Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [RNA-seq]

Many polygenic traits are associated with hundreds of single nucleotide polymorphisms (SNPs), which predominantly (>95%) reside within noncoding genomic regions, making it difficult to understand how they regulate complex traits, such as blood pressure (BP). Given the central role of the kidney in regulating BP, we hypothesized that chromatin-accessible regions in renal tissue would be enriched for BP-associated SNPs (bpSNPs). We developed chromatin state and transcriptomic maps of the proximal tubules (PT) and medullary thick ascending limbs (mTAL) isolated from humans and rats. These maps revealed shared cis-regulatory elements (CREs) across humans and rats, including upstream transcriptional regulators. Notably, bpSNPs were significantly enriched within open chromatin regions, suggesting they potentially alter the activity of CREs and near genes critical to renal development and function. Collectively, this work lays a foundation for interrogating how intergenic SNPs may regulate polygenic traits such as BP. Overall design: We used manually dissected human and rat kidney segments; proximal tubule (PT) and medullary thick ascending limb (mTAL). We have performed bulk ATAC-seq analysis to delinate the chromatin map, and bulk RNA-seq analysis to analyze the transcriptome of these two segments. For ATAC seq analysis, we have used three replicates of mTAL samples and four replicates PT samples from both human and rat. For RNA-seq analysis, we have used three and six replicates of mTAL and PT from human and rat, respectively.