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

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-ß) 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. Overall design: To investigate the functional role of VILMIR during the human interferon response, we generated an A549 cell line overexpressing ectopic VILMIR as well as an empty vector control line. The control cell line as well as the VILMIR-overexpressing cell line were treated with or without human IFN-ß at 1 ng/mL or 10 ng/mL for 6 hours in triplicate. RNA-sequencing and differential expression analysis was then performed to identify the impact of VILMIR overexpression on host transcription before and after IFN-ß treatment.