Suzanne de Bruijn

299 General discussion and perspectives transcript that turned out to be the predominant transcript in the retina. 99 Considering the high percentage of alternative spliced transcripts in both the retina and inner ear 98,99 , it can be speculated that a considerable percentage of missing heritability resides in these “hidden” exons or in sequences that determine the splicing pattern. Single cell approaches can also be employed to map the single-molecule 3D or regulatory landscape. Previously, TAD domains were considered to be conserved among tissues and cells, but there is accumulating evidence that this view is incomplete. Recent reports indicate that 20-80% of the CTCF-enriched TAD boundaries are not shared between cell types. 100 Additionally, there is great intra-TAD variability of interactions within TADs that is mainly caused by differences in enhancer accessibility. 101 Single-cell platforms are rapidly being developed that allowmapping of the epigenome landscape of cell subpopulations via e.g. single cell CUT&Tag 102 , ATAC sequencing 103 and Hi-C. 104 Chapter 2 describes the presence of a long, ubiquitous KIAA1549 transcript, and a short, retina-specific, KIAA1549 transcript. Depending on the variant type and the affected KIAA1549 transcript, pathogenic variants in KIAA1549 lead to mild or more severe forms of RP. This study left some questions unresolved, including the function of the individual isoforms, the signaling pathways involved and the cellular localization of the encoded proteins within the retina. A scRNA-seq approach could help to elucidate the function of the different transcripts and map the transcripts to retinal cellular subtypes. This could increase our understanding related to the different transcripts, their interplay and possibly the regulatory elements involved. With this, potentially, essential insights can be gained that will help in variant interpretation and patient counseling. A complete understanding of tissue-specific alternative splicing patterns is not only crucial for diagnostic purposes, modulation of alternative splicing has also been shown to be instrumental in the design of novel genetic therapeutic strategies such as exon skipping. 116 Together with the arrival of long-read sequencing technologies, that allow full-length transcript annotation, the application of scRNA-seq will allow the generation of a complete atlas optimally representing the diverse retina and inner ear transcriptome landscape. Nevertheless, as discussed in Box 1 , the limited availability of tissue samples to study vision and hearing disorders severely hampers an efficient (diagnostic) application of this technique.