Regulation of gene expression revealed by genome editing of repetitive and polymorphic cis-elements

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The project aims to identify variable tandem repeats (VNTRs) at potential regulatory features, like promoters and enhancers, to inform functional analyses in human iPSCs by gene editing. The candidate developed a computational pipeline to detect tandem repeats at candidate enhancer regions (cCREs) on the ENCODE dataset. The candidate also identified VNTRs in the literature which are proposed to be involved in human disease. The project aims to develop gene editing methods to generate variants in healthy iPSCs. The candidate succeeded in editing repeat contractions at two loci in iPSCs: ADGRG1 (reducing two copies to one copy) and TRIB3 (reducing three or five copies to one copy). TRIB3 editing results have been sequenced using Nanopore long-read technology and an analysis pipeline to genotype the editing results is being established. Moreover, the candidate developed a method based on a novel formulation of gene editing reagents which could be used to generate intermediate numbers of DNA repeat variants. These achievements lay the groundwork for a streamlined pipeline for the analysis of the rest of the identified gene editing sites, enabling the subsequent goals of the project.