Cr(VI) Promotes Differential Binding of CTCF to its Cognate Sites
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA646103 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12215057.fastq.gz | Fastqsanger.gz | |||
| SRR12215058.fastq.gz | Fastqsanger.gz | |||
| SRR12215059.fastq.gz | Fastqsanger.gz | |||
| SRR12215060.fastq.gz | Fastqsanger.gz | |||
| SRR12215061.fastq.gz | Fastqsanger.gz |
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Project description:Using ChIP-seq, we characterize the differential binding of CTCF following 48 hours of low-dose, Cr(VI) treatment. Differentially-bound sites are enriched in regions near genes that are actively transcribed in the basal state and strength of initial binding may be a factor in determining the directionality of binding affinity fluctuations. CTCF and cohesin samples were used to predict intra-TAD chromatin loops in an effort to provide an initial characterization of how Cr(VI) potentially disrupts chromatin-chromatin contacts important for the regulation of transcription, serving as a foundation for future studies.
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Project description:Hexavalent chromium (Cr(VI)) is a highly toxic contaminant, some bacteria are able to transform it to less toxic and less soluble trivalent chromium (Cr(III)). Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically, and resists up 35 mM of Cr(VI); Subculturing of AqSCr in the presence of Cr(VI) conduces to adaptation. In this study, we performed RNA-Seq of Cr(VI) adapted stage, finding 255 genes upregulated and 240 downregulated with respect to controls without Cr(VI). Genes differentially expressed are mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid metabolism, ribosomal subunits and energy metabolism. Among them, genes not previously associated with chromium resistance as cybB, encoding a putative superoxide oxidase, gltA2, encoding an alternative citrate synthase, and des, encoding a fatty acid desaturase were upregulated. The alternative sigma factors fecl, rpoE and rpoS were upredgulated in Cr(VI) adapted cells, then they participate in orchestate the Cr(VI)-resistance mechanisms in AqSCr strain
2021-05-20 | GSE160968 | GEO
Project description:Cr(VI) is a common bioavailable toxic metal that can cause oxidative stress, DNA adducts, and perturb normal gene expression. Changes in gene expression are useful biomarkers of toxicant exposure that provide information about the health of an organism, its ability to adapt to its environment, and indicate potential toxicant-specific effects. Therefore, we developed a toxicology array to the estuarine sentinel species Fundulus heteroclitus, or mummichog. Juvenile mummichog were exposed to potassium dichromate for thirty days at concentrations from 0 to 24 mg/L of Cr(VI), and growth was measured to determine the NOEC (1.5 mg/L or 0.0288 mM) and LOEC (3 mg/L or 0.0577 mM). Body burdens from Cr(VI) exposed fish demonstrated a dose dependent increase and were inversely correlated to body weight. Cr(VI)-exposed juvenile mummichog differentially expressed greater than 20 genes in a dose-dependent manner, including hepatic glucose transporter 2, liver fatty acid binding protein, ATPase synthase 8, type II keratin, TBT binding protein, and complement component C3-2. Many of these genes are involved in energy metabolism or growth, which is consistent with the reduced growth caused by Cr(VI). Keywords: dose response
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Project description:Hexavalent chromium compounds are well-established respiratory carcinogens utilized in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal carcinogen, affecting millions of people throughout the world. Cr(VI) is genotoxic, by forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. We have used FAIRE to show that Cr(VI) elicits broad changes in chromatin accessibility resulting from disruption of the binding of transcription factors CTCF and AP-1 to their cognate sites in chromatin. Here, we have used two complementary approaches to test the hypothesis that chromium perturbs chromatin organization and dynamics. DANPOS2 analyses of MNase.seq data identified several chromatin alterations induced by Cr(VI) affecting nucleosome architecture, including occupancy changes at specific genome locations; position shifts of 10 nucleotides or more; and fuzziness, or changes in signal amplitude. Using ATAC to analyze changes in chromatin accessibility, we found that Cr(VI) opened differentially accessible chromatin domains in a dose-dependent manner. These domains were enriched for the previously identified binding motifs for CTCF and AP-1, many located in promoters of differentially expressed genes. Cr(VI)-enriched CTCF sites were confirmed by ChIP.seq and, when compared with ENCODE-validated CTCF site datasets from mouse liver, correlated with evolutionarily conserved similar sites occupied in vivo. Our results show that Cr(VI) exposure promotes broad changes in chromatin accessibility and suggest that the subsequent dysregulation of transcription may result from the disruption of CTCF binding and nucleosome spacing, suggesting that transcription regulatory mechanisms are primary Cr(VI) targets.
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Project description:Hexavalent chromium compounds are well-established respiratory carcinogens utilized in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal carcinogen, affecting millions of people throughout the world. Cr(VI) is genotoxic, by forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. We have used FAIRE to show that Cr(VI) elicits broad changes in chromatin accessibility resulting from disruption of the binding of transcription factors CTCF and AP-1 to their cognate sites in chromatin. Here, we have used two complementary approaches to test the hypothesis that chromium perturbs chromatin organization and dynamics. DANPOS2 analyses of MNase.seq data identified several chromatin alterations induced by Cr(VI) affecting nucleosome architecture, including occupancy changes at specific genome locations; position shifts of 10 nucleotides or more; and fuzziness, or changes in signal amplitude. Using ATAC to analyze changes in chromatin accessibility, we found that Cr(VI) opened differentially accessible chromatin domains in a dose-dependent manner. These domains were enriched for the previously identified binding motifs for CTCF and AP-1, many located in promoters of differentially expressed genes. Cr(VI)-enriched CTCF sites were confirmed by ChIP.seq and, when compared with ENCODE-validated CTCF site datasets from mouse liver, correlated with evolutionarily conserved similar sites occupied in vivo. Our results show that Cr(VI) exposure promotes broad changes in chromatin accessibility and suggest that the subsequent dysregulation of transcription may result from the disruption of CTCF binding and nucleosome spacing, suggesting that transcription regulatory mechanisms are primary Cr(VI) targets.
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Project description:Hexavalent chromium compounds are well-established respiratory carcinogens utilized in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal carcinogen, affecting millions of people throughout the world. Cr(VI) is genotoxic, by forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. We have used FAIRE to show that Cr(VI) elicits broad changes in chromatin accessibility resulting from disruption of the binding of transcription factors CTCF and AP-1 to their cognate sites in chromatin. Here, we have used two complementary approaches to test the hypothesis that chromium perturbs chromatin organization and dynamics. DANPOS2 analyses of MNase.seq data identified several chromatin alterations induced by Cr(VI) affecting nucleosome architecture, including occupancy changes at specific genome locations; position shifts of 10 nucleotides or more; and fuzziness, or changes in signal amplitude. Using ATAC to analyze changes in chromatin accessibility, we found that Cr(VI) opened differentially accessible chromatin domains in a dose-dependent manner. These domains were enriched for the previously identified binding motifs for CTCF and AP-1, many located in promoters of differentially expressed genes. Cr(VI)-enriched CTCF sites were confirmed by ChIP.seq and, when compared with ENCODE-validated CTCF site datasets from mouse liver, correlated with evolutionarily conserved similar sites occupied in vivo. Our results show that Cr(VI) exposure promotes broad changes in chromatin accessibility and suggest that the subsequent dysregulation of transcription may result from the disruption of CTCF binding and nucleosome spacing, suggesting that transcription regulatory mechanisms are primary Cr(VI) targets.
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Project description:Cr(VI) is a common bioavailable toxic metal that can cause oxidative stress, DNA adducts, and perturb normal gene expression. Changes in gene expression are useful biomarkers of toxicant exposure that provide information about the health of an organism, its ability to adapt to its environment, and indicate potential toxicant-specific effects. Therefore, we developed a toxicology array to the estuarine sentinel species Fundulus heteroclitus, or mummichog. Adults males were exposed to Cr(VI) for 7-days at 0, 1.5 (NOEC), or 3 mg/L (LOEC). Livers were excised and RNA isolated. Adults are used in the laboratory experiments so that we can compare laboratory studies to fish caught at chromium-contaminated field sites. Cr(VI) altered the expression of 12 genes in adult liver, including hepatic growth factor activator, heart fatty acid binding protein, and complement component C3-2. Keywords: dose response
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Project description:Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. The rice variety IR-64 was germinated and allowed to grow for 5 d at 37 C and then transferred to Hewitt solution for growth. After 10 d of growth, seedlings of uniform size and growth were treated with 100 µM of Cr (VI), As (V), Cd, and Pb under standard physiological conditions of 16 h light (115 μmol m−2 s−1) and 8 h dark photoperiod at 25 ± 2 C for 24 h. Total RNA was extracted from the treated rice roots and microarray was performed using one-cycle target labeling and control reagents (Affymetrix platform).
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Project description:Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice.
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