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

• 成果类型: Article
• 署名作者: Vicary, Alison C.; Jordan, Sydney N. Z.; Mendes, Marisa; Swaminath, Sharmada; Castro, Lennice K.; Porter, Justin S.; Vo, Kevin D.; Russell, Alistair B.
• 署名单位: University of California System; University of California San Diego
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9602
• DOI: 10.1073/pnas.2515564122
• 发表日期: 2025-09-02
• 关键词: rna-polymerase-ii; structural basis; cap-binding; a virus; rig-i; activation; induction; promoter; identification; endonuclease

摘要

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.