEO | 2016/09/24
SECONDARY ACCESSION(S): PRJNA297697
REPOSITORIES: GEO
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Project description:5-Azacytidine or 5-aza-2’-deoxycytidine is a chemical analogue of the cytosine nucleoside used in DNA and RNA. Cells in the presence of 5-azacytidine incorporate it into DNA during replication and RNA during transcription. The incorporation of 5-azacytidine into DNA or RNA inhibits methyltransferase thereby causing demethylation in that sequence, affecting the way that cell regulation proteins are able to bind to the DNA/RNA substrate. Inhibition of DNA occurs through the formation of stable complexes between the molecule and with DNA methyltransferases, thereby saturating the cells methylation machinery. 5-azacytidine is mainly used in the treatment of myelodysplastic syndrome. Changes in gene expression levels in Erbb2 transfected murine fibroblast cell line after treatment with Azacytidine in two different concentrations were analysed. Keywords: cDNA microarray, murine fibroblast, azacytidine treatment, carcinogenesis
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Project description:5-Azacytidine or 5-aza-2â??-deoxycytidine is a chemical analogue of the cytosine nucleoside used in DNA and RNA. Cells in the presence of 5-azacytidine incorporate it into DNA during replication and RNA during transcription. The incorporation of 5-azacytidine into DNA or RNA inhibits methyltransferase thereby causing demethylation in that sequence, affecting the way that cell regulation proteins are able to bind to the DNA/RNA substrate. Inhibition of DNA occurs through the formation of stable complexes between the molecule and with DNA methyltransferases, thereby saturating the cells methylation machinery. 5-azacytidine is mainly used in the treatment of myelodysplastic syndrome. Changes in gene expression levels in Erbb2 transfected murine fibroblast cell line after treatment with Azacytidine in two different concentrations were analysed. Keywords: cDNA microarray, murine fibroblast, azacytidine treatment, carcinogenesis Gene expression levels of Erbb2 transfected NIH3T3 cell lines treated with 5µM and 10µM Azacytidine were compared to Erbb2 transfected but non-treated NIH3T3 cell line. For each Azacytidine concentration 4-8 experiments were performed including 50% dye swaps. As a controll experiments gene expression levels of NIH3T3 cells with and without Azacytidine treatment were analysed
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Project description:The non-methylable cytosine analogs, 5-azacytidine and zebularine, are widely used to disrupt DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that 5-azacytidine and zebularine-treated seedlings have nearly indistinguishable patterns of DNA methylation genome-wide and that 5-azacytidine, despite being more unstable in aqueous solution, has a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of up-regulated genes and transposable element genes, particularly CACTA-like elements, demonstrating that chemical demethylating agents have a disproportionately large effect on loci that are silenced by DNA methylation.
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Project description:TET2 is a know tumorsuppressor gene involved in the demethylation of DNA. TET2 catalyses the conversion of 5-methyl cytosine (5-mC) to 5-hydroximethyl cytosine (5-hmC), an important step in the removal of methylation from the DNA. In T-All mutations in TET2 are rare, however we have found that it is often silenced by DNA Methylation. 5-Azacytidine (5-AZA) is a an effective demethylating agent used as a cancer treatment and has been showed to be able to reactivate methylated genes. Similarly, Vitamin C is an important co-factor for TET2 and has been shown to have synergistic effects with 5-Azacytidine. By treating the TET2 methylated T-ALL cell lines Loucy and DND41 and comparing to TET2 expressing T-ALL cells lines such as SUP-T1 and Jurkat we aimed to explore if 5-AZA could reactivate TET2 in T-ALL, what effects this would have on tumorgenicity and whether Vitamin C had any synergy with these effects in T-ALL. As part of this effort we treated the cell lines SUP-T1, Jurkat, Loucy and DND41 with 5-AZA and Vitamin C and performed Total RNA-seq to explore the effects of 5-AZA and Vitamin C on the expression of genes and non-coding elements such as retrotransponsons.
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