Suzanne de Bruijn

221 Structural variants cause ectopic enhancer-gene contact in retinitis pigmentosa Regulatory elements 200 kb hg19 57,150,000 57,200,000 57,250,000 57,300,000 57,350,000 57,400,000 57,450,000 57,500,000 57,550,000 57,600,000 57,650,000 57,700,000 57,750,000 GM12878 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad K562 CTCF Histone Mods by ChIP-seq Signal from ENCODE/Broad MCF-7 CTCF TFBS ChIP-seq Raw Signal 1 from ENCODE/UW K562 CTCF ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan MCF-7 CTCF ChIA-PET Interactions Rep 1 from ENCODE/GIS-Ruan GeneHancer Regulatory Elements and Gene Interactions Human retina CTCF ChIP-seq from CHERRY et al. Human retina NRLChIP-seq from CHERRY et al. Human retina H3K27ac ChIP-seq from CHERRY et al. TRIM37 SKA2 PRR11 SMG8 GDPD1 YPEL2 MIR4729 DHX40 CLTC PTRH2 VMP1 GM12878 200 _ 1 _ K562 200 _ 1 _ Human retina 55 _ 0 _ MCF-7 200 _ 1 _ H3K27AC 55 _ 0 _ NRL 55 _ 0 _ LINC01476 A K562 MCF-7 B C Figure S7. CTCF sites insulate contacts within the YPEL2 TAD. (A) CTCF ChIP-seq data showed that YPEL2 is located within an insulated TAD that is present in multiple cell and tissue types, including human retina. (B) ChIA-PET CTCF interaction data established in K562 and MCF-7 cells revealed strong interactions between the CTCF binding sites on the 5’ side of the YPEL2 TAD, and the single CTCF binding site on the 3’ side of the YPEL2 TAD. (C) The structured YPEL2 TAD contains retina-specific enhancer elements as shown in Figure 3 . These regulatory elements are also described in the Genehancer database 32 and interactions with the YPEL2 promoter region were experimentally validated.