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

Virologica Sinica volume 36, pages 75–84 (2021)Cite this article

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.

References

  • Ai JW, Weng SS, Cheng Q, Cui P, Li YJ, Wu HL, Zhu YM, Xu B, Zhang WH (2018) Human endophthalmitis caused by pseudorabies virus infection, China, 2017. Emerg Infect Dis 24:1087–1090

    Article  PubMed  PubMed Central  Google Scholar 

  • Cao R, Wu W, Zhou X, Liu K, Li B, Huang X, Zhang Y, Liu H (2015) Let-7 g induces granulosa cell apoptosis by targeting MAP3K1 in the porcine ovary. Int J Biochem Cell Biol 68:148–157

    Article  CAS  PubMed  Google Scholar 

  • Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY (2017) Sensing self and foreign circular RNAs by intron identity. Mol Cell 67:228–238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cramer SD, Campbell GA, Njaa BL, Morgan SE, Smith SN, McLin WT, Brodersen BW, Wise AG, Scherba G, Langohr IM, Maes RK (2011) Pseudorabies virus infection in Oklahoma hunting dogs. J Vet Diagn Invest 23:915–923

    Article  PubMed  Google Scholar 

  • Curtale G, Mirolo M, Renzi TA, Rossato M, Bazzoni F, Locati M (2013) Negative regulation of Toll-like receptor 4 signaling by IL-10-dependent microRNA-146b. Proc Natl Acad Sci U S A 110:11499–11504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Damas ND, Fossat N, Scheel T (2019) Functional interplay between RNA viruses and non-coding RNA in mammals. Noncoding RNA 5:7

    CAS  PubMed Central  Google Scholar 

  • Diel DG, Luo S, Delhon G, Peng Y, Flores EF, Rock DL (2011) Orf virus ORFV121 encodes a novel inhibitor of NF-kappaB that contributes to virus virulence. J Virol 85:2037–2049

    Article  CAS  PubMed  Google Scholar 

  • Engel EA, Song R, Koyuncu OO, Enquist LW (2015) Investigating the biology of alpha herpesviruses with MS-based proteomics. Proteomics 15:1943–1956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Enquist LW (1999) Life beyond eradication: veterinary viruses in basic science. Arch Virol Suppl 15:87–109

    CAS  PubMed  Google Scholar 

  • Forero A, Tisoncik-Go J, Watanabe T, Zhong G, Hatta M, Tchitchek N, Selinger C, Chang J, Barker K, Morrison J, Berndt JD, Moon RT, Josset L, Kawaoka Y, Katze MG (2015) The 1918 influenza virus PB2 protein enhances virulence through the disruption of inflammatory and Wnt-mediated signaling in mice. J Virol 90:2240–2253

    Article  PubMed  CAS  Google Scholar 

  • Grunwell JR, Yeligar SM, Stephenson S, Ping XD, Gauthier TW, Fitzpatrick AM, Brown L (2018) TGF-beta1 suppresses the type I IFN response and induces mitochondrial dysfunction in alveolar macrophages. J Immunol 200:2115–2128

    Article  CAS  PubMed  Google Scholar 

  • Guarnerio J, Bezzi M, Jeong JC, Paffenholz SV, Berry K, Naldini MM, Lo-Coco F, Tay Y, Beck AH, Pandolfi PP (2016) Oncogenic role of fusion-circRNAs derived from cancer-associated chromosomal translocations. Cell 165:289–302

    Article  CAS  PubMed  Google Scholar 

  • Guethlein LA, Older AA, Abi-Rached L, Parham P (2007) Evolution of killer cell Ig-like receptor (KIR) genes: definition of an orangutan KIR haplotype reveals expansion of lineage III KIR associated with the emergence of MHC-C. J Immunol 179:491–504

    Article  CAS  PubMed  Google Scholar 

  • Hafezi W, Lorentzen EU, Eing BR, Muller M, King NJ, Klupp B, Mettenleiter TC, Kuhn JE (2012) Entry of herpes simplex virus type 1 (HSV-1) into the distal axons of trigeminal neurons favors the onset of nonproductive, silent infection. PLoS Pathog 8:e1002679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495:384–388

    Article  CAS  PubMed  Google Scholar 

  • Hoshina S, Sekizuka T, Kataoka M, Hasegawa H, Hamada H, Kuroda M, Katano H (2016) Profile of exosomal and intracellular microRNA in gamma-herpesvirus-infected lymphoma cell lines. PLoS ONE 11:e162574

    Article  CAS  Google Scholar 

  • Hou T, Liao J, Zhang C, Sun C, Li X, Wang G (2018) Elevated expression of miR-146, miR-139 and miR-340 involved in regulating Th1/Th2 balance with acute exposure of fine particulate matter in mice. Int Immunopharmacol 54:68–77

    Article  CAS  PubMed  Google Scholar 

  • Huang J, Ma G, Fu L, Jia H, Zhu M, Li X, Zhao S (2014) Pseudorabies viral replication is inhibited by a novel target of miR-21. Virology 456–457:319–328

    Article  PubMed  CAS  Google Scholar 

  • Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, Marzluff WF, Sharpless NE (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19:141–157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jin Y, Zhang K, Huang W, Tang W, Li H, Dong W, Gu J, Zhou J (2020) Identification of functional lncRNAs in pseudorabies virus type II infected cells. Vet Microbiol 242:108564

    Article  PubMed  CAS  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  CAS  PubMed  Google Scholar 

  • Kimman TG, Binkhorst GJ, van den Ingh TS, Pol JM, Gielkens AL, Roelvink ME (1991) Aujeszky’s disease in horses fulfils Koch’s postulates. Vet Rec 128:103–106

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, Zhu P, Chang Z, Wu Q, Zhao Y, Jia Y, Xu P, Liu H, Shan G (2015) Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 22:256–264

    Article  PubMed  CAS  Google Scholar 

  • Li LJ, Zhao W, Tao SS, Leng RX, Fan YG, Pan HF, Ye DQ (2017a) Competitive endogenous RNA network: potential implication for systemic lupus erythematosus. Expert Opin Ther Targets 21:639–648

    Article  CAS  PubMed  Google Scholar 

  • Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL (2017b) Coordinated circRNA biogenesis and function with NF90/NF110 in viral infection. Mol Cell 67:214–227

    Article  CAS  PubMed  Google Scholar 

  • Li J, Lu M, Huang B, Lv Y (2018a) Porcine circovirus type 2 inhibits inter-beta expression by targeting Karyopherin alpha-3 in PK-15 cells. Virology 520:75–82

    Article  CAS  PubMed  Google Scholar 

  • Li X, Yang L, Chen LL (2018b) The biogenesis, functions, and challenges of circular RNAs. Mol Cell 71:428–442

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Hu Y, Yin J, Yan XY, Chen WJ, Jiang CY, Hu XS, Wang XY, Zhu JG, Yu ZB, Han SP (2019) Profiles analysis reveals circular RNAs involving zebrafish physiological development. J Cell Physiol 234:15922–15933

    Article  CAS  Google Scholar 

  • Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Luo X, Guo L, Zhang J, Xu Y, Gu W, Feng L, Wang Y (2017) Tight junction protein occludin is a porcine epidemic diarrhea virus entry factor. J Virol 91:e00202-17

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma X, Zhao X, Zhang Z, Guo J, Guan L, Li J, Mi M, Huang Y, Tong D (2018) Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-kappaB pathway in porcine intestinal epithelial cell line. BMC Genom 19:747

    Article  CAS  Google Scholar 

  • Masic M, Ercegan M, Petrovic M (1965) The significance of the tonsils in the pathogenesis and diagnosis of Aujeszyk’s disease in pigs. Zentralbl Vet B 12:398–405

    Article  CAS  Google Scholar 

  • Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333–338

    Article  CAS  PubMed  Google Scholar 

  • Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Li P, Wu M (2017) CircRNA: functions and properties of a novel potential biomarker for cancer. Mol Cancer 16:94

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Muller T, Hahn EC, Tottewitz F, Kramer M, Klupp BG, Mettenleiter TC, Freuling C (2011) Pseudorabies virus in wild swine: a global perspective. Arch Virol 156:1691–1705

    Article  CAS  PubMed  Google Scholar 

  • Nishitsuji H, Sawada L, Sugiyama R, Takaku H (2015) ZNF10 inhibits HIV-1 LTR activity through interaction with NF-kappaB and Sp1 binding motifs. FEBS Lett 589:2019–2025

    Article  CAS  PubMed  Google Scholar 

  • Nishitsuji H, Ujino S, Yoshio S, Sugiyama M, Mizokami M, Kanto T, Shimotohno K (2016) Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc Natl Acad Sci U S A 113:10388–10393

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng L, Chen G, Zhu Z, Shen Z, Du C, Zang R, Su Y, Xie H, Li H, Xu X, Xia Y, Tang W (2017) Circular RNA ZNF609 functions as a competitive endogenous RNA to regulate AKT3 expression by sponging miR-150-5p in Hirschsprung’s disease. Oncotarget 8:808–818

    Article  PubMed  Google Scholar 

  • Pomeranz LE, Reynolds AE, Hengartner CJ (2005) Molecular biology of pseudorabies virus: impact on neurovirology and veterinary medicine. Microbiol Mol Biol Rev 69:462–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pontes MS, Van Waesberghe C, Nauwynck H, Verhasselt B, Favoreel HW (2016) Pseudorabies virus glycoprotein gE triggers ERK1/2 phosphorylation and degradation of the pro-apoptotic protein Bim in epithelial cells. Virus Res 213:214–218

    Article  CAS  PubMed  Google Scholar 

  • Qu S, Yang X, Li X, Wang J, Gao Y, Shang R, Sun W, Dou K, Li H (2015) Circular RNA: a new star of noncoding RNAs. Cancer Lett 365:141–148

    Article  CAS  PubMed  Google Scholar 

  • Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7:e30733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sathiyamoorthy K, Chen J, Longnecker R, Jardetzky TS (2017) The COMPLEXity in herpesvirus entry. Curr Opin Virol 24:97–104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi J, Hu N, Li J, Zeng Z, Mo L, Sun J, Wu M, Hu Y (2017) Unique expression signatures of circular RNAs in response to DNA tumor virus SV40 infection. Oncotarget 8:98609–98622

    Article  PubMed  PubMed Central  Google Scholar 

  • Shi J, Hu N, Mo L, Zeng Z, Sun J, Hu Y (2018) Deep RNA sequencing reveals a repertoire of human fibroblast circular RNAs associated with cellular responses to herpes simplex virus 1 infection. Cell Physiol Biochem 47:2031–2045

    Article  CAS  PubMed  Google Scholar 

  • Sun Y, Luo Y, Wang CH, Yuan J, Li N, Song K, Qiu HJ (2016) Control of swine pseudorabies in China: opportunities and limitations. Vet Microbiol 183:119–124

    Article  PubMed  Google Scholar 

  • Tagawa T, Gao S, Koparde VN, Gonzalez M, Spouge JL, Serquina AP, Lurain K, Ramaswami R, Uldrick TS, Yarchoan R, Ziegelbauer JM (2018) Discovery of Kaposi’s sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA. Proc Natl Acad Sci U S A 115:12805–12810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian H, He Z (2018) miR-215 enhances HCV replication by targeting TRIM22 and inactivating NF-kappaB signaling. Yonsei Med J 59:511–518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, Fang L (2018) Advances in circular RNAs and their roles in breast cancer. J Exp Clin Cancer Res 37:206

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang H, Zhao Y, Chen M, Cui J (2017a) Identification of novel long non-coding and circular RNAs in human papillomavirus-mediated cervical cancer. Front Microbiol 8:1720

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Wang D, Xie G, Yin Y, Zhao E, Tao K, Li R (2017b) MicroRNA-152 regulates immune response via targeting B7-H1 in gastric carcinoma. Oncotarget 8:28125–28134

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang S, Cui S, Zhao W, Qian Z, Liu H, Chen Y, Lv F, Ding HG (2018) Screening and bioinformatics analysis of circular RNA expression profiles in hepatitis B-related hepatocellular carcinoma. Cancer Biomark 22:631–640

    Article  CAS  PubMed  Google Scholar 

  • Wu TH, Pan CY, Lin MC, Hsieh JC, Hui CF, Chen JY (2012) In vivo screening of zebrafish microRNA responses to bacterial infection and their possible roles in regulating immune response genes after lipopolysaccharide stimulation. Fish Physiol Biochem 38:1299–1310

    Article  CAS  PubMed  Google Scholar 

  • Yang H, Wang G, Sun H, Shu R, Liu T, Wang CE, Liu Z, Zhao Y, Zhao B, Ouyang Z, Yang D, Huang J, Zhou Y, Li S, Jiang X, Xiao Z, Li XJ, Lai L (2014) Species-dependent neuropathology in transgenic SOD1 pigs. Cell Res 24:464–481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang ZG, Awan FM, Du WW, Zeng Y, Lyu J, Wu GS, Yang W, Yang BB (2017) The circular RNA interacts with STAT3, increasing its nuclear translocation and wound repair by modulating Dnmt3a and miR-17 function. Mol Ther 25:2062–2074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang X, Guan H, Li C, Li Y, Wang S, Zhao X, Zhao Y, Liu Y (2019) Characteristics of human encephalitis caused by pseudorabies virus: a case series study. Int J Infect Dis 87:92–99

    Article  CAS  PubMed  Google Scholar 

  • Ye C, Zhang QZ, Tian ZJ, Zheng H, Zhao K, Liu F, Guo JC, Tong W, Jiang CG, Wang SJ, Shi M, Chang XB, Jiang YF, Peng JM, Zhou YJ, Tang YD, Sun MX, Cai XH, An TQ, Tong GZ (2015) Genomic characterization of emergent pseudorabies virus in China reveals marked sequence divergence: evidence for the existence of two major genotypes. Virology 483:32–43

    Article  CAS  PubMed  Google Scholar 

  • Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang GL, Li YX, Zheng SQ, Liu M, Li X, Tang H (2010) Suppression of hepatitis B virus replication by microRNA-199a-3p and microRNA-210. Antivir Res 88:169–175

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Liu H, Hou L, Wang G, Zhang R, Huang Y, Chen X, Zhu J (2017) Circular RNA_LARP4 inhibits cell proliferation and invasion of gastric cancer by sponging miR-424-5p and regulating LATS1 expression. Mol Cancer 16:151

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang L, Qin Y, Chen M (2018a) Viral strategies for triggering and manipulating mitophagy. Autophagy 14:1665–1673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang M, Huang N, Yang X, Luo J, Yan S, Xiao F, Chen W, Gao X, Zhao K, Zhou H, Li Z, Ming L, Xie B, Zhang N (2018b) A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis. Oncogene 37:1805–1814

    Article  CAS  PubMed  Google Scholar 

  • Zhou L, Chen J, Li Z, Li X, Hu X, Huang Y, Zhao X, Liang C, Wang Y, Sun L, Shi M, Xu X, Shen F, Chen M, Han Z, Peng Z, Zhai Q, Chen J, Zhang Z, Yang R, Ye J, Guan Z, Yang H, Gui Y, Wang J, Cai Z, Zhang X (2010) Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PLoS ONE 5:e15224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou M, Li C, Lu C, Zhang X, Pan Y, Liu X, Liu G, Zhao Z, Sun B (2016) miRNA29 promotes viral replication during early stage of PRRSV infection in vitro. DNA Cell Biol 35:636–642

    Article  CAS  PubMed  Google Scholar 

  • Zou F, Mao R, Yang L, Lin S, Lei K, Zheng Y, Ding Y, Zhang P, Cai G, Liang X, Liu J (2016) Targeted deletion of miR-139-5p activates MAPK, NF-kappaB and STAT3 signaling and promotes intestinal inflammation and colorectal cancer. FEBS J 283:1438–1452

    Article  CAS  PubMed  Google Scholar 

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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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  • DOI: https://doi.org/10.1007/s12250-020-00255-w

Keywords

  • Pseudorabies virus infection
  • RNA-seq
  • CircRNA