Fig. 7

CRISPR interference-based enhancer inactivation in iPSMs. a A differential eRNA and ATAC region at chr1q23.3 containing a GWAS lead SNP associated with MS risk (rs6427540 [35]). The differential ATAC peak identified in both MDMs and iPSMs is highlighted in a grey bar, eRNA expression in MDMs is indicated by a black arrow, and the sgRNA sites for CRISPRi are highlighted by red arrows. The normalized RNA and ATAC signals across the replicates of each cell type are shown on the y axis. b, c Quantifications of the ATAC peak (highlighted in a in MDMs (b, upper panel) and iPSMs (b, lower panel) and the expression of its proximal genes SLAMF1 (c, upper panel) and CD48 (c, upper panel) in MDMs. Each coloured line represents samples from one donor across different treatment conditions. The significance was determined by linear regression, comparing normalized sequencing counts upon LPS response (HD vs. UT) or LPS tolerance (LDHD vs. HD). ***p < 0.001; **p < 0.005; n.s: not significant. d–f A MDMs/iPSMs shared differential ATAC peak at chr10p15.1 contains GWAS lead SNPs associated with RA (rs10795791 [36]) and SC disease risk (rs4147359 [37]) (d) and the quantifications of the ATAC (e) and proximal gene expression (f) as described above. g, h Bar plots of gene expression, measured using qRT-PCR normalized to GAPDH (2^–∆∆Ct) in CRISPRi edited iPSMs with either a non-target sgRNA control (green bars) or sgRNAs targeting enhancers as indicated (red bars). Error bars represent SEM of 4 independent replicates. P value was calculated by two-tailed Student’s t-test. See also Figs. S7, S8 and S9