Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation

Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here, we link the ZIKV-induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R loops at specific loci strongly enriched in the interferon (IFN)-stimulated genes (ISGs). Bromouridine sequencing results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of IFN receptor eliminated the R loops on ISGs and partially rescued S-phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN-dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.