Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

ABSTRACT: Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

PROVIDER: PRJNA477708 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7417410.fastq.gz	Fastqsanger.gz
	SRR7417420.fastq.gz	Fastqsanger.gz
	SRR7417430.fastq.gz	Fastqsanger.gz
	SRR7417440.fastq.gz	Fastqsanger.gz
	SRR7417450.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 149

Similar Datasets

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

Project description:To fully comprehend how genetic variants influence phenotypes, we must understand the functions of the epigenome. To assess the degree to which genetic variants influence epigenome activity, we integrate epigenetic and genotypic data from lupus patient lymphoblastoid cell lines to identify variants that induce allelic imbalance in the magnitude of histone post-translational modifications, referred to herein as histone quantitative trait loci (hQTLs). We demonstrate that enhancer hQTLs are enriched on autoimmune disease risk haplotypes and disproportionately influence gene expression variability compared with non-hQTL variants in strong linkage disequilibrium. We show that the epigenome regulates HLA class II genes differently in individuals who carry HLA-DR3 or HLA-DR15 haplotypes, resulting in differential 3D chromatin conformation and gene expression. Finally, we identify significant expression QTL (eQTL) x hQTL interactions that reveal substructure within eQTL gene expression, suggesting potential implications for functional genomic studies that leverage eQTL data for subject selection and stratification.

2018-06-25 | GSE116193 | GEO

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

Project description:Genetic variants can confer risk to complex genetic diseases by modulating gene expression through changes to the epigenome. To assess the degree to which genetic variants influence epigenome activity, we integrate epigenetic and genotypic data from lupus patient lymphoblastoid cell lines to identify variants that induce allelic imbalance in the magnitude of histone post-translational modifications, referred to herein as histone quantitative trait loci (hQTLs). We demonstrate that enhancer hQTLs are enriched on autoimmune disease risk haplotypes and disproportionately influence gene expression variability compared with non-hQTL variants in strong linkage disequilibrium. We show that the epigenome regulates HLA class II genes differently in individuals who carry HLA-DR3 or HLA-DR15 haplotypes, resulting in differential 3D chromatin conformation and gene expression. Finally, we identify significant expression QTL (eQTL) x hQTL interactions that reveal substructure within eQTL gene expression, suggesting potential implications for functional genomic studies that leverage eQTL data for subject selection and stratification.

| S-EPMC6060153 | biostudies-literature

Transcriptome profile Carnegie Stage 22 gut of different RET haplotypes

Project description:Total mRNA seq was perfomed on human fetal gut tissue at CS22 on 3 samples having different RET haplotype which progressively reduce expression of RET. R haplotypes are resistant and S haplotypes are susceptible to Hirschsprung disease

2018-10-30 | GSE111341 | GEO

Transcription profiling of 148 Arabidopsis recombinant inbred lines treated with Silwet solution to develop genetic markers and derive high-density haplotypes

Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We surveyed recombinant inbred lines (RILs) from a population derived from a cross of inbred Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) in order to map e-QTLs controlling ELPs. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 28 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for 148 RILs, plus replicated Bay-0 and Sha control samples grown at the same time as the RILs. These GeneChips were used to develop genetic markers and derive high-density haplotypes for the RILs

2007-01-10 | E-TABM-62 | biostudies-arrayexpress

Novel haplotypes Emilia-Romagna region

Project description:Apis mellifera mitochondrial haplotypes

| PRJEB67526 | ENA

Microarray expression analysis of PRF1 (perforin 1) haplotypes in patients with primary progressive multiple sclerosis

Project description:A genetic study of the PRF1 gene has shown association of several polymorphisms with multiple sclerosis (MS). Haplotype analysis identified risk haplotypes strongly associated with male patients having the primary-progressive form of MS (PPMS). Gene expression microarrays were performed in 10 male PPMS patients carrying the risk (n=6) and protective haplotypes (n=4) in order to identify pathways associated with the risk haplotypes. Pathway analysis revealed overrepresentation of the cell killing gene ontology category among down-regulated genes in patients carrying risk haplotypes compared with patients carrying protective haplotypes.

2010-07-28 | GSE23205 | GEO

Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases

Project description:We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on SLE and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared to other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships between genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.

2024-03-10 | GSE254502 | GEO

ClassII haplotypes

Project description:Unravelling the architecture of Major Histocompatibility Complex class II haplotypes in rhesus macaques

| PRJEB70961 | ENA

Mitochondrial DNA haplotypes induce differential patterns of DNA methylation that result in differential chromosomal gene expression patterns

Project description:Mitochondrial DNA (mtDNA) haplotypes are associated with phenotypes and disease. To understand how mtDNA haplotypes induce these characteristics, we used four embryonic stem cell lines that have the same set of chromosomes but possess different mtDNA haplotypes. We show that mtDNA haplotypes influence changes in chromosomal gene expression and affinity for nuclear-encoded mtDNA replication factors to modulate mtDNA copy number, two events that act synchronously during differentiation. Global DNA methylation analysis showed that each haplotype induces distinct DNA methylation patterns, which, when modulated by DNA demethylation agents resulted in skewed gene expression patterns that highlight the effectiveness of the new DNA methylation patterns established by each haplotype. The haplotypes differentially regulate α-ketoglutarate, a metabolite from the TCA cycle that modulates the TET family of proteins, which catalyse the transition from 5-methylcytosine (DNA methylation) to 5-hydroxymethylcytosine (DNA demethylation). Our outcomes show a direct link between mtDNA haplotypes and DNA methylation profiles.

2017-11-01 | GSE94918 | GEO

Transcription profiling of peripheral blood from patients with primary progressive multiple sclerosis to compare risk and protective PRF1 haplotypes

2010-07-28 | E-GEOD-23205 | biostudies-arrayexpress