Non-destructive transcriptomics via vesicular export (NTVE)
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ABSTRACT:
PROVIDER: PRJNA1192227 | ENA |
REPOSITORIES: ENA
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Project description:RNA turnover is critical for regulating gene expression and cellular homeostasis, with nuclear export representing a key step in mRNA fate. During lytic reactivation of Kaposi’s Sarcoma-associated Herpesvirus (KSHV), widespread host mRNA decay is mediated by the viral endonuclease SOX, which depletes cytoplasmic transcripts and induces secondary nuclear RNA processing defects. One such defect includes transcript hyperadenylation, which typically promotes nuclear retention and decay. However, a subset of host mRNAs escapes both SOX-mediated degradation and nuclear retention, raising questions about their export mechanisms and stability. Here, we investigate the impact of KSHV infection on mRNA poly(A) tail length and nuclear export dynamics using high-throughput poly(A)-sequencing of nuclear and cytoplasmic RNA fractions from KSHV-positive cells. Our data confirm a global increase in poly(A) tail length during KSHV lytic infection, consistent with transcript hyperadenylation. Nevertheless, we identified a group of hyperadenylated transcripts that remain cytoplasmically localized, suggesting active evasion of nuclear retention. Notably, we focused on interleukin-6 (IL-6), a known SOX escapee, which retains cytoplasmic expression during lytic infection despite acquiring a longer poly(A) tail. Using G/I tailing and sPAT assays, we confirmed IL-6 hyperadenylation and demonstrate that its export is CRM1-dependent rather than through the canonical NXF1-NXT1 pathway, which is suppressed during host shutoff. Pharmacological inhibition of CRM1 impairs IL-6 nuclear export and reduces steady-state RNA levels, implicating CRM1 export in the stabilization of this transcript. Our findings reveal a previously unrecognized mechanism by which select host mRNAs, including IL-6, bypass KSHV-imposed nuclear export blocks and escape nuclear decay, thereby preserving their function during viral infection. This study highlights viral manipulation of RNA processing and export pathways as a critical determinant of transcript fate and identifies CRM1 as a key mediator of selective host transcript preservation during KSHV lytic reactivation.
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