Jacob C. Ulirsch, Satish K. Nandakumar, Li Wang, Felix C. Giani, Xiaolan Zhang et al.
Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.
Jacob C. Ulirsch, Satish K. Nandakumar, Li Wang, Felix C. Giani, Xiaolan Zhang, Peter Rogov, Alexandre Melnikov, Patrick McDonel, Ron Do, Tarjei S. Mikkelsen, Vijay G. Sankaran. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. 2016-06-02. https://doi.org/10.1016/j.cell.2016.04.048
A 145-bp variant-focused oligonucleotide library representing major/reference and minor/alternate alleles across three variant-centered sliding windows was transfected into K562 cells overexpressing GATA1. Reporter RNA was measured 48 hours after transfection and normalized to plasmid DNA input across four GATA1-condition RNA replicates.
A 145-bp variant-focused oligonucleotide library representing major/reference and minor/alternate alleles across three variant-centered sliding windows was transfected into standard human K562 cells. Reporter RNA was measured 48 hours after transfection and normalized to plasmid DNA input across six RNA replicates.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 4 files (ZIP)article_bioc.jsonGSE87711_design.txt.gzGSE87711_design_barcodes.txt.gzGSE87711_RBC_MPRA_minP_raw.txt.gz