ArticleJournal of the American Society of Nephrology : JASN2019
Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci.
Article in Journal of the American Society of Nephrology : JASN, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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19 citing papers in PubMed, 1 synthesis or guideline pooled it, 34 citations in OpenAlex.
- A catalog of genetic loci associated with kidney function from analyses of a million individuals.Nature genetics · 2019Pooled it
- Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects.Molecular ecology · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- INSIGHTS INTO ACUTE KIDNEY INJURY AND TRANSITION TO CHRONIC KIDNEY DISEASE BY SINGLE-CELL TECHNOLOGIES.Transactions of the American Clinical and Climatological Association · 2025Review
- Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.Nature genetics · 2024Article
- Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.bioRxiv : the preprint server for biology · 2024Article
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- Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing.Nature communications · 2024Article
- Multi-omic analysis of human kidney tissue identified medulla-specific gene expression patterns.Kidney international · 2024Article
- Soluble uric acid inhibits β2 integrin-mediated neutrophil recruitment in innate immunity.Blood · 2022Article
- Serum Protein Exposure Activates a Core Regulatory Program Driving Human Proximal Tubule Injury.Journal of the American Society of Nephrology : JASN · 2022Article
- Article
- Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney.Nature communications · 2021Article
- Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants.BMC biology · 2021Article
- Integrative Omics Analyses Reveal Epigenetic Memory in Diabetic Renal Cells Regulating Genes Associated With Kidney Dysfunction.Diabetes · 2020Article
- Complexities of Understanding Function from CKD-Associated DNA Variants.Clinical journal of the American Society of Nephrology : CJASN · 2020Review
- Epigenomics and the kidney.Current opinion in nephrology and hypertension · 2020Review
- Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.Nature communications · 2019Article
- Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma.EBioMedicine · 2019Article
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21 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundLinking genetic risk loci identified by genome-wide association studies (GWAS) to their causal genes remains a major challenge. Disease-associated genetic variants are concentrated in regions containing regulatory DNA elements, such as promoters and enhancers. Although researchers have previously published DNA maps of these regulatory regions for kidney tubule cells and glomerular endothelial cells, maps for podocytes and mesangial cells have not been available.
methodsWe generated regulatory DNA maps (DNase-seq) and paired gene expression profiles (RNA-seq) from primary outgrowth cultures of human glomeruli that were composed mainly of podocytes and mesangial cells. We generated similar datasets from renal cortex cultures, to compare with those of the glomerular cultures. Because regulatory DNA elements can act on target genes across large genomic distances, we also generated a chromatin conformation map from freshly isolated human glomeruli.
resultsWe identified thousands of unique regulatory DNA elements, many located close to transcription factor genes, which the glomerular and cortex samples expressed at different levels. We found that genetic variants associated with kidney diseases (GWAS) and kidney expression quantitative trait loci were enriched in regulatory DNA regions. By combining GWAS, epigenomic, and chromatin conformation data, we functionally annotated 46 kidney disease genes.
conclusionsWe demonstrate a powerful approach to functionally connect kidney disease-/trait-associated loci to their target genes by leveraging unique regulatory DNA maps and integrated epigenomic and genetic analysis. This process can be applied to other kidney cell types and will enhance our understanding of genome regulation and its effects on gene expression in kidney disease.
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