Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (ChIP-seq)

Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. Using the Human Umbilical Derived Erythroid Progenitor 2 (HUDEP-2) cell line we have modelled the effects of two variants associated with red blood cell traits using CRISPR/Cas9 facilitated HDR editing. CRISPR/Cas9 editing was carried out to generate homozygous clones at two trait associated variants (rs10758656 and rs9349205) as well as a non-disease associated SNP (rs4508712) as an editing control. Following editing clonal populations were isolated by single cell sorting and expansion. Effects of edited variants were determined by ATAC-seq (carried out in technical duplicates), ChIP-seq, and RNA-seq on multiple days for at least 3 independent clones. Experiments were carried out during growth in both expansion, and erythroid differentiation media.