Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [ChIP-Seq]

ABSTRACT: Purpose: Using a selected carrier (C) allele of rs10846744 SNP associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele, chromatin immunoprecipitation of a protein of interest, NR2F2, overexpressed and bound to the rs10846744 region in the risk (CC) cells was performed in triplicate. Methods: Using NR2F2 as the target protein, chromatin was immunoprecipitated from each cell type and subjected to Next-gen sequencing. Input controls for each cell type were also sequenced. Results: MACS (Zhang et al., 2008) was utilized for analysis. The narrow peak results were visualized using the Washington University EpiGenome Browser (Zhou and Wang, 2013) and bedgraph files were visualized in the Integrative Genomics Viewer (Thorvaldsdóttir et al., 2013) as bigwig files. Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE110756 | GEO | 2019/10/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [4C-Seq]

Project description:Purpose: Isolating chromatin interactions from a specific viewpoint, we utilized Next-generation sequencing (NGS) to profile specific chromatin interaction differences between two populations, a selected carrier (C) alele of SNP (rs10846744) associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele. Methods: Chromatin was isolated from two subjects, one homozygous for the rs10846744 reference (G) allele and one homozygous for the rs10846744 risk (C) allele, processed for 4C-Seq (van de Werken et al., 2012). Results: 4C-ker (Raviram et al, 2016) analyzed the chromatin interaction data from the specific viewpoint. The results were visualized using the Washington University EpiGenome Browser (Zhou and Wang, 2013). Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

2019-10-04 | GSE110752 | GEO

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [Hi-C]

Project description:Purpose: Utilized Next-generation sequencing (NGS) to profile global chromatin interaction differences between two populations, a selected carrier (C) alele of SNP (rs10846744) associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele. Methods: Chromatin was isolated from two subjects, one homozygous for the rs10846744 reference (G) allele and one homozygous for the rs10846744 risk (C) allele, processed for dilution HiC (Lieberman-Aiden, van Berkum et al., 2009) and then subjected next-gen sequencing. Results: HiC-Pro integrated pipeline (with default parameters) was used for generating the HiC contact probability matrices (Servant et al., 2015). The results were visualized using HiCPlotter (Akdemir and Chin, 2015) and HiTC (Servant et al., 2012) and the Washington University EpiGenome Browser (Zhou and Wang, 2013). Juicebox (Durand et al., 2016) was utilized to extract observed/expected KR (Knight-Ruiz) normalized contacts for chromosome 12. Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

2019-10-04 | GSE110757 | GEO

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks

Project description:Increased high density lipoprotein (HDL) cholesterol levels have been associated with mutations in the cholesterol efflux receptor gene SCARB1, contributing to coronary artery disease (CAD). Using chromatin capture techniques (4C-Seq and HiC), ChIP-Seq and RNA-Seq, we identified a potential mechanism between a non-coding SNP (rs10846744) within the first intron of SCARB1 and LAG3, a negative regulator of T cells, both on chromosome 12. We previously demonstrated how loss of LAG3 is associated with inflammation and CAD found in carriers of the rs10846744 risk allele (C) both in our hyperalphalipoproteinemia (HALP) participants and the Multi-Ethnic Study of Atherosclerosis (MESA), increasing the risk of a coronary event by 45% (PMID: 27777974). NR2F2 transcription factor binding, as detected by (yeast 1 hybrid assay, ChIP, and ChIP-Seq) to the rs10846744 risk (C) allele, bridges NR2F2, SCARB1, and LAG3 loci, altering gene networks associated with a CAD proinflammatory signature. This SuperSeries is composed of the SubSeries listed below.

2019-10-04 | GSE110761 | GEO

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [RNA-Seq]

Project description:Purpose: Utilized Next-generation sequencing (NGS) to profile transcriptional differences between two populations, a selected carrier (C) alele of SNP (rs10846744) associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele. Methods: RNA was isolated from three subjects homozygous for the rs10846744 reference (G) allele and three subjects homozygous for the rs10846744 risk (C) allele and then subjected to full transcriptome sequencing. Triplicates of one sample from each group were also sequences to overlay with chromatin data from each group. Knockdown of NR2F2 using lentiviral particles assessed differential expression between the treated and untreated risk replicates. The Illumina NextSeq 500 next gen sequencing platform (UCONN CGI, Storrs, CT) was used for RNA-Seq. HiSeq 2000 was used for biological replicates at Perkin Elmer. RNA targets of interest were validated by qPCR using TaqMan assays and proteins were blotted using standard western methodologies. Results: We normalized the raw read count by FPKM and using Cufflinks, identified differential transcripts. RNA-seq data confirmed differential expression of NR2F2 and LAG3, validated by qPCR. Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks.

2019-10-04 | GSE108274 | GEO

Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice

Project description:RNA alternative splicing (AS) expands the regulatory potential of eukaryotic genomes. The mechanisms regulating liver-specific AS profiles and their contribution to liver function are poorly understood. Here, we identify a key role for the splicing factor RNA-binding Fox protein-2 (RBFOX2) in maintaining cholesterol homeostasis in an obesogenic environment in the liver. Using enhanced individual-nucleotide resolution UV-crosslinking and immunoprecipitation (eiCLIP), we identify physiologically relevant targets of RBFOX2 in mouse liver, including the scavenger receptor class B type I (Scarb1). RBFOX2 function is decreased in the liver in diet-induced obesity, causing a Scarb1 isoform switch and alteration of hepatocyte lipid homeostasis. Our findings demonstrate that specific AS programmes actively maintain liver physiology, and underlie the lipotoxic effects of obesogenic diets when dysregulated. Splice-switching oligonucleotides targeting this network alleviate obesityinduced inflammation in the liver and promote an anti-atherogenic lipoprotein profile in the blood, underscoring the potential of isoform-specific RNA therapeutics for treating metabolism-associated diseases.

2022-11-28 | PXD036976 | Pride

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks

Project description:Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks

| PRJNA434469 | ENA

Lymphocyte activation gene3 and coronary artery disease.

Project description:Purpose: Utilized Next-generation sequencing (NGS) to profile transcriptional differences between two populations, carriers (CC) of rs10846744 SNP associated with cardiovascular disease (CVD) and non-carriers (GG) who are disease free. Methods: Total RNA was isolated from three subjects homozygous for the rs10846744 reference (GG) allele and three subjects homozygous for the rs10846744 risk (CC) allele and then subjected to full transcriptome sequencing using the Perkin Elmer next gen sequencing platform (Perkin Elmer, Branford, CT). Bioinformatics was performed using Perkin Elmer GeneSifter software program. The data was adjusted by selecting total map reads, quality reads >20, log transformation, and using Benjamini Hochberg to correct for multiple testing. RNA targets of interest were validated by qRT–PCR using TaqMan assays and western blotting using standard methodologies. Results: Using Perkin Elmer's Genesifter Analysis Edition Software, we mapped about 100 million sequence reads per sample to the human genome (build 37.2), normalized the raw read count by total mapped million reads and identified 937 upregulated and 587 downregulated transcripts in the EBV (Epstein Barr Virus)-transformed B lymphocyte cells isolated from 3 carriers of the risk (CC) allele and 3 non-carriers of the (GG) reference allele with BWA workflow. RNA-seq data confirmed differential expression of LAG3 and this was validated with qRT–PCR. Conclusions: Our study represents the first detailed analysis of differential LAG3 expression, contributing to CVD, with biologic replicates, generated by RNA-seq technology.

2016-10-20 | GSE87891 | GEO

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [RNA-Seq]

Project description:Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [RNA-Seq]

| PRJNA423020 | ENA

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [4C-Seq]

Project description:Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [4C-Seq]

| PRJNA434463 | ENA

Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [Hi-C]

Project description:Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [Hi-C]

| PRJNA434487 | ENA