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Differential CircRNA Expression Profiles in PK-15 Cells Infected with Pseudorabies Virus Type II

  • RESEARCH ARTICLE
  • Published:
Virologica Sinica

Abstract

Circular RNAs (circRNAs) belong to a class of non-coding RNAs with diverse biological functions. However, little is known about their roles in case of pseudorabies virus (PrV) infection. Here, we analyzed the expression profile of host circRNAs from a virulent PrV type II strain DX (PrV-DX) infected and an attenuated gE/TK deficient (gE−TK−PrV) strain of PrV infected PK-15 cells. CircRNAs were identified by find_circ and analyzed with DESeq 2. Compared with the mock cells, 449 differentially expressed (DE) circRNAs (233 down-regulated and 216 up-regulated) from PrV-DX infected and 578 DE circRNAs (331 down-regulated and 247 up-regulated) from gE−TK− PrV infected PK-15 cells were identified. In addition, 459 DE circRNAs (164 down-regulated and 295 up-regulated) between the PrV-DX and gE−TK−PrV infected cells were identified. The expression patterns of 13 circRNAs were validated by reverse transcription quantitative real-time PCR (RT-qPCR) and results were similar as of RNA-seq. The putative target miRNA binding sites of DE circRNAs were predicted by using miRanda and psRobot. The circRNA-miRNA-mRNA network was constructed and certain miRNAs that have possible roles in antiviral immune response, such as miR-210 and miR-340, were predicted. GO and KEGG pathway analysis demonstrated that DE circRNAs were enriched in the processes such as cellular metabolism, protein binding, RNA degradation and regulation of actin cytoskeleton. Collectively, these findings might provide the useful information for a better understanding of mechanisms underlying the interaction between PrV-II and host cells.

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Data Availability

The data of RNA-seq was deposited in the Gene Expression Omnibus (GEO) database with the Accession Number of GSE139424.

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Acknowledgements

We thank Dr. Tianqi Yu for the assistance of data analysis. This work was supported by the National Key Research & Development Program of China (2016YFD0500102), Key Research & Development Program of Zhejiang Province (Grant No. 2020C02011) and the Fundamental Research Funds for the Central Universities (2017FZA6018).

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Authors and Affiliations

  1. MOA Key Laboratory of Animal Virology, Center of Veterinary Sciences, Zhejiang University, Hangzhou, 310058, China

    Haimin Li, Wen Tang, Yulan Jin, Weiren Dong, Yan Yan & Jiyong Zhou

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  1. Haimin Li
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  2. Wen Tang
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  3. Yulan Jin
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  4. Weiren Dong
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  5. Yan Yan
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Contributions

JZ designed the study and supervised the experiment. YJ and YY prepared the samples. HL validated and analyzed the RNA-seq data and drafted the manuscript. WD and WT helped to analyze the data. JZ finalized the manuscript. All authors read and approved the final version of the manuscript.

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Correspondence to Jiyong Zhou.

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Li, H., Tang, W., Jin, Y. et al. Differential CircRNA Expression Profiles in PK-15 Cells Infected with Pseudorabies Virus Type II. Virol. Sin. 36, 75–84 (2021). https://doi.org/10.1007/s12250-020-00255-w

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