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ABSTRACT: Vitamin D Receptor Gene and interleukin polymorphisms

PROVIDER: PRJNA947482 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24000400.fastq.gz	Fastqsanger.gz
	SRR24000401.fastq.gz	Fastqsanger.gz
	SRR24000402.fastq.gz	Fastqsanger.gz
	SRR24000403.fastq.gz	Fastqsanger.gz
	SRR24000404.fastq.gz	Fastqsanger.gz

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Effect of long-term vitamin D supplementation on colonic gene expression in IL-10 Knockout mice at young adulthood

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Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression

Project description:Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression

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Effects of cis-regulatory elements on proteome

Project description:Background Genomic variations contribute to the phenotypic diversity of individuals. A number of polymorphisms in protein-coding regions that alter drug efficacy or lead to adverse reactions have been characterized; however, noncoding regions that affect drug responses are largely overlooked, except for a limited number of well-studied enhancers. Results We conducted a quantitative assessment of cis-regulatory elements (CREs) based on transcription initiation profiling of mRNAs and noncoding RNAs, including enhancer RNAs, by using CAGE (Cap Analysis of Gene Expression). Candidate CREs identified in a hepatocellular carcinoma HepG2 cell line with stable expression of drug-responsive transcription factor pregnane X receptor (PXR) were further narrowed down by integrating data of PXR-binding sites in human primary hepatocytes and genome-wide association studies. We found more than 100-fold enrichments of the candidates to genetically associated loci with circulating levels of bilirubin and vitamin D, which implicated a link to adverse reactions of PXR ligands. We uncovered novel enhancers of UGT1A1 and TSKU through CRISPR/Cas9 knockout experiments. We identified alleles altering regulatory activities of UGT1A1 and CYP24A1enhancers by using luciferase reporter assay. Furthermore, our siRNA experiments revealed an unexpected impact of TSKU on the expression of vitamin D-metabolizing enzymes. Conclusions Our transcriptome-based assessment of CREs expanded the list of drug-inducible and PXR-mediated enhancers and super-enhancers. We identified regulatory alleles that alter drug-induced gene expressions, and discovered a novel molecular cascade associated with an adverse reaction. Our results contribute a precise understanding of the noncoding elements of the human genome underlying drug responses.

2025-04-17 | PXD060446 | Pride

Homo sapiens

Project description:Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression [ChIP-Seq]

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Homo sapiens

Project description:Vitamin D/Vitamin D Receptor (VDR) Axis Regulates LMNA gene expression [RNA-Seq]

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Vitamin D Receptor (VDR) ChIP-seq reported in "Vitamin D receptor and STAT3 cooperate to TET2-mediated acquisition of tolerogenesis"

Project description:The active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), induces stable tolerogenesis in dendritic cells (DC). This process involves the Vitamin D receptor (VDR) which translocates to the nucleus, binds its cognate genomic sites and promotes epigenetic and transcriptional remodeling. In this study, we investigated the interplay between the vitamin D receptor (VDR) and transcription factors to induce DNA methylation changes, which might provide phenotypic stability to the tolerogenic phenotype of DCs.

2022-02-23 | GSE145584 | GEO

Homo sapiens

Project description:Association of vitamin D anabolism-related gene polymorphisms and susceptibility to uterine leiomyomas

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Project description:The genotyping of eight single nucleotide polymorphisms of vitamin D metabolizing enzyme gene

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Transcriptomics of vitamin D treatment effects in Mycobacterium tuberculosis-infected THP-1 cells

Project description:Previous reports have shown low vitamin D serum levels and polymorphisms in the vitamin D receptor (VDR) to be associated with increased risk for TB. Given that 1α,25-dihydroxyvitamin D3 has a role in lipid metabolism control, we tested whether the link between 1α,25-dihydroxyvitamin D3 and tuberculosis involves macrophage lipid metabolism. Since formation of lipid droplets (LD) is a hallmark of lipid dysregulation in M. tuberculosis-infected macrophages, we measured LD content as a readout of altered lipid metabolism in infected THP-1 cells. Induction of LD, which peaked by 24 hours post-infection was prevented by addition of 1α,25-dihydroxyvitamin D3 at the time of infection. To investigate the mechanism of 1α,25-dihydroxyvitamin D3 modulation of LD formation, we analyzed the transcriptome of M. tuberculosis-infected THP-1 cells with and without 1α,25-dihydroxyvitamin D3 treatment.

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Effect of long-term vitamin D supplementation on colonic gene expression in IL-10 Knockout mice at young adulthood

Project description:Low vitamin D status has been implicated in the progression of inflammatory bowel disease (IBD). This study used interleukin (IL)-10 knockout (KO) mice, that develop an intestinal inflammation when housed in a non-sterile environment, to determine if supplementation with vitamin D throughout life impacts colonic gene expression. Results provide important information on the intestinal response to vitamin D in inflamed mice. Female IL-10 knock out mice were randomized to 25 (Low, L) or 5000 (High, H) IU vitamin D/kg of diet throughout pregnancy and lactation. At weaning, offspring received the same or opposite diet as their mother until age 3 months. This resulted in four vitamin D interventions: HH, HL, LH, or LL where the first letter represents the diet consumed by dams during pregnancy and lactation and the second letter represents the diet consumed by offspring from weaning through to 3 months of age. Global gene expression was analyzed in the proximal colon of 3 months old mice (n=6 per group, for a total of 24 samples; samples came from different litters and moms IDs are given in the samples table below). Samples were stored at -80C.

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