Understanding enhancer regulation in single-cell CRISPR screens using scMAGeCK
Open AccessGenome-wide CRISPR-Cas9 screening allows scientists to identify genes or non-coding elements that are associated with various phenotypes. Single-cell CRISPR-Cas9 screening provides a more powerful tool to monitor gene expression changes upon gene or enhancer perturbations at a single-cell level. Here, we use the scMAGeCK-Linear Regression (LR) module, in combination with the annotated gene sets in Gene Set Enrichment Analysis (GSEA) to directly link enhancer perturbations with possible phenotypic changes. We utilize a recently published single-cell CRISPR enhancer screening data in a leukemia cell line (K-562) and search for potential gene regulation pathways that are disrupted upon enhancer perturbation. Our results show that the CBFA2T3 and RUNX1-RUNX1T1 shared similar regulating gene sets from GSEA. Protein-protein interaction, pathway enrichment analysis, and transcription factor binding analysis further uncover possible interactions between CBFA2T3 and its target genes. Finally, we studied the potential roles of CBFA2T3 and their downstream target genes in leukemia using CRISPR-VIEW, an online genome-wide CRISPR-Cas9 and RNAi screening database that we recently developed.
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