Suzanne de Bruijn

176 Chapter 4 mechanism could account for the RP17-SVs, as a combination of (micro)homology- mediated repair and non-homologous end joining events were identified ( Table S7-S8 , Figure S5 , Supplementary Results ). Consistent autosomal dominant retinitis pigmentosa phenotype for RP17-affected families The SVs identified were fully penetrant in all families. Available clinical data are presented in Table S9 . Twenty-four cases from seventeen pedigrees were evaluated retrospectively. There is significant correlation of phenotype across all genotypes, with relatively mild disease, decreased visual acuity, visual field constriction, nyctalopia, and slow progression consistent with adRP. Many cases have preserved central visual function and acuity until the 6 th -7 th decade. Foveal sparing and cystoid macular edema were a common finding in individuals with UK-SV2. Based on a small number of cases (n=2) UK-SV6 (with a triplicated SV) may be associated with an earlier age of onset and more severe phenotype ( Figure S6 ). Topologically associating domain structure and epigenetic landscape of the RP17 genomic region All of theRP17-SVs lead todisruptionof thegenomic region spanning YPEL2 to LINC01476 ( Figure 2E ). SVs that interfere with genome structure can have distinct effects on gene regulation, depending on the type and extent of the SV and landscape of the genomic region. 17 TADs are separated by boundaries, regions of low chromatin interaction that insulate the regulatory activities of neighboring TADs. The transcription factor CTCF (CCTC-binding factor) typically binds in these regions where it plays a pivotal role in the maintenance of boundaries. SVs can cause loss-of-function by disconnecting enhancers from their target genes; however, disruption of TAD structures and boundaries can also exert a gain-of-function effect. Deletions, for example, can lead to the fusing of two previously separated TADs (TAD-fusion), inversions can result in the exchange of regulatory material between TADs (TAD-shuffling), whereas duplications can give rise to the generation of novel domains, so called neo-TADs. 14,15 In each case, SVs result in the generation of ectopic contacts of enhancers with the promoters of novel target genes resulting in aberrant gene activation. The human limb malformations caused by SVs that alter the CTCF-associated boundary of the WNT6/IHH/EPHA4/PAX3 locus are a prominent example. The SVs result in ectopic interactions between EPHA4 limb enhancers and the neighboring developmental genes that are normally insulated, driving ectopic expression in the limb. 16 Similarly, the deletion of a CTCF site located between the Xist and Tsix TADs on the X-chromosome resulted in a novel domain by