Genome-wide CRISPR screen to identify IncRNAs affecting SARS-CoV-2 cell entry

SARS-CoV-2 is the causative agent of the Coronavirus disease 2019 (COVID-19) pandemic. Discovering host factors critical for SARS-CoV-2 infection will facilitate the development of novel therapeutic treatments for COVID-19, as well as elucidate SARS-CoV-2 pathogenesis. While most studies focus on identifying protein-coding genes crucial for the injection, the non-coding genome is largely understudied. Long non-coding RNA (lncRNA) is the largest and most diverse group of ncRNA, defined as transcripts longer than 200 nucleotides and have no open reading frame. lncRNAs can regulate all levels of gene expression by interacting with DNA, RNA, and proteins. Considering lncRNAs involvement in many cellular processes, we can assume they also play a role in SARS-CoV-2 infection. CRISPR based screening is a robust, high-throughput approach to study lncRNAs. Specifically, CRISPR interference (CRISPRi), can modulate gene expression at the transcription level without the requirement of genome editing. In this study, we performed a CRISPR screen of lncRNAs affecting SARS-CoV-2 infection in SNU449 human cells, originating from liver Carcinoma and modified to express the ACE2 receptor. Our screen identified many pro-viral and antiviral lncRNA genes. We validated RP11-977G19.11 and RP11-314A20.5 as critical for SAR-CoV-2 infection. Both genes were found to regulate the expression of neighboring protein-coding genes. Specifically, RP11-977G19.11 regulate the expression of Citrate synthase, a key member of energy metabolism, and RP11-314A20.5 regulate Chemokine (C-X-C motif) ligand 16 (CXCL16), which is involved in the immunity response. Our findings will be relevant for the current pandemic, as well as novel viral pathogens sharing the same host factors.