flu-splicing

flu-splicing analyzes RNA-seq data to quantify influenza A virus (IAV)-induced alterations in host mRNA splicing, including changes in exon inclusion, intron retention, and virus-specific alternative splicing events.

Key Features:

• RNA-Seq data analysis: Uses RNA-seq datasets to quantify IAV-induced host mRNA splicing changes, reporting shifts such as increased exon inclusion and decreased intron retention.
• Differential splicing detection: Focuses on identifying alternative splicing events and differential exon usage specifically associated with IAV infection.
• Specificity of splicing changes: Identifies that over half of IAV-sensitive splicing events show no significant changes in mRNA abundance or 3' end termination sites and that many events are absent under vesicular stomatitis virus (VSV) infection, interferon induction, or osmotic stress.
• Mechanistic association with RED: Associates IAV-sensitive splicing alterations with hijacking of the RNA-binding protein RED, including promotion of viral NS1 mRNA splicing and overlap with splicing changes observed in RED-depleted cells.

Scientific Applications:

• Virology and host interaction studies: Characterizes how IAV alters host splicing programs to inform studies of virus–host molecular interactions.
• Gene expression regulation research: Provides datasets and analyses to investigate splicing-mediated regulation of host gene expression under viral infection.
• Therapeutic target identification: Identifies specific IAV-associated splicing events and regulatory links (e.g., RED involvement) that can guide exploration of antiviral intervention points.

Methodology:

Performs comparative computational analysis of RNA-seq data to detect differential splicing events between IAV-infected samples and multiple control conditions.