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Natural and synthetic genetic regulation in stimulated CD4+ T cells


Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the 3D chromatin organization measured by in situ Hi-C in T cells. 15% of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (ATAC-QTLs). ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression, and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.

To elucidate the trans regulatory network governing activation and polarization of CD4+ T cells 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 Th2 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.

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