Suzanne de Bruijn

179 Structural variants cause ectopic enhancer-gene contact in retinitis pigmentosa Control SV2 Subtraction Control-SV2 57.5 Mb 57.6 Mb 57.7 Mb 57.4 Mb 57.3 Mb 57.2 Mb 57.1 Mb 21 0 5.9 - 5.9 36 0 Genes B A C Chromosome 17 neo-TAD 2 neo-TAD 1 YPEL2 TAD SMG8 LINC01476 GDPD1 PRR11 YPEL2 DHX40 G H E D SMG8 GDPD1 PRR11 DHX40 B B Neo-TAD 1 Neo-TAD 2 SMG8 LINC01476 LINC01476 DHX40 GDPD1 PRR11 YPEL2 YPEL2 GDPD1 SMG8 YPEL2 YPEL2 TAD PRR11 Inversion D E E G H G F Duplication Retinal enhancer Boundary Enhancer interaction B Neo-TAD YPEL2 TAD YPEL2 TAD SMG8 SMG8 GDPD1 YPEL2 GDPD1 YPEL2 Genes Genes Wildtype NL-SV1 UK-SV2 Genes LINC01476 B B C A PRR11 DHX40 YPEL2 LINC01476 B B B B B F ** Retinal enhancer CTL UK-SV2 0.0 5.0 10.0 15.0 Fold changes B Figure 4. RP17-SVs create novel domains (neo-TADs) and hyper-activation of retinal enhancers. (A) Schematic modeling of the genome architecture spanning the RP17 region using Hi-C maps. The wildtype Hi-C map derived from neuronal tissue shows a TAD with CTCF boundaries containing YPEL2 and retinal enhancers, flanked by unstructured domains. TAD models of NL-SV1 and UK-SV2 (dotted vertical lines represent SV breakpoints) predict the formation of neo-TADs and ectopic interactions of the retinal enhancer with GDPD1 . (B) Hi-C performed on retinal organoids (ROs) derived from control (top) and RP17 UK-SV2 individuals (bottom) (10 kb resolution; raw count map). The chromatin organization in control ROs shows the YPEL2 TAD (indicated by dashed lines). Two novel domains (neo-TAD 1 and 2) are visible in the UK-SV2 ROs, and neo-TAD 2 allows ectopic retinal enhancer contacts to GDPD1 and SMG8 . Dashed circle indicates the strong chromatin contact between retinal enhancers and the GDPD1 promoter. (C) qPCR revealed significantly upregulated retinal enhancer RNA expression in UK-SV2 ROs compared to controls. (n=3, mean ± standard error of the mean, **p≤0.01).