![]() We validated these interactions by ribonucleoprotein (RNP) immunoprecipitation (RIP) analysis and investigated the impact of NF90 on the stability and translation of these target mRNAs. We found several RNAs that encoded proteins implicated in RNA metabolism, the response to viral infection, and signaling through RAP1. In order to systematically identify the collection of NF90 target mRNAs and further determine the sites of interaction with target mRNAs, we carried out iCLIP (individual nucleotide resolution UV cross-linking and immunoprecipitation) analysis in HEK-293 cells. Our studies found that NF90 regulates the stability of several cytokines following exposure to Plasmodium falciparum antigens 17, repressed the translation of the cytokine BAFF in THP-1 cells, and cooperated with microRNA miR-15a in binding BAFF mRNA to inhibit translation 18, 19. NF90 was found to suppress the translation of several mRNAs encoding proinflammatory factors NF90 levels declined in senescent fibroblasts, leading to derepression and increased translation of several inflammatory cytokines 16. NF90 stabilizes the mRNAs encoding the cyclin-dependent kinase inhibitor CDKN1A (p21) and the myogenic transcription factor MYOD in developing skeletal muscle 13, while it promotes cell proliferation by binding the 3'UTR of CCNE1 mRNA, encoding cyclin E1, and stabilizing it, an effect that was further enhanced by the long noncoding (lnc) RNA LINC00470 14, 15. NF90 was shown to bind a subset of RNAs containing AU-rich sequences in the 3'UTR, including IL2 mRNA during T cell activation and MKP-1 mRNA in response to oxidative damage 9, 12. NF90 regulates mRNA stability and translation efficiency by binding to the 3'-untranslated region (UTR) of target mRNAs, many of them encoding proteins involved in cell proliferation and in the immune response. In turn, NF90 modulates RNA metabolism by influencing mRNA splicing, export to the cytoplasm, turnover, and translation 5, 9, 10, 11. Deeper characterization of NF90 as transcription factor revealed that it induces the proliferation of K562 erythroleukemia cells and regulates the expression of immediate early genes 4, 5, genes which are rapidly activated in response to several stimuli 6, 7.Īs an RBP, NF90 possesses two double-stranded RNA-binding motifs (dsRBM), a zinc finger domain (ZNF), and a nucleic acid-binding arginine/glycine-rich (RGG) motif 8, through which it binds single- and double-stranded RNA from viruses and mammalian cells 4. The role of NF90 as a DNA-binding transcription factor was first identified in 1994 by Crothesy and colleagues while studying the human transcription factor complex NFAT (nuclear factor of activated T cells), which is involved in the transcriptional regulation of the IL2 and IL13 genes 2, 3. Nuclear Factor 90 (NF90) is a multifunctional DNA- and RNA-binding protein found mainly in the nucleus and encoded by the interleukin enhancer-binding factor 3 ( ILF3) gene. Consequently, RBPs are major factors in the response of cells to both intracellular and extracellular stimuli. RNA-binding proteins (RBPs) robustly influence gene expression programs by modulating a range of post-transcriptional steps, including pre-mRNA splicing and processing, as well as mRNA export to the cytoplasm, mRNA turnover, and translation 1. Our results support a role for NF90 in modulating key genes implicated in the immune response and offer insight into the immunological response to the SARS-CoV-2 infection. Two of the top targets, IRF3 and IRF9 mRNAs, encode the proteins IRF3 and IRF9, crucial regulators of the interferon pathway involved in the SARS-CoV-2 immune response. We validated a subset of targets and investigated the impact of NF90 on their expression levels. Interestingly, many of the identified RNAs encoded proteins involved in the response to viral infection and RNA metabolism. To systematically identify the RNAs that interact with NF90, we carried out iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) analysis in the human embryonic fibroblast cell line HEK-293. Nuclear Factor 90 (NF90) is an RBP encoded by the interleukin enhancer-binding factor 3 ( ILF3) gene that has been found to influence RNA metabolism at several levels, including pre-RNA splicing, mRNA turnover, and translation. RNA-binding proteins (RBPs) interact with and determine the fate of many cellular RNAs directing numerous essential roles in cellular physiology.
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