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Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

ABSTRACT: Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

PROVIDER: PRJNA609633 | ENA |

REPOSITORIES: ENA

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Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

Project description:We employ omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production in Escherichia coli. As a result, we identify 56 beneficial genes , including 46 novel targets functioning in cell structure and division, and signaling transduction that efficiently facilitate FFAs production.

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Genome-wide targets identification for high-titer production of free fatty acids in Escherichia coli

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Project description:Volatile fatty acids (VFAs) production through anaerobic fermentation

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Free fatty acids and TNF-alpha in hepg2/c3a cell culture

Project description:free fatty acids(palmitate, oleate, linoleate) 0.7mM and tnf-alpha (0 20,100 ng/ml) were subjected to HepG2 cell line to study the cytotoxicity induced by these two factors Keywords: stress response

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Free fatty acids and TNF-alpha in HepG2 cell culture

Project description:The regulation of complex cellular activities in palmitate treated HepG2 cells, and the ensuing cytotoxic phenotype, involves cooperative interactions between genes. While previous approaches have largely focused on identifying individual target genes, elucidating interacting genes has thus far remained elusive. We applied the concept of information synergy to reconstruct a ?gene-cooperativity? network for palmititate-induced cytotoxicity in liver cells. Our approach integrated gene expression data with metabolic profiles to select a subset of genes for network reconstruction. Subsequent analysis of the network revealed insulin signaling as the most significantly enriched pathway, and desmoplakin (DSP) as its top neighbor. We determined that palmitate significantly reduces DSP expression, and treatment with insulin restores the lost expression of DSP. Insulin resistance is a common pathological feature of fatty liver and related ailments, whereas loss of DSP has been noted in liver carcinoma. Reduced DSP expression can lead to loss of cell-cell adhesion via desmosomes, and disrupt the keratin intermediate filament network. Our findings suggest that DSP expression may be perturbed by palmitate and, along with insulin resistance, may play a role in palmitate induced cytotoxicity, and serve as potential targets for further studies on non-alcoholic fatty liver disease (NAFLD). free fatty acids(palmitate, oleate, linoleate) 0.7mM and tnf-alpha (0 20,100 ng/ml) were subjected to HepG2 cell line to study the cytotoxicity induced by these two factors. control(Hepg2 medium and BSA medium) treatment(combinations of TNFa+FFAs) two biological replicates for each condition, color swap for each sample

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ATAC-seq and multi-omics analysis of human liver highlight a hepatocyte-specific enhancer for ACOT1 regulating the balance of acyl-CoA and free fatty acids in type 2 diabetes.

Project description:ATAC-seq (assay for transposase-accessible chromatin followed by sequencing) is widely used to decode chromatin accessibility. Here we performed high-sensitive ATAC-seq in 9 human liver samples from normal and T2D donors, and identified a set of differentially accessible regions (DARs). DARs were overlapped with publicly available CREs databases and integrated with multi-omics data to identify candidates for further experimental validations. We identified 7 DARs that mark putative regulatory elements including a candidate enhancer for the ACOT1 gene that regulates the balance of acyl-CoA and free fatty acids in the cytoplasm. The relevance of ACOT1 regulation in T2D was supported by the analysis of transcriptomics and proteomics data in liver tissue. Conclusions: Our strategy that integrates chromatin accessibility with DNA binding and other types of omics provides novel insights towards the role of genetic regulation in complex multifactorial diseases such as T2D.

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Project description:Multi-omics approach reveals miR-SNPs affecting muscle fatty acids profile in the Nelore cattle

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RNASeq of Developing Arabidopsis Seeds Producing Hydroxy-Fatty Acids

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