Effect of deleting ultra-conserved elements PAX6_Tarzan, PBX3_Claudia on gene expression in K562 cells

Non-coding regulatory elements (NCRE) represent a major fraction of the human genome, play important roles in different biological pathways, and have the potential as genomic medicine targets. We developed a straightforward dual-CRISPR screening system capable of deleting thousands of NCREs genome-wide to study their functions in distinct biological contexts in K562 cells. Here we reported 4 top hits from the genome-wide screen of ultra-conserved elements (UCE), i.e. PAX6_Tarzan(chr11:31810437-31810870, hg19) and PBX3_Claudia(chr9:128457564-128457785, hg19) play essential roles in cell growth and drug response. To investigate the function of the 2 top hits from the genome-wide ultra-conserved elements (UCE) genetic screen by the established dual-CRISPR system, we first generated the homologous ultra-conserved element deleted cell lines using our dual-CRISPR system. We then performed the gene expression analysis from the total RNA-seq of the different UCE-KO cell lines. By comparative gene expression profiling analysis using DESeq2, we identified the differentially expressed genes between the wild-type K562 cells and 2 derivatives UCE-KO cell lines.