LncRNAs regulate many biological processes including gene imprinting, cell growth, cell differentiation, apoptosis, immune responses, the p53 pathway, stem cell self-renewal, and DNA damage response [24–29]. LncRNA expression is usually tissue-specific or affects specific developmental stages [30–32]. SARS coronavirus-infected mice were found to contain 500 annotated lncRNAs and 1,000 non-annotated genomic regions [33]. LncRNA GAS5 has been found to suppress hepatitis C virus (HCV) replication via interaction with viral NS protein [34]. LncRNA NEAT1 is crucial for the nucleocytoplasmic transport of mRNA in response to stimuli [35]. Recent studies have also shown that virus lncRNA, or lncRNA produced during the viral life cycle, can regulate the host’s antiviral immune response, thus playing an important role in promoting the replication and proliferation of the virus and packaging of the genome into the virions [36, 37]. Cellular lncRNA and virus-encoded lncRNA can form chimeric lncRNA, which impacts virus infection [38, 39]. Some studies have shown that lncRNAs regulate the host’s innate immune response, including pathogen recognition receptor-related signaling and the production of interferons and cytokines [40, 41].
In-depth study of lncRNAs has shown that they act as a medium for molecular scaffolds, guides, decoys, or signals in chromatin remodeling, transcription, post-transcription, or post-translational regulation [42, 43]. lncRNAs exhibit both negative and positive functions for host’s innate immunity and virus replication [44, 45]. Different forms of miRNAs lead to mRNA degradation through base pairing to mRNA sequence motifs; thus, lncRNAs utilize specific sequences or structural motifs to bind with DNA, RNA, or proteins, to modulate gene expression and protein activity including cis (impacting neighboring genes) and trans (impacting gene expression via chromosome conformation) functions [42, 46]. In this study, we found that upregulation of lncRNA-NONSUST006715.1 transcription levels inhibited the expression of JEV nonstructural protein NS3 and JEV mRNA levels (Fig. 1C and D), and knockdown of lncRNA-NONSUST006715.1 promoted JEV proliferation (Fig. 2C and D). NS3 is a multifunctional protein with protease, helicase, and nucleoside triphosphatase activities [47–49]. NS3 can also form a viral replication complex with NS5 and dsRNA [47, 50], to participate in JEV replication and assembly [51, 52]. We speculate that lncRNA-NONSUST006715.1 could suppress JEV proliferation by inhibiting NS3.
CCR1, also called CD191, is a G protein-coupled receptor that can serve a therapeutic target for the treatment of inflammatory diseases. Mouse homolog studies have suggested that this gene plays roles in host protection, including the inflammatory response and susceptibility to viruses and parasites [53]. CCR1 also directs leukocytes to inflammation sites [54]. CCR1 is mainly expressed in lymphocytes, neutrophils, and monocytes [55, 56]; its known ligands include CCL3, CCL5, CCL7, and CCL23 [57]. In humans, CCR1 is highly expressed on monocytes, whereas in rodents, it is primarily expressed on neutrophils [54, 58]. CCR1 recruits monocytes and type-1 T helper cells to activate inflammation after chronic HCV infection [59]. In rheumatoid arthritis, CCR1 regulates the expression of TNFα and IL-10, and is therefore an efficient therapeutic target [60]. Since lncRNA-NONSUST006715.1 suppresses JEV proliferation, CCR1 may play a positive role in promoting JEV proliferation post-infection. Downregulation of CCR1 expression has been reported after infection with Leishmania infantum or coronavirus [61, 62]. In the present study, we found that CCR1 expression was negatively correlated with lncRNA-NONSUST006715.1 expression after JEV infection, CCR1 expression was downregulated at 36 h after JEV infection, but recovered at 48 h (Fig. 3D). By contrast, lncRNA-NONSUST006715.1 expression was very high at 36 h after JEV infection, but decreased sharply at 48 h (Fig. 1A); therefore, we concluded that the regulation of lncRNA-NONSUST006715.1 expression by CCR1 is crucial for JEV proliferation. In this study, we found the transcript factor SP1 could regulate the expression of the lncRNA-NONSUST006715.1 (Fig. 4C and D), and found that CCR1 inhibited lncRNA-NONSUST006715.1 expression via the transcript factor SP1 (Fig. 4A and B, Fig. 5A-C); however, the mechanism by which CCR1 regulates SP1 remains unclear. Furthermore, the mechanism by which lncRNA-NONSUST006715.1 suppresses JEV proliferation requires further study.