Figure 5.

Patient variants in VISTA enhancers reduce enhancer activity in the nervous system

(A–E) Genomic intervals containing hs1066.1 and OTX1 (A) or hs576 and SIM1 (C and D). Coordinates are in hg19. The locations of ASD patient variants are in red, control variants are in gray, and obesity-associated variants⁹⁴ are in orange. (A) The pale yellow bar in the alignment to Rhesus indicates missing sequence (Ns) in that region. (D) The core region of hs576 recapitulates most of the enhancer activity of the entire element.⁹⁴ Constructs containing hs1066.1 (B) or hs576 (E) without or with ASD patient variant(s) upstream of a minimal promoter driving the lacZ gene were integrated into the safe-harbor H11 locus and analyzed for lacZ expression at E11.5 (STAR Methods). Representative embryos are shown (all embryos are in Figures S18 and S19). E11.5 embryos have an average crown-rump length of 6 mm. (B) d, diencephalon; m, midbrain; and h, hindbrain. (E) Arrowheads indicate cranial nerves where the inclusion of the two ASD patient variants reduces enhancer activity.