Fig. 5: APN is the most dominant gene suppressed by UHRF1 for HCoV-229E infection.
From: UHRF1 restricts HCoV-229E infection through epigenetic silencing of the viral receptor APN
A Volcano plot of RNA-seq analysis. Total cellular RNA was extracted from control and UHRF1-knockout A549-ACE2 cells and subjected to RNA-seq. Genes with an absolute Log2 fold change >2 and adjusted P-value < 0.05 were considered as differentially expressed. Differential expression analysis was performed using DESeq2 with a two-sided Wald test. P-values were adjusted for multiple comparisons using the Benjamini-Hochberg method. B Schematic of focused CRISPR activation screening. A sub-library targeting 2172 of the 2210 upregulated genes identified from RNA-seq analysis of UHRF1-knockout cells, with ~4 sgRNAs per gene, was generated and transduced into A549-ACE2-dCas9 cells. Cells were infected with HCoV-229E-mGreen (MOI 0.5, 24 h) or SARS-CoV-2 transcription- and replication-competent virus-like particles in which the N gene is replaced by the reporter GFP (trVLP-GFP)38 (MOI 0.5, 24 h). Infected reporter-positive cells were sorted for genomic DNA extraction and sgRNA sequence analysis. Created in BioRender. Wang, P. (2025) https://BioRender.com/35yt09k. C, D Genes identified from CRISPR screens for HCoV-229E (C) and SARS-CoV-2 (D). Genes were analyzed by MAGeCK software and sorted based on -log10 (MAGeCK score) and P-values. The algorithm employs a one-sided test to identify genes under positive selection, and P-values were adjusted for multiple testing using the Benjamini-Hochberg method.
