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Research Paper

Differential expression of long non-coding RNAs under Peste des petits ruminants virus (PPRV) infection in goats

, ORCID Icon, , , , , , , , , , , , , & show all
Pages 310-322 | Received 02 Dec 2020, Accepted 03 Jan 2022, Published online: 06 Feb 2022

References

  • Gibbs PJ, Taylor WP, Lawman MJP, et al. Classification of peste des petits ruminants virus as the fourth member of the genus Morbillivirus. Intervirology. 1979;11(5):268–274.
  • Banyard AC, Parida S, Batten C, et al. Global distribution of peste des petits ruminants virus and prospects for improved diagnosis and control. J Gen Virol. 2010;91(12):2885–2897.
  • Delil F, Asfaw Y, Gebreegziabher B. Prevalence of antibodies to peste des petits ruminants virus before and during outbreaks of the disease in Awash Fentale district, Afar, Ethiopia. Trop Anim Health Prod. 2012;44(7):1329–1330.
  • Dhar P, Sreenivasa BP, Barrett T, et al. Recent epidemiology of peste des petits ruminants virus (PPRV). Vet Microbiol. 2002;88(2):153–159.
  • Lefevre PC, Diallo A. Peste des petits ruminants. Rev Sci Tech. 1990;9(4):935–981.
  • Nanda YP, Chatterjee A, Purohit AK, et al. The isolation of peste des petits ruminants virus from northern India. Vet Microbiol. 1996;51(3–4):207–216.
  • Singh RP, Saravanan P, Sreenivasa BP, et al. Prevalence and distribution of peste des petits ruminants virus infection in small ruminants in India. Rev Sci Tech. 2004a;23(3):807–819.
  • Truong T, Boshra H, Embury-Hyatt C, et al. Peste des petits ruminants virus tissue tropism and pathogenesis in sheep and goats following experimental infection. PLoS One. 2014;9(1):e87145.
  • Skroblin P, Mayr M. “Going Long”: long Non-Coding RNAs as Biomarkers. Circulationresearch. 2014;115(7):607–609.
  • Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell. 2013;154(1):26–46.
  • Heward JA, Lindsay MA. Long non-coding RNAs in the regulation of the immune response. Trends Immunol. 2014;35(9):408–419.
  • Huarte M, Guttman M, Feldser D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 2010;142(3):409–419.
  • Wang P, YiquanXue YH, Lin L, et al. The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science. 2014;344(6181):310–313.
  • Ginn L, La Montagna M, Wu Q, et al. Diverse roles of long non‐coding RNAs in viral diseases. Rev Med Virol. 2020. Published 2020 Nov 27. DOI:10.1002/rmv.2198.
  • Grace CY, Satpathy AT, Chang HY. Gene regulation in the immune system by long noncoding RNAs. Nat Immunol. 2017;18(9):962.
  • Elling R, Chan J, Fitzgerald KA. Emerging role of long noncoding RNAs as regulators of innate immune cell development and inflammatory gene expression. Eur J Immunol. 2016;46(3):504–512.
  • Ouyang J, Hu J, Chen J-L. lncRNAs regulate the innate immune response to viral infection. WIREs RNA. 2016;7(1):129–143.
  • Wang Y, Huo Z, Lin Q, et al. Positive Feedback Loop of Long Noncoding RNA OASL-IT1 and Innate Immune Response Restricts the Replication of Zika Virus in Epithelial A549 Cells. J Innate Immun. 2021;13(3):179–193.
  • Wang Y, Tian L, Yang Q, et al. LncRNA THUMPD3-AS1 enhances the proliferation and inflammatory response of chondrocytes in osteoarthritis. Int Immunopharmacol. 2021;100:108138.
  • Luo D, Dai W, Feng X, et al. Suppression of lncRNA NLRP3 inhibits NLRP3-triggered inflammatory responses in early acute lung injury. Cell Death Dis. 2021;12(898). DOI:10.1038/s41419-021-04180-y
  • Liu S, Yu T, Zhang Y, et al. Integrated analysis of mRNA and long non-coding RNA expression profiles reveals the potential roles of lncRNA-mRNA network in carp macrophage immune regulation [published online ahead of print, 2021 Sep 23]. In Vitro Cell Dev Biol Anim. 2021;57(8):835–847.
  • Ouyang J, Zhu X, Chen Y, et al. NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription.”. Cell Host Microbe. 2014;16(5):616–626.
  • Imamura K, Imamachi N, Akizuki G, et al. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol Cell. 2014;53(3):393–406.
  • Koufariotis LT, Chen Y-PP, Chamberlain A, et al. A catalogue of novel bovine long noncoding RNA across 18 tissues. PloS One. 2015;10(10):e0141225.
  • Cun-Yuan L, Li X, Liu Z, et al. Identification and characterization of long non-coding RNA in prenatal and postnatal skeletal muscle of sheep. Genomics. 2018;111(2):133–141.
  • Ren H, Wang G, Chen L, et al. Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus). BMC Genomics. 2016;17(1):67.
  • Tang Z, Yang W, Yang Y, et al. Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa. Sci Rep. 2017;7(1):43166.
  • Zeng N, Wang C, Liu S, et al. Transcriptome Analysis Reveals Dynamic Gene Expression Profiles in Porcine Alveolar Macrophages in Response to the Chinese Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus. Biomed Res Int. 2018. DOI:10.1155/2018/1538127
  • Khanduri A, Sahu AR, Wani SA, et al. Dysregulated miRNAome and proteome of PPRV infected goat PBMCs reveal a coordinated immune response. Front Immunol. 2018;9. DOI:10.3389/fimmu.2018.02631.
  • Manjunath S, Mishra BP, Mishra B, et al. Comparative and temporal transcriptome analysis of peste des petits ruminants virus infected goat peripheral blood mononuclear cells. Virus Res. 2017;229:28–40.
  • Manjunath S, Kumar GR, Mishra BP, et al. Genomic analysis of host–Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways. Vet Res. 2015;46(1):15.
  • Pandey A, Sahu AR, Wani SA, et al. Modulation of Host miRNAs Transcriptome in Lung and Spleen of Peste des Petits Ruminants Virus Infected Sheep and Goats. Front Microbiol. 2017;8:1146.
  • Zhan S, Dong Y, and Zhao Wet al, Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genom. 2016; 17: 666(1-10). https://doi.org/10.1186/s12864-016-3009-3
  • Sahu AR, Wani SA, and Saminathan M, et al. Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography. Arch Virol. 2017 Jun;162((6)):1677–1693. doi:10.1007/s00705-017-3288-2.
  • Liu Y, Li M, Bo X, et al. Systematic Analysis of Long Non-Coding RNAs and mRNAs in the Ovaries of Duroc Pigs During Different Follicular Stages Using RNA Sequencing. Int J Mol Sci. 2018;19(6):1722.
  • Heo JB, Sung S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science. 2011;331(6013):76–79.
  • Carnero E, Barriocanal M, Prior C, et al. “Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication.” EMBO reports (2016): e201541763.
  • Imam H, Bano AS, Patel P, et al. The lncRNA NRON modulates HIV-1 replication in a NFAT-dependent manner and is differentially regulated by early and late viral proteins. Sci Rep. 2015;5(1):8639.
  • Pauli A, Eivind Valen MF, Lin MG, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.”. Genome Res. 2012;22(3):577–591.
  • Li T, Wang S, Rimao W, et al. Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing. Genomics. 2012;99(5):292–298.
  • van de Ven R, Oerlemans R, van der Heijden JW, et al. ABC drug transporters and immunity: novel therapeutic targets in autoimmunity and cancer. J Leukoc Biol. 2009;86(5):1075–1087.
  • Van De Ven R, Scheffer GL, Reurs AW, et al. A role for multidrug resistance protein 4 (MRP4; ABCC4) in human dendritic cell migration. Blood J Am Soc Hematol. 2008;112(6):2353–2359.
  • Bourdon M, Manet C, Montagutelli X. Host genetic susceptibility to viral infections: the role of type I interferon induction. Genes Immun. 2020;21(6):365–379.
  • Adolf GR. Human interferon omega–a review. Mult Scler. 1995;1:S44–7.
  • Wittling MC, Cahalan SR, and Levenson EA, et al. Shared and unique features of human Interferon-beta and interferon-alpha subtypes. Front Immunol. 2020;11:605673(1-13).
  • Bailey CC, Zhong G, Huang IC, et al. IFITM-family proteins: the cell’s first line of antiviral defense. Annu Rev Virol. 2014;1(1):261–283.
  • Li FJ, Won WJ, and Becker EJ, et al. Emerging roles for the FCRL family members in lymphocyte biology and disease. Fc Receptors. 2014; 382:29–50.
  • Rostamzadeh D, Kazemi T, Amirghofran Z, et al. Update on Fc receptor-like (FCRL) family: new immunoregulatory players in health and diseases. Expert Opin Ther Targets. 2018;22(6):487–502.
  • Hamdan TA, Lang PA, Lang KS. The diverse functions of the ubiquitous Fcγ receptors and their unique constituent, FcRγ subunit. Pathogens. 2020;9(2):140.
  • Song F, Qian Y, Peng X, et al. The frontline of immune response in peripheral blood. PloS One. 2017;12(8):e0182294.
  • Nitschke L. CD22 and Siglec-G regulate inhibition of B-cell signaling by sialic acid ligand binding and control B-cell tolerance. Glycobiology. 2014;24(9):807–817.
  • Zhang P, Xiaoming L, Tao K, et al. Siglec-10 is associated with survival and natural killer cell dysfunction in hepatocellular carcinoma. J Surg Res. 2015;194(1):107–113.
  • Harjunpää H, Llort Asens M, Guenther C, et al. Cell Adhesion Molecules and Their Roles and Regulation in the Immune and Tumor Microenvironment. Front Immunol. 2019;10:1078.
  • Singh RP, Sreenivasa BP, Dhar P, et al. Development of a monoclonal antibody based competitive-ELISA for detection and titration of antibodies to peste des petits ruminants (PPR) virus. Vet Microbiol. 2004c;98(1):3–15.
  • Dhinakar RG, Nachimuthu K, Mahalinga Nainar A. A simplified objective method for quantification of peste des petits ruminants virus or neutralizing antibody. J Virol Methods. 2000;89(1–2):89–95.
  • Singh RP, Sreenivasa BP, Dhar P, et al. A sandwich-ELISA for the diagnosis of Peste des petits ruminants (PPR) infection in small ruminants using anti-nucleocapsid protein monoclonal antibody. Arch Virol. 2004b;149(11):2155–2170.
  • Bryzghalov O, Makałowska I, Szcześniak MW. lncEvo: automated identification and conservation study of long noncoding RNAs. BMC Bioinformatics. 2021;22(1):1–14.
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357.
  • Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
  • Pertea M, Pertea GM, Antonescu CM, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290–295.
  • Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–515.
  • Pertea G, Pertea M (2020). GFF utilities: gffRead and GffCompare. F1000Research, 9.
  • Patro R, Duggal G, Love MI, et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417–419.
  • Kang YJ, Yang DC, Kong L, et al. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 2017;45(W1):W12–W16.
  • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140.
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842.
  • Bindea G, Mlecnik B, Hackl H, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–1093.
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.