Mapping gene regulatory networks of primary CD4+ T cells using single-cell genomics and genome engineering

Gene regulatory programs controlling the activation and polarization of CD4 + T cells are incompletely mapped and the interindividual variability in these programs remain unknown. We sequenced the transcriptomes of ~160k CD4 + T cells from 9 donors following pooled CRISPR perturbation targeting 140 regulators. We identified 134 regulators that affect T cell functionalization, including IRF2 as a positive regulator of Th 2 polarization. Leveraging correlation patterns between cells, we mapped 194 pairs of interacting regulators, including known (e.g. BATF and JUN ) and novel interactions (e.g. ETS1 and STAT6 ). Finally, we identified 80 natural genetic variants with effects on gene expression, 48 of which are modified by a perturbation. In CD4 + T cells, CRISPR perturbations can influence in vitro polarization and modify the effects of trans and cis regulatory elements on gene expression.