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Fatty acid binding proteins shape the cellular response to activation of the glucocorticoid receptor

ABSTRACT: Fatty acid binding proteins shape the cellular response to activation of the glucocorticoid receptor

PROVIDER: PRJNA747920 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15187026.fastq.gz	Fastqsanger.gz
	SRR15187027.fastq.gz	Fastqsanger.gz
	SRR15187028.fastq.gz	Fastqsanger.gz
	SRR15187029.fastq.gz	Fastqsanger.gz
	SRR15187030.fastq.gz	Fastqsanger.gz

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Fatty acid binding proteins shape the cellular response to activation of the glucocorticoid receptor

Project description:Glucocorticoids are steroid hormones that are essential for life in mammals. Therapeutically, they are some of the most cost-effective drugs for the treatment of inflammatory diseases ranging from skin rashes to COVID-19, but their use is limited by adverse effects. Glucocorticoids exert their effects via the glucocorticoid receptor, a type I nuclear hormone receptor which modulates gene expression. The transcriptional activity of some related, but nuclear restricted, type II nuclear hormone receptors can be enhanced by a family of intracellular transport proteins, the fatty acid binding proteins (FABPs). We find that the transcriptional activity of the GR can be altered by a sub-set of FABP family members dependent on the GR-ligand. The ability of some FABPs to selectively promote or limit the transcriptional activity of the GR in a ligand-dependent manner could facilitate the discovery of drugs that narrow GR activity to only the desired subset of therapeutically relevant genes.

2021-07-22 | GSE180341 | GEO

Comparative transcriptomics analysis of fatty acid-secreting Yarrowia lipolytica reveals importance of cell wall proteins

Project description:Yarrowia lipolytica has been considered one of the most promising platforms for the microbial production of fatty acids and derived products. The deletion of the faa1 gene coding for an acyl-CoA synthetase leads to the accumulation and secretion of free fatty acids (FFAs) into the extracellular space. The secretion of products is beneficial for the development of microbial cell factories to avoid intracellular inhibitory effects and reduce downstream processing costs. However, the mechanism behind the secretion of fatty acids is not well known. In this research, we compared the transcriptome of this mutant showing FFA secretion to a wildtype-like strain not showing this phenotype. Both toxicity and growth assays, as well as deletion and overexpression mutants of candidate genes were used to assess the effects of candidate genes on the export of FFAs. Although no clear transporter of fatty acids was identified, the analysis of the transcriptomic data revealed an overrepresentation of cell wall-related proteins. Based on this results, a literature search allowed to retrieve proteins related to the cell wall previously associated to lipid. Experiments performed on these candidates proved their involvement in resistance to FFAs toxicity, with one of them being a potential acyl-CoA export protein.

2025-11-06 | GSE217432 | GEO

Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins

Project description:Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins

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Fatty-acid degrading metagenome

Project description:Fatty-acid degrading metagenome

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Glucocorticoid promotes fatty acids metabolism in hypertrophic scar tissues and fibroblasts via the microRNA

Project description:Hypertrophic scar (HS) is a skin lesion due to abnormal wound healing after skin injury; histologically, HS is characterized by deposition of excessive amounts of the extracellular matrix and collagen produced by wound healing-induced proliferative fibroblasts. Clinically, HS management includes surgical resection of HS, topical glucocorticoid therapy or drug injections, pressure therapy, fractional carbon dioxide laser therapy, and cryotherapy. In terms of non-surgical therapy, glucocorticoids (like Triamcinolone acetonide, a synthetic corticosteroid medication used topically to treat various skin conditions) was able to effectively inhibit HS formation safely for decades. The effects of glucocorticoids may either be due to its anti-inflammatory, anti-allergenic and immunomodulatory effects or activate fatty acids metabolism by promotion of lipid accumulation in fibroblasts. However, it is no clear why and how glucocorticoids-upregulated fatty acid metabolisms benefit in HS treatment and prevention.And it remains to be defined how altered microRNAs regulated-fatty acid metabolism involved in pathological scars.

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Deconvolving the recognition of DNA shape from sequence

Project description:Binding of transcription factors to DNA is mediated by the recognition of the chemical signatures of the DNA bases and the three-dimensional shape of the DNA molecule. The direct contribution of DNA shape to DNA-binding specificity has been difficult to assess, as DNA shape is a consequence of its sequence. Here, we teased apart these two modes of recognition in the context of Hox-DNA binding. We made a series of mutations in Hox residues that, in a co-crystal structure, only recognize DNA shape, and tested the effect on DNA binding preferences using SELEX-seq. Analysis of shape features of selected sequences revealed that these residues are both necessary and sufficient for selection of sequences with distinct shape features. We used statistical machine learning to show that the accuracy of binding specificity predictions improves by adding shape features to a model that only depends on sequence. We conclude that shape readout is a direct and critical component of binding site selection by Hox proteins. Three rounds of SELEX were performed on a series of Hox mutants as described in Slattery et al, Cell, 2011 (PMID 22153072) and Riley et al, Methods in molecular Biology, 2014 (PMID 25151169). Briefly, His-tagged Scr and Antp mutant proteins were incubated with a randomized 16mer oligonucleotide library, and bound DNA was amplified and sequenced as described (PMID 22153072, PMID 25151169).

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Project description:Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins [ChIP-seq]

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Project description:Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins [ATAC-seq]

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Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins [RNA-seq]

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Comparative transcriptomics analysis of fatty acid-secreting Yarrowia lipolytica reveals importance of cell wall proteins

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