Expression Profiling and Bioinformatics Analysis of CircRNA in Mice Brain Infected with Rabies Virus

Abstract

Rabies virus (RABV) induces acute, fatal encephalitis in mammals including humans. The circRNAs are important in virus infection process, but whether circRNAs regulated RABV infection remains largely unknown. Here, mice brain with or without the RABV CVS-11 strain were subjected to RNA sequencing and a total of 30,985 circRNAs were obtained. Among these, 9021 candidates were shared in both groups, and 14,610 and 7354 circRNAs were expressed specifically to the control and experimental groups, indicating that certain circRNAs were specifically inhibited or induced on RABV infection. The circRNAs mainly derived from coding exons. In total, 636 circRNAs were differentially expressed in RABV infection, of which 426 significantly upregulated and 210 significantly downregulated (p < 0.05 and fold change ≥2). The expression of randomly selected 6 upregulated and 6 downregulated circRNAs was tested by RT-qPCR, and the expression trend of the 11 out of 12 circRNAs was consistent in RT- qPCR and RNA-seq analysis. Rnase R-resistant assay and Sanger sequencing were conducted to verify the circularity of circRNAs. GO analysis demonstrated that source genes of all differentially regulated circRNAs were mainly related to cell plasticity and synapse function. Both KEGG and GSEA analysis revealed that these source genes were engaged in the cGMP–PKG and MAPK signaling pathway, and HTLV-I infection. Also, pathways related to glucose metabolism and synaptic functions were enriched in KEGG analysis. The circRNA–miRNA–mRNA network was built with 25 of 636 differentially expressed circRNAs, 264 mRNAs involved in RABV infection, and 29 miRNAs. Several miRNAs and many mRNAs in the network were reported to be related to viral infection and the immune response, suggesting that circRNAs could regulate RABV infection via interacting with miRNAs and mRNAs. Taken together, this study first characterized the transcriptomic pattern of circRNAs, and signaling pathways and function that circRNAs are involved in, which may indicate directions for further research to understand mechanisms of RABV pathogenesis.

A circular RNA, circUSP36, accelerates endothelial cell dysfunction in atherosclerosis by adsorbing miR-637 to enhance WNT4 expression

“…The stability of circUSP36 was detected by the RNase R and actinomycin D assays [ 24 ]. To conduct RNase R treatment, 2 mg total RNA from endothelial cells was incubated for 0.5 h with or without 5 U/mg RNase R. For the actinomycin D assay, endothelial cells were treated with 2 μg/ml actinomycin D for different time periods (0, 4, 8, and 12 h).…”

“…Total RNA derived from endothelial cells was isolated using TRIzol reagent (Invitrogen) [ 24 ]. Reverse transcription was performed using Superscript II reverse transcriptase (Invitrogen), according to the manufacturer’s instructions.…”

Separation, Purification, Structure Analysis, In Vitro Antioxidant Activity and circRNA-miRNA-mRNA Regulatory Network on PRV-Infected RAW264.7 Cells of a Polysaccharide Derived from Arthrospira platensis

“…There are 151 circRNAs, 56 miRNAs, and 341 mRNAs differentially expressed in Orf virus-infected goatskin fibroblast cells [ 60 ]. The brains of mice infected with Rabies virus were sequenced, and the constructed circRNA-miRNA-mRNA network was composed of 25 differentially expressed circRNAs, 29 miRNAs, and 264 mRNAs [ 61 ]. In this study, there were 17 differentially expressed circRNAs, 117 miRNAs, and 2113 mRNAs between C group and CV group ( Figure 8 A–C) ( p < 0.05, FC > 1.5).…”

The Emerging Role of the Serine Incorporator Protein Family in Regulating Viral Infection

“…Changes in the circular RNA spectrum were detected in the brains of Rabies virus (RABV)-infected or uninfected mice by RNA sequencing, and RABV infection was found to significantly change the expression pattern of 636 circular RNAs. Among these circular RNAs, SERINC3 significantly improved novel_circ_017745 expression, while the mRNA expression pattern of host genes remained unchanged with RABV infection (Zhao et al, 2021). Some non-retroviruses may be sensitive to SERINC5.…”