biostudies-literatureVicary ACNIAID NIH HHSNIGMS NIH HHSHHS | NIH | National Institute of General Medical Sciences (NIGMS)HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)e2515564122https://www.ebi.ac.uk/biostudies/studies/S-EPMC12415228biostudies-literatureUnknown122(35)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 using sequencing (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 (NELF) 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.Proceedings of the National Academy of Sciences of the United States of AmericaCRISPR with Transcriptional Readout reveals influenza transcription is modulated by NELF and can precipitate an interferon response.PMC124152285R35GM147031T32GM133351T32 GM133351R01 AI1766395R01AI176639R35 GM147031Castro LKRussell ABPorter JSSwaminath SJordan SNZMendes MVo KDVicary ACfalseCRISPR 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 using sequencing (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 (NELF) 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.2025-01-01T00:00:00Z2025 Sep2026-06-03T05:58:42.561Z2026-04-25T03:17:00.649ZS-EPMC124152284086465110.1073/pnas.2515564122