Ontology highlight
ABSTRACT:
PROVIDER: PRJNA853479 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19880166_1.fastq.gz | Fastqsanger.gz | |||
| SRR19880166_2.fastq.gz | Fastqsanger.gz | |||
| SRR19880167_1.fastq.gz | Fastqsanger.gz | |||
| SRR19880167_2.fastq.gz | Fastqsanger.gz | |||
| SRR19880168_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study is to do a side-by-side comparison of the transcriptomes that are regulated under Cu and Cd stress at the early stage in rice roots. The comparison of transcriptomes between Cu and Cd treatments and the application of bioinformatics procedures (e.g. regulated gene analysis) are potentially useful approaches for determining the both general and individual early responses triggered by each metal. Identify genes and pathways that would discriminate among the actions of Cu and Cd.
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Project description:Perinereis aibuhitensis Raw sequence reads
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Project description:The cadmium-resistant Cupriavidus sp. E324 strain has been previously shown to have a high potential for use in cadmium (Cd) remediation, due to its high capacity for cadmium bioaccumulation. According to the comparative genomic analysis, the E324 strain was most closely related to C. nantongensis X1 T , indicating that the E324 strain should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of C. nantongensis E324, the transcriptional response of this strain to Cd stress was assessed using RNA-seq-based transcriptome analysis, followed by validation through qRT- PCR. The results showed that the upregulated Differentially Expressed Genes (DEGs) were significantly enriched in categories related to metal binding and transport, phosphate transport, and oxidative stress response. Consistently, we observed significant increases in both the cell wall and intracellular contents of certain essential metals (Cu, Fe, Mn, and Zn) upon Cd exposure). Among these, only the Zn pretreatment resulting in high Zn accumulation in the cell walls could enhance bacterial growth under Cd stress conditions through its role in inhibiting Cd accumulation. Additionally, the promotion of catalase activity and glutathione metabolism upon Cd exposure to cope with Cd-induced oxidative stress was demonstrated. Meanwhile, the upregulation of phosphate transport-related genes upon Cd treatment seems to be the bacterial response to Cd-induced phosphate depletion. Altogether, our findings suggest that these adaptive responses are critical mechanisms contributing to increased Cd tolerance in C. nantongensis E324 strain via the enhancement of metal-chelating and antioxidant capacities of the cells.
2024-09-03 | GSE272856 | GEO
Project description:Copper (Cu) regulates hypoxia-inducible factor-1 (HIF-1) transcription activity by affecting the selectivity of HIF-1α targeting to the promoters of the affected genes. Here, we made an effort to provide a comprehensive understanding of Cu regulation of the selectivity of HIF-1α targeting across genome. We used tetraethylenepentamine (TEPA), a Cu selective chelator, to reduce Cu content in the cells. In hypoxia, we conducted chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-seq) to globally map the binding sites of HIF-1α, Pol Ⅱ (RNA polymeraseⅡ) and histone H3K27ac. We also performed RNA-sequencing (RNA-seq) in EA.hy926 cells under hypoxia (1% O2) with or without Cu depression to determine the profile of mRNA expression. Our analyses identified 3197 HIF-1α binding sites under hypoxia. Cu depression by TEPA reduced 1820 binding sites from the 3197, but induced additional 274 new binding sites. We analyzed these binding sites in the promoter and putative enhancer regions, coupled with their mRNA expression profiles, and found 281 Cu-dependent and 10 Cu-independent HIF-1α target genes. We found that the core bases “GGAA” and “TTCC” constituted the critical motifs for the binding sites of Cu-dependent genes. This study thus revealed that Cu, by affecting the binding of HIF-1α to the critical motifs in the promoter and putative enhancer regions of HIF-1 regulated genes, leads to the selectivity of HIF-1 regulated expression of Cu-dependent genes.
2019-09-24 | GSE120524 | GEO
Project description:The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd.
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