A Previously Undiscovered Circular RNA, circTNFAIP3, and Its Role in Coronavirus Replication

circEgg inhibits BmCPV infection by regulating the transition between H3K9me3 and H3K9ac

Our previous study demonstrated that the expression level of circRNA circEgg, which is encoded by histone-lysine N-methyltransferase eggless (BmEgg), is responsive to Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection in the silkworm. However, the precise relationship between BmCPV infection and circEgg remains unclear. In this study, we observed that the expression level of circEgg in both the midguts and cultured BmN cells significantly increased after BmCPV infection, while the expression of its host gene, BmEgg, exhibited an opposite trend. Transient expression experiments revealed that circEgg acts to inhibit BmCPV infection. Additionally, Western blot analyses indicated that BmCPV infection leads to a downregulation of histone 3 lysine 9 trimethylation (H3K9me3) and an upregulation of histone 3 lysine 9 acetylation (H3K9ac). Notably, the levels of H3K9ac and H3K9me3 were found to be positively and negatively correlated with circEgg expression, respectively, suggesting that circEgg may regulate the transition between H3K9me3 and H3K9ac. Mechanistically, we discovered that circEgg inhibits BmCPV infection by enhancing the H3K9ac level through the circEgg-bmo-miR-3391-5p-histone deacetylase Rpd3 network, while simultaneously reducing the H3K9me3 level via the circEgg-encoded protein circEgg-P122. Collectively, these findings indicate that circEgg plays a crucial role in inhibiting BmCPV infection by modulating the balance between H3K9me3 and H3K9ac.

Emerging role and clinical applications of circular RNAs in human diseases

Circular RNAs (circRNAs) are a large family of non-coding RNAs characterized by a single-stranded, covalently closed structure, predominantly synthesized through a back-splicing mechanism. While thousands of circRNAs have been identified, only a few have been functionally characterized. Although circRNAs are less abundant than other RNA types, they exhibit exceptional stability due to their covalently closed structure and demonstrate high cell and tissue specificity. CircRNAs play a critical role in maintaining cellular homeostasis by influencing gene transcription, translation, and post-translation processes, modulating the immune system, and interacting with mRNA, miRNA, and proteins. Abnormal circRNA expression has been associated with a wide range of human diseases and various infections. Due to their remarkable stability in body fluids and tissues, emerging research suggests that circRNAs could serve as diagnostic and therapeutic biomarkers for these diseases. This review focuses on the emerging role of circRNAs in various human diseases, exploring their biogenesis, molecular functions, and potential clinical applications as diagnostic and therapeutic biomarkers with current evidence, challenges, and future perspectives. The key theme highlights the significance of circRNAs in regulating gene expression, their involvement in diseases like cancer, neurodegenerative disorders, cardiovascular diseases, and diabetes, and their potential use in translational medicine for developing novel therapeutic strategies. We also discuss recent clinical trials involving circRNAs. Thus, this review is important for both basic researchers and clinical scientists, as it provides updated insights into the role of circRNAs in human diseases, aiding further exploration and advancements in the field.

Advances in the understanding of circRNAs that influence viral replication in host cells

Circular RNAs (circRNAs) are non-coding RNAs discovered in recent years, which are produced by back-splicing involving the 3' and 5' ends of RNA molecules. There is increasing evidence that circRNAs have important roles in cancer, neurological diseases, cardiovascular and cerebrovascular diseases, and other diseases. In addition, host circRNAs and virus-encoded circRNAs participate in the body's immune response, with antiviral roles. This review summarizes the mechanisms by which host and viral circRNAs interact during the host immune response. Comprehensive investigations have revealed that host circRNAs function as miRNA sponges in a particular manner, primarily by inhibiting viral replication. Viral circRNAs have more diverse functions, which generally involve promoting viral replication. In addition, in contrast to circRNAs from RNA viruses, circRNAs from DNA viruses can influence host cell migration, proliferation, and apoptosis, along with their effects on viral replication. In summary, circRNAs have potential as diagnostic and therapeutic targets, offering a foundation for the diagnosis and treatment of viral diseases.

Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2

Virus-encoded circular RNA (circRNA) participates in the immune response to viral infection, affects the human immune system, and can be used as a target for precision therapy and tumor biomarker. The coronaviruses SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) that have emerged in recent years are highly contagious and have high mortality rates. In coronaviruses, little is known about the circRNA encoded by the SARS-CoV-1/2. Therefore, this study explores whether SARS-CoV-1/2 encodes circRNA and characteristics and functions of circRNA. Based on RNA-seq data of SARS-CoV-1 and SARS-CoV-2 infections, we used circRNA identification tools (circRNA_finder, find_circ and CIRI2) to identify circRNAs. The number of circRNAs encoded by SARS-CoV-1 and SARS-CoV-2 was identified as 151 and 470, respectively. It can be found that SARS-CoV-2 shows more prominent circRNA encoding ability than SARS-CoV-1. Expression analysis showed that only a few circRNAs encoded by SARS-CoV-1/2 showed high expression levels, and the positive strand produced more abundant circRNAs. Then, based on the identified SARS-CoV-1/2-encoded circRNAs, we performed circRNA identification and characterization using the previously developed CirRNAPL. Finally, target gene prediction and functional enrichment analysis were performed. It was found that viral circRNA is closely related to cancer and has a potential role in regulating host cell functions. This study studied the characteristics and functions of viral circRNA encoded by coronavirus SARS-CoV-1/2, providing a valuable resource for further research on the function and molecular mechanism of coronavirus circRNA.

Influenza A Virus-Induced circRNA circMerTK Negatively Regulates Innate Antiviral Responses

Circular RNAs (circRNAs) are an important subclass of noncoding RNAs implicated in the regulation of multiple biological processes. However, the functional involvement of circRNAs in the pathogenesis of influenza A viruses (IAVs) remains largely unknown. Here, we employed RNA sequencing (RNA-Seq) to examine the differentially expressed circRNAs in mouse lung tissues challenged or not challenged with IAV to evaluate the impact of viral infection on circRNAs in vivo. We observed that 413 circRNAs exhibited significantly altered levels following IAV infection. Among these, circMerTK, the derivative of myeloid-epithelial-reproductive tyrosine kinase (MerTK) pre-mRNA, was highly induced by IAV. Interestingly, circMerTK expression was also increased upon infection with multiple DNA and RNA viruses in human and animal cell lines, and thus it was selected for further studies. Poly(I:C) and interferon β (IFN-β) stimulated circMerTK expression, while RIG-I knockout and IFNAR1 knockout cell lines failed to elevate circMerTK levels after IAV infection, demonstrating that circMerTK is regulated by IFN signaling. Furthermore, circMerTK overexpression or silencing accelerated or impeded IAV and Sendai virus replication, respectively. Silencing circMerTK enhanced the production of type I IFNs and interferon-stimulating genes (ISGs), whereas circMerTK overexpression suppressed their expression at both the mRNA and protein levels. Notably, altering circMerTK expression had no effect on the MerTK mRNA level in cells infected or not infected with IAV, and vice versa. In addition, human circMerTK and mouse homologs functioned similarly in antiviral responses. Together, these results identify circMerTK as an enhancer of IAV replication through suppression of antiviral immunity. IMPORTANCE CircRNAs are an important class of noncoding RNAs characterized by a covalently closed circular structure. CircRNAs have been proven to impact numerous cellular processes, where they conduct specialized biological activities. In addition, circRNAs are believed to play a crucial role in regulating immune responses. Nevertheless, the functions of circRNAs in the innate immunity against IAV infection remain obscure. In this study, we employed transcriptomic analysis to investigate the alterations in circRNAs expression following IAV infection in vivo. It was found that expression of 413 circRNAs was significantly altered, of which 171 were upregulated, and 242 were downregulated following the IAV infection. Interestingly, circMerTK was identified as a positive regulator of IAV replication in both human and mouse hosts. CircMerTK was shown to influence IFN-β production and its downstream signaling, enhancing IAV replication. This finding provides new insights into the critical roles of circRNAs in regulating antiviral immunity.

BmNPV circular RNA-encoded peptide VSP39 promotes viral replication

CircRNAs are covalently closed single-stranded circular RNA molecules, which are not easily degraded by endonucleases and play vital roles in many biological processes. Currently, most studies on circRNAs focus on endogenous circRNAs in cells, and there are few studies on virus-encoded circRNAs. In this study, a viral circRNA (circRNA-000010) derived from the region (-/bp: 114514-115,319) of the complementary strand of Bombyx mori Nucleopolyhedrovirus (BmNPV) genome was identified with the circRNA-sequencing. The authenticity of viral circRNA-000010 was further confirmed by reverse transcription PCR, reverse transcription-rolling circle amplification (TCA), in situ hybridization, immunofluorescent staining, and Northern blotting. The results of overexpression and knockdown experiments showed that circRNA-000010 promoted viral replication. Furthermore, a viral small peptide VSP39 with 39 amino acid residues translated by circRNA-000010 but not its linear molecule was confirmed. Finally, VSP39 was found to promote viral replication. Our findings indicated that a viral circRNA encoded by BmNPV promoted viral replication. These findings will provide new clues for further understanding coding information of the BmNPV genome and open a new insight for investigating host-virus interactions.

Regulatory circular RNAs in viral diseases: applications in diagnosis and therapy

Circular RNA (circRNA) forms closed loops via back-splicing in precursor mRNA, resisting exonuclease degradation. In higher eukaryotes, protein-coding genes create circRNAs through exon back-splicing. Unlike mRNAs, circRNAs possess unique production and structural traits, bestowing distinct cellular functions and biomedical potential. In this review, we explore the pivotal roles of viral circRNAs and associated RNA in various biological processes. Analysing the interactions between viral circRNA and host cellular machinery yields fresh insights into antiviral immunity, catalysing the development of potential therapeutics. Furthermore, circRNAs serve as enduring biomarkers in viral diseases due to their stable translation within specific tissues. Additionally, a deeper understanding of translational circRNA could expedite the establishment of circRNA-based expression platforms, meeting the rising demand for broad-spectrum viral vaccines. We also highlight the applications of circular RNA in biomarker studies as well as circRNA-based therapeutics. Prospectively, we expect a technological revolution in combating viral infections using circRNA.

Non-coding RNA in SARS-CoV-2: Progress toward therapeutic significance

The recently developed pathogenic virus, SARS-CoV-2, was found in the Hubei Province, China. Giving rise to a broad spectrum of symptoms, SARS-CoV-2 rapidly spread across the globe, causing multi-systemic and dangerous complications, with death in extreme cases. Thereby, the number of research cases increases every day on preventing infection and treating its resulting damage. Accumulating evidence suggests noncoding RNAs (ncRNAs) are necessary for modifying virus infection and antiviral immune reaction, along with biological processes regulating SARS-CoV-2 and subsequent disease states. Therefore, understanding these mechanisms might provide a further understanding of the pathogenesis and feasible therapy alternatives against SARS-CoV2. Consequently, the molecular biology of SARS-CoV-2, ncRNA's role in its infection, and various RNA therapy tactics against the virus have been presented in this review section.

Downregulation of the Long Noncoding RNA IALNCR Targeting MAPK8/JNK1 Promotes Apoptosis and Antagonizes Bovine Viral Diarrhea Virus Replication in Host Cells

Bovine viral diarrhea virus (BVDV) is the causative agent of the bovine viral diarrhea-mucosal disease, which is a leading cause of economic losses in the cattle industry worldwide. To date, many underlying mechanisms involved in BVDV-host interactions remain unclear, especially the functions of long noncoding RNAs (lncRNAs). In our previous study, the lncRNA expression profiles of BVDV-infected Madin-Darby bovine kidney (MDBK) cells were obtained by RNA-seq, and a significantly downregulated lncRNA IALNCR targeting MAPK8/JNK1 (a key regulatory factor of apoptosis) was identified through the lncRNA-mRNA coexpression network analysis. In this study, the function of IALNCR in regulating apoptosis to affect BVDV replication was further explored. Our results showed that BVDV infection-induced downregulation of the lncRNA IALNCR in the host cells could suppress the expression of MAPK8/JNK1 at both the mRNA and protein levels, thereby indirectly promoting the activation of caspase-3, leading to cell-autonomous apoptosis to antagonize BVDV replication. This was further confirmed by the small interfering RNA (siRNA)-mediated knockdown of the lncRNA IALNCR. However, the overexpression of the lncRNA IALNCR inhibited apoptosis and promoted BVDV replication. In conclusion, our findings demonstrated that the lncRNA IALNCR plays an important role in regulating host antiviral innate immunity against BVDV infection. IMPORTANCE Bovine viral diarrhea-mucosal disease caused by BVDV is an important viral disease in cattle, causing severe economic losses to the cattle industry worldwide. The molecular mechanisms of BVDV-host interactions are complex. To date, most studies focused only on how BVDV escapes host innate immunity. By contrast, how the host cell regulates anti-BVDV innate immune responses is rarely reported. In this study, a significantly downregulated lncRNA, with a potential function of inhibiting apoptosis (inhibiting apoptosis long noncoding RNA, IALNCR), was obtained from the lncRNA expression profiles of BVDV-infected cells and was experimentally evaluated for its function in regulating apoptosis and affecting BVDV replication. We demonstrated that downregulation of BVDV infection-induced lncRNA IALNCR displayed antiviral function by positively regulating the MAPK8/JNK1 pathway to promote cell apoptosis. Our data provided evidence that host lncRNAs regulate the innate immune response to BVDV infection.

circEZH2 inhibits opening of mitochondrial permeability transition pore via interacting with PiC and up-regulating RSAD2

Transmissible gastroenteritis virus (TGEV) infection can lead to mitochondrial damage in porcine intestinal epithelial cells-jejunum 2 (IPEC-J2) cell line. The abnormal opening of mitochondrial permeability transition pore (mPTP) is the most important factor for mitochondrial damage. We previously demonstrated that circEZH2 could inhibit the abnormal opening of mPTP by binding miR-22. However, circEZH2 binding to miR-22 cannot completely enable mPTP opening to recover to normal level compared with the control group. So, we assume that circEZH2 also regulates the mPTP opening in other ways. To prove it, we identified the differentially expressed proteins (DEPs) caused by circEZH2 and circEZH2-interacting proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS). It turns out there are 123 DEPs (0.83 ≤ fold change ≥ 1.2) upon overexpression circEZH2 and 200 proteins interacted with circEZH2. The kyoto encyclopedia of genes and genomes (KEGG) analysis, gene ontology (GO) analysis, subcellular localization analysis, and protein interaction network results show that the DEPs and circEZH2-interacting proteins may involve in the regulation of mPTP opening. RNA immunoprecipitation (RIP) assay and flow cytometry (FCM) results indicate that circEZH2 can inhibit the opening of mPTP by interacting with Pi carrier (PiC, also named SLC25A3). Quantitative real-time polymerase chain reaction (qRT-PCR), western blotting, and FCM results reveal that circEZH2 can inhibit mPTP opening by promoting the expression of radical s-adenosyl methionine domain-containing protein 2 (RSAD2). In addition, PiC can promote RSAD2 expression. The data indicate that circEZH2 inhibits TGEV-induced mPTP opening by interacting with PiC and upregulating RSAD2.

The Cellular and Viral circRNAs Induced by Fowl Adenovirus Serotype 4 Infection

Circular RNAs (circRNAs) are a new class of noncoding RNAs that play vital roles in many biological processes. Virus infection induces modifications in cellular circRNA transcriptomes and expresses viral circRNAs. The outbreaks of Hydropericardium-hepatitis syndrome (HHS) caused by fowl adenovirus serotype 4 (FAdV-4) have resulted in huge economic losses to the poultry industry worldwide. To investigate the expression of circRNAs during FAdV-4 infection, we performed transcriptome analysis of FAdV-4-infected leghorn male hepatoma (LMH) cells. In total, 19,154 cellular circRNAs and 135 differentially expressed (DE) cellular circRNAs were identified. The characteristics of the DE cellular circRNAs were analyzed and most of them were related to multiple biological processes according to GO and KEGG enrichment analysis. The accuracy of 10 cellular circRNAs were verified by semiquantitative RT-PCR and sequencing. The change trend was consistent with the RNA sequencing results. Moreover, 2014 viral circRNAs were identified and 10 circRNAs were verified by the same methods. Our analysis showed that seven circRNAs with the same 3′ terminal and variable 5′ terminal regions were located at pTP protein and DNA pol protein of FAdV-4, which may be generated via alternative splicing events. Moreover, the expression level of viral circRNAs was closely related to the replication efficiency of the virus and partial of the viral circRNAs promoted the replication of FAdV-4. Competing endogenous RNA analysis further showed that the effects of cellular and viral circRNAs on host or viral genes may act via miRNAs. Collectively, our findings first indicate that FAdV-4 infection induced the differential expression of cellular circRNAs and FAdV-4 also expressed viral circRNAs, some of which affected FAdV-4 replication. These findings will provide new clues for further understanding FAdV-4 and provide a basis for investigating host-virus interactions.