Gene expression profiling of teloHAEC cells with CRISPR-Cas9-mediated deletion of candidate enhancer regions

Functional consequences of genetic variation in the non-coding human genome are difficult to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional non-coding SNPs with effects in human endothelial cells (EC), we utilized our previous molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation to nominate a set of likely functional non-coding SNPs. Together with information from Genome-Wide Association Studies (GWAS) for vascular disease traits, we tested the ability of more than 34,000 genetic variants to perturb enhancer function in ECs using the highly multiplexed reporter assay. Based on these results, CRISPR-mediated deletion followed by mRNA-Seq was carried out for SNP-containing regulatory elements near SMAD3 and LDAH (C2orf43) in order to functionally verify the target genes of the regulatory elements. Overall design: mRNA expression profiling of teloHAEC cells following CRISPR treatment