Extended Data Fig. 4: HCR-FlowFISH and CASA identify CREs for multiple loci.

a,b, Connectogram diagrams showing K562 DHS (light blue), K562 H3K27ac (dark blue), guide coverage (black), HCR-FlowFISH composite guide score tracks, and CASA CREs calls for MYC (teal), PVT1 (salmon), LMO2 (orange), CAPRIN1 (navy), and CAT (lilac). CASA-derived CRE activity scores are shown as lines connecting the CRE to the target gene, and colored by effect on transcript abundance (black decreases abundance, red increases abundance). In a, ‘Pro’ and ‘e1-4’ denote the promoter and enhancers identified at this locus in Fulco et al.¹⁷. In b, ‘P’, ‘I’, ‘D’, denote the proximal, intermediate and distal promoters of LMO2, respectively. c, Relative mRNA expression compared to unperturbed cells for CRISPRi perturbations of distal, intermediate + distal, and proximal + distal promoters. Three technical replicates shown, bars represent standard deviation.