Ontology highlight
ABSTRACT:
PROVIDER: PRJNA680302 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Identifying the regulatory mechanisms of genome-wide association study (GWAS) loci affecting adipose tissue has been restricted due to limited characterization of adipose transcriptional regulatory elements. We profiled chromatin accessibility in three frozen human subcutaneous adipose tissue needle biopsies and preadipocytes and adipocytes from the Simpson Golabi-Behmel Syndrome (SGBS) cell strain using an assay for transposase-accessible chromatin (ATAC-seq). We identified 68,571 representative accessible chromatin regions (peaks) across adipose tissue samples (FDR<5%). GWAS loci for eight cardiometabolic traits were enriched in these peaks (p<0.005), with the strongest enrichment for waist-hip ratio. Of 110 recently described cardiometabolic GWAS loci colocalized with adipose tissue eQTLs, 59 loci had one or more variants overlapping an adipose tissue peak. Annotated variants at the SNX10 waist-hip ratio locus and the ATP2A1-SH2B1 body mass index locus showed allelic differences in regulatory assays. These adipose tissue accessible chromatin regions elucidate genetic variants that may alter adipose tissue function to impact cardiometabolic traits.
2019-01-01 | GSE110734 | GEO
Project description:Aptamer Proteomics of Cardiometabolic and Renal Traits in African Americans
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Project description:The Kibbutzim Family Study (KFS) aimed to investigate the environmental and genetic determinants of cardiometabolic traits (phenotype is LDL-C)
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Project description:Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. The caQTL variants are enriched in liver tissue promoter and enhancer states and frequently disrupt binding motifs of transcription factors expressed in liver. We predicted target genes for 861 caQTL peaks using proximity, chromatin interactions, correlation with promoter accessibility or gene expression, and colocalization with expression QTL. Using GWAS signals for 19 liver function and/or cardiometabolic traits, we identified 110 colocalized caQTL and GWAS signals, 56 of which contained a predicted caPeak target gene. At the LITAF LDL-cholesterol GWAS locus, we validated that a caQTL variant showed allelic differences in protein binding and transcriptional activity. These caQTL contribute to the epigenomic characterization of human liver and help identify molecular mechanisms and genes at GWAS loci.
2021-05-01 | GSE164870 | GEO
Project description:Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. The caQTL variants are enriched in liver tissue promoter and enhancer states and frequently disrupt binding motifs of transcription factors expressed in liver. We predicted target genes for 861 caQTL peaks using proximity, chromatin interactions, correlation with promoter accessibility or gene expression, and colocalization with expression QTL. Using GWAS signals for 19 liver function and/or cardiometabolic traits, we identified 110 colocalized caQTL and GWAS signals, 56 of which contained a predicted caPeak target gene. At the LITAF LDL-cholesterol GWAS locus, we validated that a caQTL variant showed allelic differences in protein binding and transcriptional activity. These caQTL contribute to the epigenomic characterization of human liver and help identify molecular mechanisms and genes at GWAS loci.
2021-05-01 | GSE164938 | GEO
Project description:Adipose tissue is a primary regulator of energy balance and metabolism. The distribution of adipose tissue depots is of clinical interest because the accumulation of upper-body subcutaneous (ASAT) and visceral adipose tissue (VAT) is associated with cardiometabolic diseases, whereas lower-body gluteal-femoral adipose tissue (GFAT) appears to be protective. There is heterogeneity in the morphological and metabolic traits of adipocytes obtained from different regions of the body, but detailed knowledge of the constituent proteins in each depot is lacking. Here, we determined the human adipocyte proteome from ASAT, VAT and GFAT using high-resolution SWATH mass spectrometry proteomics.
2021-04-19 | PXD018314 | Pride
Project description:Allele-specific expression (ASE) quantifies the relative expression of two alleles in a diploid individual, and such expression imbalance potentially contributes to phenotypic variation and disease pathophysiology among individuals. We developed ASEP, a method that is able to detect gene-level ASE under one condition, as well as, ASE difference between two conditions (e.g., pre- vs post-treatment) across individuals. Application of ASEP to human macrophage RNA-seq dataset has illustrated its ability to uncover ASE / differential ASE genes related to cardiometabolic traits.
2020-05-06 | GSE149638 | GEO
Project description:Open chromatin profiling in adipose tissue marks genomic regions with functional roles in cardiometabolic traits
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