Fig. 4

Results from CRISPRi interrogation of JIA risk loci to identify target genes of intergenic enhancers harboring MPRA-screened SNPs in the TRAF1 (rs10985080) and LNPEP/ERAP2 (rs1216565) loci. Panel A provides the sequences and positions of the gRNAs used to interrogate these regions. Panel B shows results from the interrogation of the TRAF1 locus. Ablation of this intergenic enhancer significantly reduces the expression of PHF1, which encodes a polycomb family transcriptional repressor, but not C5, another expressed gene within the same topologically-associated domain as this enhancer. Off-target effects were assessed by examining the effects of these same gRNAs on the expression of HBE1. The gRNAs showed no effects on HBE1 expression, although specifically targeted gRNAs to an HBE1 enhancer reduced expression by 50%. Panel C shows results from interrogation of the intergenic enhancer within the LNPEP/ERAP2 locus. Attenuating this enhancer, which is situated between the LNPEP and ERAP2 genes, significantly reduced expression of both genes. ** = p < 0.01. *** = p < 0.001