CRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response

Transcription of interferons upon viral infection is critical for cell-intrinsic innate immunity. This process is influenced by many host and viral factors. To identify host factors that modulate interferon induction within cells infected by influenza A virus, we developed CRISPR with Transcriptional Readout (CRITR-seq). CRITR-seq is a method linking CRISPR guide sequence to activity at a promoter of interest. Employing this method, we find that depletion of the Negative Elongation Factor complex increases both flu transcription and interferon expression. We find that the process of flu transcription, both in the presence and absence of viral replication, is a key contributor to interferon induction. Taken together, our findings highlight innate immune ligand concentration as a limiting factor in triggering an interferon response, identify NELF as an important interface with the flu life cycle, and validate CRITR-seq as a tool for genome-wide screens for phenotypes of gene expression. To perform a genome-wide CRISPR screen of factors influencing type III interferon induction by influenza virus infection we developed a new method, called CRITR-seq. These files are the sequencing output of that method. A549-Cas9 cells bearing our vector were allowed to undergo editing for ten days, after which they were infected by influenza A virus lacking NS1 at an MOI of 2 and gDNA and RNA harvested for sequencing and analysis 8 hours post infection.