Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

The vast majority of complex disease associations cannot be cleanly mapped to a gene, as they often lie within the non-cding fraction of the genome. Immune disease-associated variants are enriched within regulatory elements, such as distal enhancers, found in T cell-specific open chromatin regions. To identify the genes modulated by these regulatory elements, we developed a CRISPRi-based single-cell functional screening approach in primary human CD4+ T cells. We performed a proof-of-concept screen targeting 45 non-coding regulatory elements and 35 transcription start sites, each targeted by 4 different gRNAs. We profiled approximately 250,000 CD4+ T cell single-cell transcriptomes using 3' 10X Genomics.