Suzanne de Bruijn

177 Structural variants cause ectopic enhancer-gene contact in retinitis pigmentosa fusion of the adjacent TADs (fused-TAD). 26 As a consequence, previously insulated enhancers activated genes in the adjacent TAD, leading to the dysregulation of these genes. Hi-C data were not available for human retina, therefore we generated Hi-C maps of control human 3D ROs to obtain maps of the chromatin organization of our region of interest. Hi-C revealed a structured domain containing YPEL2 ( YPEL2 TAD) flanked by less structured neighboring domains ( Figure 3A ). CTCF binding is present on both boundaries ( Figure 3B ) supporting the TAD structure at this locus. CTCF ChIA-PET data highlighted interactions between the CTCF binding sites at the 5’ and the 3’ boundary of the YPEL2 TAD ( Figure S7B ). Assay for transposase accessible chromatin using sequencing (ATAC)-seq data from human retina shows that the chromatin in the YPEL2 TAD is accessible andH3K27Ac ChIP- seq data revealed that there are several active enhancers located within the YPEL2 TAD that are expected to drive YPEL2 expression in the retina ( Figure 3B ). 27 Importantly, the YPEL2 TAD harbors two regions of active enhancers with binding sites for transcription factor (TFs) known to be required for photoreceptor function, including NRL, CRX, and OTX2 ( Figure 3B ). NRL is a TF that is preferentially expressed in rod photoreceptors. These TF binding sites correlated with H3K27Ac and ATAC-seq peaks in retina. The published GeneHancer dataset shows that these regulatory elements have interactions with the YPEL2 promoter ( Figure S7C ). 28 Collectively, these analyses revealed that YPEL2 is located within an active compartment that contains retinal-specific enhancers ( Figure 3C ). Expression of YPEL2 and GDPD1 Expression of YPEL2 and GDPD1 was assessed by qPCR in multiple healthy human tissues, including retina ( Figure S8 ). YPEL2 is ubiquitously expressed in the tissues studied, including retina, with highest relative expression in brain. Single cell retina RNA-seq datasets revealed YPEL2 is expressed at higher levels in rod photoreceptor cells, which is the primary cell type affected in retinitis pigmentosa, compared to cone photoreceptors ( Figure S8 ). 25 GDPD1 is detected at low levels in all tissue types, with higher levels of expression in testis and the brain. These data support the hypothesis that YPEL2 expression is regulated by retinal enhancers within the YPEL2 TAD.