VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells

John, K.; Smith, E.; Istishin, A.; Mahmood, N.; Diveley, K.; Tollison, T. S.; Carpenter, S.; Peng, X.

doi:10.1101/2025.08.18.670784

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bioRxiv · 10.1101/2025.08.18.670784

VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells

John, K.·Smith, E.·Istishin, A.·Mahmood, N.·Diveley, K.·Tollison, T. S.·Carpenter, S.·Peng, X.

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Abstract

Long noncoding RNAs (lncRNAs) have been found to play significant regulatory roles within antiviral and immune responses. We previously identified the novel lncRNA virus-inducible lncRNA modulator of interferon response (VILMIR), that was found to broadly regulate the host transcriptional response to interferon-beta (IFN-{beta}) treatment in A549 human lung epithelial cells. Here, we investigated the mechanism by which VILMIR regulates the host interferon response in trans by identifying interacting proteins and gene regulatory networks of VILMIR. Through an RNA pull-down assay, we found that VILMIR interacted with both nuclear and cytoplasmic proteins in vitro, including the transcriptional regulators FUBP1 and PUF60 in the nucleus, as well as the antiviral proteins IFIT1 and IFIT3 and the aminoacyl-tRNA synthetases QARS1 and KARS1 in the cytoplasm. In addition, we found that overexpression of VILMIR in A549 cells resulted in an overall enhancement of host interferon response genes and identified a core set of interferon-stimulated genes that were consistently regulated by VILMIR knockdown and overexpression. Finally, we proposed several possible mechanisms by which VILMIR may interact with the identified proteins to regulate the interferon response, such as by interacting with FUBP1 and PUF60 in the nucleus to regulate host transcription in trans or by interacting with the IFIT proteins and aminoacyl-tRNA synthetases in the cytoplasm to regulate translation. IMPORTANCEDespite thousands of long noncoding RNAs (lncRNAs) being differentially expressed after immune responses and viral infections, there is very limited knowledge on their individual functions in these contexts. We previously identified a novel lncRNA, VILMIR, that was found to be an interferon-stimulated gene that regulated the host transcriptional response to interferon-beta treatment in human epithelial cells. Here, we investigated the mechanism by which VILMIR regulates the interferon response in trans. Through in vitro studies, we identified several nuclear and cytoplasmic proteins that interact with VILMIR, including proteins involved in transcriptional and translational regulation. In addition, we demonstrated that the overexpression of VILMIR results in an enhancement of host interferon response genes, supporting our hypothesis that VILMIR plays an activating role in the host interferon response. Finally, we propose several potential models for the mechanism of VILMIR, providing a foundation for the investigation of VILMIR as a novel therapeutic target in antiviral immunity.

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John, K., Smith, E., Istishin, A., Mahmood, N., Diveley, K., Tollison, T. S., Carpenter, S., Peng, X.. 2025-08-22. VILMIR is a trans-acting long noncoding RNA that enhances the host interferon response in human epithelial cells. https://doi.org/10.1101/2025.08.18.670784

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