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

该项目旨在识别潜在调控功能的可变串联重复序列(VNTRs)，如启动子和增强子，以通过基因编辑为人类IPSCs的功能分析提供信息。候选人开发了一种计算管道来检测ENCODE数据集上候选增强子区(CCRE)的串联重复序列。候选人还在文献中确定了被认为与人类疾病有关的VNTRs。该项目旨在开发基因编辑方法，在健康的IPSCs中产生变异。候选人成功地编辑了ipscs中两个基因座的重复收缩：ADGRG1(将两个拷贝减少为一个拷贝)和TRIB3(将三个或五个拷贝减少为一个拷贝)。已经使用纳米孔长读技术对TRIB3编辑结果进行了测序，并正在建立一条对编辑结果进行基因分型的分析管道。此外，候选人还开发了一种基于一种新的基因编辑试剂配方的方法，该试剂可以用来产生中间数量的DNA重复变体。这些成就为分析其余已确定的基因编辑点奠定了流水线的基础，使该项目的后续目标得以实现。

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.