A Dinucleotide-barcode reporter system and application in dissecting the causal rule of regulatory risk SNPs

We adapted the DiR barcode-based parallel reporter assay systems strategy to systematically identify the SNPs that affect gene expression by modulating activities of regulatory elements. Among 293 SNPs linked with GWAS-identified prostate cancer-risk SNPs, we found 32, 9, and 11 regulatory SNPs in 22Rv1, PC-3, and LNCaP cells. Further mechanism study indicates that one SNP regulates gene expression in prostate cancer malignancy. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases. Our findings hold great promise in benefiting prostate cancer patients with prognostic prediction. Overall design: Blank DiR-seq bias analysis in LNCaP cell lines (3 replicates), Input plasmid library 10lib before transfection (3 replicates). Blank DiR-seq report analysis in LNCaP and MCF7 cell lines (3 replicates, respectively), Input plasmid library before transfection (3 replicates). SNP DiR-seq report analysis in 22Rv1, PC-3 and LNCaP cell lines (3 replicates, respectively), Input plasmid library before transfection (2 replicates).