Ascura, A. | bioRxiv Science

bioRxiv2025

The Incoming Influenza Genome Assembles a Host RBP Network that Orchestrates Viral RNA Synthesis

Influenza A virus (IAV) replication initiates within minutes of entry, yet the earliest host determinants acting on the incoming viral genome remain undefined. Here, using VIR-CLASP to capture protein interactions with progenitor vRNA prior to any detectable viral transcription, we map the first host-viral RNA interface and identify [~]700 human RNA binding proteins (RBPs) proactively recruited by the negative-sense genome. These factors are enriched in pathways essential for RNA metabolism, chromatin remodeling, transcriptional regulation, and nuclear condensate organization, revealing that the vRNA engages a far broader host network than previously appreciated. Functional interrogation of top candidates demonstrates that GMPS, TOP2A, SRRM2, and SPEN serve as critical proviral factors operating at distinct stages of the IAV synthesis program: GMPS and SPEN are required for efficient production of vRNA, cRNA, and mRNA; TOP2A promotes mRNA capping and early transcript accumulation; and SRRM2, together with SR-proteins, coordinates splicing of viral M and NS transcripts. These findings support a model in which the incoming vRNA acts not merely as a transcriptional template but as a scaffold that initiates assembly of nuclear machinery required for productive viral replication. By defining the pre-replicative viral RNA interactome and its functional consequences, this work exposes an unrecognized layer of host control over IAV permissivity and establishes new points of vulnerability for antiviral intervention.

molecular biology↗

bioRxiv2025

Early Host-Virus RNA Interactions Reveal SPEN-Driven m6A Regulation as a Major Determinant of Henipavirus Infection

Early interactions between viral RNA and host-encoded RNA-binding proteins are pivotal in shaping the trajectory of RNA virus infection. Henipaviruses are emerging, highly lethal BSL-4 pathogens whose mechanisms of pathogenesis remain largely elusive. To illuminate the earliest moments of host-virus interplay, we employed Viral Cross-linking and Solid-phase Purification (VIR-CLASP) to capture host proteins bound to the incoming henipavirus genome within the first hour of infection. This approach establishes the first henipavirus RNA-host protein interactome, revealing 146 human proteins directly associated with the primary viral RNA. Among these, SPEN, RBM15, and RBM15B - canonical regulators of lncRNA Xist - emerged as key host factors that actively promote viral infection. Direct RNA sequencing further uncovered that SPEN depletion induces widespread hypomethylation, affecting ~98% of differentially modified m6A sites, ~87% of which localize to the L mRNA transcript encoding the viral RNA-dependent RNA polymerase. Collectively, these findings expose a critical layer of host dependency at the very onset of infection and reveal a previously unappreciated role for SPEN family proteins in facilitating henipavirus infection.

biochemistry↗