Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLOS ONE. 2014;9:91918.
Article
Google Scholar
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL. The Pfam protein families database. Nucleic Acids Res. 2002;30:276–80.
Article
CAS
Google Scholar
Chai WJ, Li J, Shangguan QL, Liu Q, Li XD, Qi DD, Tong XM, Liu WJ, Ye X. Lnc-ISG20 inhibits influenza a virus replication by enhancing ISG20 expression. J Virol. 2018;92:0053918.
Article
Google Scholar
Chen J, Shi XB, Zhang XZ, Wang AP, Wang L, Yang YY, Deng RG, Zhang GP. MicroRNA 373 facilitates the replication of porcine reproductive and respiratory syndrome virus by its negative regulation of type I interferon induction. J Virol. 2017;91:01311.
Google Scholar
Dokland T. The structural biology of prrsv. Virus Res. 2010;154(1–2):86–97.
Article
CAS
Google Scholar
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009;458:223–7.
Article
CAS
Google Scholar
Gao J, Pan Y, Xu Y, Zhang W, Wang Y. Unveiling the long non-coding RNA profile of porcine reproductive and respiratory syndrome virus-infected porcine alveolar macrophages. BMC Genomics. 2021;22:177.
Article
CAS
Google Scholar
Kim O, Sun Y, Lai FW, Song C, Yoo D. Modulation of type I interferon induction by porcine reproductive and respiratory syndrome virus and degradation of CREB-binding protein by non-structural protein 1 in MARC-145 and HeLa cells. Virology. 2010;402:315–26.
Article
CAS
Google Scholar
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35:W345–9.
Article
Google Scholar
Li AM, Zhang JY, Zhou ZY, Wang L, Liu YJ, Liu YJ. ALDB: a domestic-animal long noncoding RNA database. PLOS ONE. 2015;10:0124003.
Google Scholar
Li X, Guo G, Lu M, Chai W, Ye X. Lnc-MxA inhibits IFN-β transcription via forming RNA-DNA triplexes at its promoter. J Virol. 2019;93:00786.
Google Scholar
Li Y, Wang X, Bo K, Wang X, Tang B, Yang B, Jiang W, Jiang P. Emergence of a highly pathogenic porcine reproductive and respiratory syndrome virus in the Mid-Eastern region of China. Vet J. 2007;174:577–84.
Article
CAS
Google Scholar
Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011;27:I275–82.
Article
CAS
Google Scholar
Luo XG, Chen XX, Qiao SL, Li R, Xie S, Zhou XY, Deng RG, Zhou EM, Zhang GP. Porcine reproductive and respiratory syndrome virus enhances self-replication via AP-1-dependent induction of SOCS1. J Immunol. 2020;204:394–407.
Article
CAS
Google Scholar
Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155–9.
Article
CAS
Google Scholar
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49:D412–9.
Article
CAS
Google Scholar
Nishitsuji H, Ujino S, Yoshio S, Sugiyama M, Mizokami M, Kanto T, Shimotohno K. Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc Natl Acad Sci USA. 2016;113:10388–93.
Article
CAS
Google Scholar
Ouyang J, Zhu X, Chen Y, Wei H, Chen Q, Chi X, Qi B, Zhang L, Zhao Y, Gao GF, Wang G, Chen JL. NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription. Cell Host Microbe. 2014;16:616–26.
Article
CAS
Google Scholar
Sagong M, Lee C. Porcine reproductive and respiratory syndrome virus nucleocapsid protein modulates interferon-beta production by inhibiting IRF3 activation in immortalized porcine alveolar macrophages. Arch Virol. 2011;156:2187–95.
Article
CAS
Google Scholar
Satpathy AT, Chang HY. Long noncoding RNA in hematopoiesis and immunity. Immunity. 2015;42:792–804.
Article
CAS
Google Scholar
Snijder EJ, Kikkert M, Fang Y. Arterivirus molecular biology and pathogenesis. J Gen Virol. 2013;94:2141–63.
Article
CAS
Google Scholar
Sun Y, Han MY, Kim C, Calvert JG, Yoo D. Interplay between interferon-mediated innate immunity and porcine reproductive and respiratory syndrome virus. Viruses-Basel. 2012;4:424–46.
Article
CAS
Google Scholar
Sun Z, Chen Z, Lawson SR, Fang Y. The cysteine protease domain of porcine reproductive and respiratory syndrome virus nonstructural protein 2 possesses deubiquitinating and interferon antagonism functions. J Virol. 2010;84:7832–46.
Article
CAS
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-U174.
Article
CAS
Google Scholar
Wang J, Zhang YX, Li QJ, Zhao JY, Yi DR, Ding JW, Zhao F, Hu SQ, Zhou JM, Deng T, Li XY, Guo F, Liang C, Cen S. Influenza virus exploits an interferon-independent lncRNA to preserve viral RNA synthesis through stabilizing viral RNA polymerase PB1. Cell Rep. 2019;27:3295.
Article
CAS
Google Scholar
Wang P, Xu JF, Wang YJ, Cao XT. An interferon-independent lncRNA promotes viral replication by modulating cellular metabolism. Science. 2017;358:1051–5.
Article
CAS
Google Scholar
Wang Y, Jing N, Willard B, Xin W, Stark GR. Negative regulation of type i ifn signaling by phosphorylation of stat2 on t387. EMBO J. 2017;36:202–12.
Article
CAS
Google Scholar
Wensvoort G, Terpstra C, Pol JM, ter Laak EA, Bloemraad M, de Kluyver EP, Kragten C, van Buiten L, den Besten A, Wagenaar F, et al. Mystery swine disease in the Netherlands: the isolation of Lelystad virus. Vet Q. 1991;13:121–30.
Article
CAS
Google Scholar
Wilkinson JM, Bao H, Ladinig A, Hong LJ, Stothard P, Lunney JK, Plastow GS, Harding JCS. Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus. BMC Genomics. 2016;17:1–7.
Article
Google Scholar
Wu JJ, Peng XW, Qiao M, Zhao HZ, Li MB, Liu GS, Mei SQ. Genome-wide analysis of long noncoding RNA and mRNA profiles in PRRSV-infected porcine alveolar macrophages. Genomics. 2020;112:1879–88.
Article
CAS
Google Scholar
Xiao SQ, Wang X, Ni HB, Li N, Zhang AK, Liu HL, Pu FX, Xu LL, Gao JM, Zhao Q, Mu Y, Wang CB, Sun YN, Du TF, Xu XG, Zhang GP, Hiscox JA, Goodfellow IG, Zhou EM. MicroRNA miR-24-3p promotes porcine reproductive and respiratory syndrome virus replication through suppression of heme oxygenase-1 expression. J Virol. 2015;89:4494–503.
Article
CAS
Google Scholar
Xie C, Mao XZ, Huang JJ, Ding Y, Wu JM, Dong S, Kong L, Gao G, Li CY, Wei LP. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39:W316–22.
Article
CAS
Google Scholar
Yang L, He J, Wang R, Zhang X, Lin S, Ma Z, Zhang Y. Nonstructural protein 11 of porcine reproductive and respiratory syndrome virus induces STAT2 degradation to inhibit interferon signaling. J Virol. 2019;93:01352.
Google Scholar
Zhang J, Sun P, Gan L, Bai W, Wang Z, Li D, Cao Y, Fu Y, Li P, Bai X, Ma X, Bao H, Chen Y, Liu Z, Lu Z. Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing. Sci Rep. 2017;7:4952.
Article
Google Scholar
Zhen YR, Wang FQ, Liang W, Liu JJ, Gao GL, Wang Y, Xu XW, Su QJ, Zhang QD, Liu B. Identification of differentially expressed non-coding RNA in porcine alveolar macrophages from Tongcheng and large white pigs responded to PRRSV. Sci Rep-Uk. 2018;8:1–11.
CAS
Google Scholar
Zhou L, Wang Z, Ding Y, Ge X, Guo X, Yang H. NADC30-like strain of porcine reproductive and respiratory syndrome virus, China. Emerg Infect Dis. 2015;21:2256–7.
Article
CAS
Google Scholar