Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316(5830):1484–8.
Article
CAS
PubMed
Google Scholar
Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 2011;147(7):1537–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sarangdhar MA, Chaubey D, Srikakulam N, Pillai B. Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment. Nucleic Acids Res. 2018;46(18):9726–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Golicz AA, Bhalla PL, Singh MB. lncRNAs in plant and animal sexual reproduction. Trends Plant Sci. 2018;23(3):195–205.
Article
CAS
PubMed
Google Scholar
Wang P, Xu JF, Wang YJ, Cao XT. An interferon-independent lncRNA promotes viral replication by modulating cellular metabolism. Science. 2017;358(6366):1051–5.
Article
CAS
PubMed
Google Scholar
Du M, Yuan L, Tan X, Huang DD, Wang XJ, Zheng Z, Mao XX, Li XR, Yang L, Huang K. The LPS-inducible lncRNA Mirt2 is a negative regulator of inflammation. Nat Commun. 2017;8(1):2049.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell. 2005;122(4):553–63.
Article
CAS
PubMed
Google Scholar
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136(4):629–41.
Article
CAS
PubMed
Google Scholar
Wang Y, Xu ZY, Jiang JF, Xu C, Kang JH, Xiao L, Wu MJ, Xiong J, Guo XC, Liu HQ. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell. 2013;25(1):69–80.
Article
CAS
PubMed
Google Scholar
Shan YJ, Ma J, Pan Y, Hu JL, Liu B, Jia L. LncRNA SNHG7 sponges miR-216b to promote proliferation and liver metastasis of colorectal cancer through upregulating GALNT1. Cell Death Dis. 2018;9(7):722–2.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liang LL, Xu JC, Wang M, Xu GR, Zhang N, Wang GZ, Zhao YF. LncRNA HCP5 promotes follicular thyroid carcinoma progression via miRNAs sponge. Cell Death Dis. 2018;9(3):372.
Article
PubMed
PubMed Central
CAS
Google Scholar
Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang H, Huo XS, Yang XR, He J, Cheng LJ, Wang N, Deng X, Jin HJ, Wang N, Wang C, et al. STAT3-mediated upregulation of lncRNA HOXD-AS1 as a ceRNA facilitates liver cancer metastasis by regulating SOX4. Mol Cancer. 2017;16(1):136.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chen DL, Lu YX, Zhang JX, Wei XL, Wang F, Zeng ZL, Pan ZZ, Yuan YF, Wang FH, Pelicano H, et al. Long non-coding RNA UICLM promotes colorectal cancer liver metastasis by acting as a ceRNA for microRNA-215 to regulate ZEB2 expression. Theranostics. 2017;7(19):4836–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abdollahzadeh R, Daraei A, Mansoori Y, Sepahvand M, Amoli MM, Tavakkoly-Bazzaz J. Competing endogenous RNA (ceRNA) cross talk and language in ceRNA regulatory networks: A new look at hallmarks of breast cancer. J Cell Physiol. 2019;234(7):10080–100.
Article
CAS
PubMed
Google Scholar
Luo HL, Yang HZ, Lin Y, Zhang YD, Pan CY, Feng PF, Yu YL, Chen XH. LncRNA and mRNA profiling during activation of tilapia macrophages by HSP70 and Streptococcus agalactiae antigen. Oncotarget. 2017;8(58):98455–70.
Article
PubMed
PubMed Central
Google Scholar
Paneru B, Al-Tobasei R, Palti Y, Wiens GD, Salem M. Differential expression of long non-coding RNAs in three genetic lines of rainbow trout in response to infection with Flavobacterium psychrophilum. Sci Rep. 2016;6:36032.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang BB, Luo G, Zhao LM, Huang LX, Qin YX, Su YQ, Yan QP. Integration of RNAi and RNA-seq uncovers the immune responses of Epinephelus coioides to L321_RS19110 gene of Pseudomonas plecoglossicida. Fish Shellfish Immunol. 2018;81:121–9.
Article
CAS
PubMed
Google Scholar
Tarifeño-Saldivia E, Valenzuela-Miranda D, Gallardo-Escárate C. In the shadow: The emerging role of long non-coding RNAs in the immune response of Atlantic salmon. Dev Comp Immunol. 2017;73:193–205.
Article
PubMed
CAS
Google Scholar
Tarifeño-Saldivia E, Valenzuela-Miranda D, Gallardo-Escárate C. Comparative analysis of long non-coding RNAs in Atlantic and Coho salmon reveals divergent transcriptome responses associated with immunity and tissue repair during sea lice infestation. Dev Comp Immunol. 2018;87:36–50.
Article
CAS
Google Scholar
Wang M, Jiang S, Wu W, Yu F, Chang WG, Li PF, Wang K. Non-coding RNAs function as immune regulators in teleost fish. Front Immunol. 2018;9:2801.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xiu YJ, Jiang GP, Zhou S, Diao J, Liu HJ, Su BF, Li C. Identification of potential immune-related circrna-mirna-mrna regulatory network in intestine of Paralichthys olivaceus during Edwardsiella tarda infection. Front Genet. 2019;10:731.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu B, Yuan R, Liang Z, Zhang TT, Zhu M, Zhang X, Geng W, Fang P, Jiang MS, Wang ZY, et al. Comprehensive analysis of circRNA expression pattern and circRNA-mRNA-miRNA network in Ctenopharyngodon idellus kidney (CIK) cells after grass carp reovirus (GCRV) infection. Aquaculture. 2019;512:734349.
Article
CAS
Google Scholar
Chu Q, Xu TJ, Zheng WW, Chang RJ, Zhang L. Long noncoding RNA MARL regulates antiviral responses through suppression miR-122-dependent MAVS downregulation in lower vertebrates. PLoS Pathog. 2020;16(7):e1008670.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seikai T. Flounder culture and its challenges in Asia. Rev Fish Sci. 2002;10(3–4):421–32.
Article
Google Scholar
Egidius E. Vibriosis - pathogenicity and pathology - a Review. Aquaculture. 1987;67(1–2):15–28.
Article
Google Scholar
Xing J, Xu HS, Tang XQ, Sheng XZ, Zhan WB. A DNA vaccine encoding the VAA gene of Vibrio anguillarum induces a protective immune response in flounder. Front Immunol. 2019;10:499.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xing J, Zhang ZQ, Luo KK, Tang XQ, Sheng XZ, Zhan WB. T and B lymphocytes immune responses in flounder (Paralichthys olivaceus) induced by two forms of outer membrane protein K from Vibrio anguillarum: Subunit vaccine and DNA vaccine. Mol Immunol. 2020;118:40–51.
Article
CAS
PubMed
Google Scholar
Zhou XJ, Xing J, Tang XQ, Zhan WB. Evaluation of bivalent vaccines candidates among VAA, OmpK and OmpR from Vibrio anguillarum in flounder (Paralichthys olivaceus). Dev Comp Immunol. 2018;85:1–9.
Article
CAS
PubMed
Google Scholar
Ning XH, Sun L. Gene network analysis reveals a core set of genes involved in the immune response of Japanese flounder (Paralichthys olivaceus) against Vibrio anguillarum infection. Fish Shellfish Immunol. 2020;98:800–9.
Article
CAS
PubMed
Google Scholar
Ning XH, Sun L. Micro-transcriptome analysis reveals immune-related microrna regulatory networks of Paralichthys olivaceus induced by Vibrio anguillarum infection. Int J Mol Sci. 2020;21:4252.
Article
CAS
PubMed Central
Google Scholar
Khorkova O, Hsiao J, Wahlestedt C. Basic biology and therapeutic implications of lncRNA. Adv Drug Deliv Rev. 2015;87:15–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dorn GW, Matkovich SJ. Menage a Trois intimate relationship among a microRNA, long noncoding RNA, and mRNA. Circ Res. 2014;114(9):1362–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li BJ, Jiang DL, Meng ZN, Zhang Y, Zhu ZX, Lin HR, Xia JH. Genome-wide identification and differentially expression analysis of lncRNAs in tilapia. BMC Genom. 2018;19(1):729.
Article
CAS
Google Scholar
Xu HG, Cao L, Sun B, Wei YL, Liang MQ. Transcriptomic analysis of potential “lncRNA-mRNA” interactions in liver of the marine teleost Cynoglossus semilaevis fed diets with different DHA/EPA ratios. Front Physiol. 2019;10:331.
Article
PubMed
PubMed Central
Google Scholar
Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 2012;22(3):577–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Núñez-Acuña G, Détrée C, Gallardo-Escárate C, Gonçalves AT. Functional diets modulate lncRNA-coding RNAs and gene interactions in the intestine of rainbow trout Oncorhynchus mykiss. Mar Biotechnol. 2017;19(3):287–300.
Article
CAS
Google Scholar
Fitzgerald KA, Caffrey DR. Long noncoding RNAs in innate and adaptive immunity. Curr Opin Immunol. 2014;26:140–6.
Article
CAS
PubMed
Google Scholar
Zhang Y, Cao XT. Long noncoding RNAs in innate immunity. Cell Mol Immunol. 2016;13(2):138–47.
Article
PubMed
CAS
Google Scholar
Basavappa M, Cherry S, Henao-Mejia J. Long noncoding RNAs and the regulation of innate immunity and host-virus interactions. J Leukoc Biol. 2019;106(1):83–93.
Article
CAS
PubMed
Google Scholar
Hacker G. Apoptosis in infection. Microbes Infect. 2018;20(9–10):552–9.
Article
PubMed
CAS
Google Scholar
Wu RH, Sheng XZ, Tang XQ, Xing J, Zhan WB. Transcriptome analysis of flounder (Paralichthys olivaceus) gill in response to lymphocystis disease virus (LCDV) infection: novel insights into fish defense mechanisms. Int J Mol Sci. 2018;19(1):160.
Article
PubMed Central
CAS
Google Scholar
Song YX, Sun JX, Zhao JH, Yang YC, Shi JX, Wu ZH, Chen XW, Gao P, Miao ZF, Wang ZN. Non-coding RNAs participate in the regulatory network of CLDN4 via ceRNA mediated miRNA evasion. Nat Commun. 2017;8(1):289.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu XS, Wang F, Li HF, Hu YP, Jiang L, Zhang F, Li ML, Wang XA, Jin YP, Zhang YJ, et al. LncRNA-PAGBC acts as a microRNA sponge and promotes gallbladder tumorigenesis. Embo Reports. 2017;18(10):1837–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu HN, Jiang Y, Xu XQ, Su XP, Liu Y, Ma YM, Zhao Y, Shen ZY, Huang B, Cao XT. Inducible degradation of lncRNA Sros1 promotes IFN-gamma-mediated activation of innate immune responses by stabilizing Stat1 mRNA. Nat Immunol. 2019;20(12):1621–30.
Article
CAS
PubMed
Google Scholar
Carty M, Goodbody R, Schroder M, Stack J, Moynagh PN, Bowie AG. The human adaptor SARM negatively regulates adaptor protein TRIF-dependent Toll-like receptor signaling. Nat Immunol. 2006;7(10):1074–81.
Article
CAS
PubMed
Google Scholar
Carty M, Bowie AG. SARM: From immune regulator to cell executioner. Biochem Pharmacol. 2019;161:52–62.
Article
CAS
PubMed
Google Scholar
Peng J, Yuan QA, Lin B, Panneerselvam P, Wang XW, Luan XL, Lim SK, Leung BP, Ho B, Ding JL. SARM inhibits both TRIF- and MyD88-mediated AP-1 activation. Eur J Immunol. 2010;40(6):1738–47.
Article
CAS
PubMed
Google Scholar
Yan NN, Su JG, Yang CR, Rao YL, Feng XL, Wan QY, Lei CZ. Grass carp SARM1 and its two splice variants negatively regulate IFN-I response and promote cell death upon GCRV infection at different subcellular locations. Dev Comp Immunol. 2015;48(1):102–15.
Article
CAS
PubMed
Google Scholar
Sottrup-Jensen L, Stepanik TM, Kristensen T, Lonblad PB, Jones CM, Wierzbicki DM, Magnusson S, Domdey H, Wetsel RA, Lundwall A, et al. Common evolutionary origin of alpha 2-macroglobulin and complement components C3 and C4. Proc Natl Acad Sci. 1985;82(1):9–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Armstrong PB, Quigley JP. Alpha2-macroglobulin: an evolutionarily conserved arm of the innate immune system. Dev Comp Immunol. 1999;23(4–5):375–90.
Article
CAS
PubMed
Google Scholar
Pathirana A, Diao M, Huang SB, Zuo LL, Liang YJ. Alpha 2 macroglobulin is a maternally-derived immune factor in amphioxus embryos: New evidence for defense roles of maternal immune components in invertebrate chordate. Fish Shellfish Immunol. 2016;50:21–6.
Article
CAS
PubMed
Google Scholar
Chen JW, Li XJ, Li L, Zhang T, Zhang Q, Wu FM, Wang DY, Hu HZ, Tian CL, Liao DS, et al. Coagulation factors VII, IX and X are effective antibacterial proteins against drug-resistant Gram-negative bacteria. Cell Res. 2019;29(9):711–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arasu A, Kumaresan V, Sathyamoorthi A, Arasu MV, Al-Dhabi NA, Arockiaraj J. Coagulation profile, gene expression and bioinformatics characterization of coagulation factor X of striped murrel Channa striatus. Fish Shellfish Immunol. 2016;55:149–58.
Article
CAS
PubMed
Google Scholar
Ho JL, Reed SG, Wick EA, Giordano M. Granulocyte-macrophage and macrophage colony-stimulating factors activate intramacrophage killing of Leishmania mexicana amazonensis. J Infect Dis. 1990;162(1):224–30.
Article
CAS
PubMed
Google Scholar
Grayfer L, Hanington PC, Belosevic M. Macrophage colony-stimulating factor (CSF-1) induces pro-inflammatory gene expression and enhances antimicrobial responses of goldfish (Carassius auratus L.) macrophages. Fish Shellfish Immunol. 2009;26(3):406–13.
Article
CAS
PubMed
Google Scholar
Spooren A, Kooijman R, Lintermans B, Van Craenenbroeck K, Vermeulen L, Haegeman G, Gerlo S. Cooperation of NFkappaB and CREB to induce synergistic IL-6 expression in astrocytes. Cell Signal. 2010;22(5):871–81.
Article
CAS
PubMed
Google Scholar
Zhang QZ, Shi KC, Yoo D. Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by nsp1. Virology. 2016;489:252–68.
Article
CAS
PubMed
Google Scholar
Lee FS, Peters RT, Dang LC, Maniatis T. MEKK1 activates both IκB kinase α and IκB kinase β. Proc Natl Acad Sci. 1998;95:9319–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao Q, Lee FS. Mitogen-activated protein kinase/ERK kinase kinases 2 and 3 activate nuclear factor-κB though IκB kinase-α and IκB kinase-β. J Biol Chem. 1999;274(13):8355–8.
Article
CAS
PubMed
Google Scholar
Yang JH, Lin Y, Guo ZJ, Cheng J, Huang J, Deng L, Liao W, Chen Z, Liu Z, Su B. The essential role of MEKK3 in TNF-induced NF-kappaB activation. Nat Immunol. 2001;2(7):620–4.
Article
CAS
PubMed
Google Scholar
Li MM, Dong CX, Sun B, Lei HZ, Wang YL, Gong YB, Sun LL, Sun ZW. LncRNA-MALAT1 promotes tumorogenesis of infantile hemangioma by competitively binding miR-424 to stimulate MEKK3/NF-kappaB pathway. Life Sci. 2019;239:116946.
Article
CAS
PubMed
Google Scholar
Kumaresan V, Ravichandran G, Nizam F, Dhayanithi NB, Arasu MV, Al-Dhabi NA, Harikrishnan R, Arockiaraj J. Multifunctional murrel caspase 1, 2, 3, 8 and 9: Conservation, uniqueness and their pathogen-induced expression pattern. Fish Shellfish Immunol. 2016;49:493–504.
Article
CAS
PubMed
Google Scholar
Bamberg A, Redente EF, Groshong SD, Tuder RM, Cool CD, Keith RC, Edelman BL, Black BP, Cosgrove GP, Wynes MW, et al. Protein tyrosine phosphatase-n13 promotes myofibroblast resistance to apoptosis in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2018;198(7):914–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harris G, Bossler A. PTPN13 expression correlates with survival in HPV + HNSCC. Otolaryngol Head Neck Surg. 2010;143(2):P70–0.
Google Scholar
Pageon SV, Tabarin T, Yamamoto Y, Ma Y, Nicovich PR, Bridgeman JS, Cohnen A, Benzing C, Gao Y, Crowther MD, et al. Functional role of T-cell receptor nanoclusters in signal initiation and antigen discrimination. Proc Natl Acad Sci. 2016;113(37):E5454–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang J, Reth M. Receptor dissociation and B-cell activation. Curr Top Microbiol Immunol. 2016;393:27–43.
CAS
PubMed
Google Scholar
Hibi M, Hirano T. Gab-family adapter molecules in signal transduction of cytokine and growth factor receptors, and T and B cell antigen receptors. Leuk Lymphoma. 2000;37(3–4):299–307.
Article
CAS
PubMed
Google Scholar
Chia YL, Ng CH, Lashmit P, Chu KL, Lew QJ, Ho JP, Lim HL, Nissom PM, Stinski MF, Chao SH. Inhibition of human cytomegalovirus replication by overexpression of CREB1. Antiviral Res. 2014;102:11–22.
Article
CAS
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sun L, Luo HT, Bu DC, Zhao GG, Yu KT, Zhang CH, Liu YN, Chen RS, Zhao Y. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;41(17):e166.
Article
CAS
PubMed
PubMed Central
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
PubMed
PubMed Central
Google Scholar
Zhao Y, Li H, Fang SS, Kang Y, Wu W, Hao YJ, Li ZY, Bu DC, Sun NH, Zhang MQ, et al. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res. 2016;44(D1):D203–8.
Article
CAS
PubMed
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Article
CAS
PubMed
PubMed Central
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(5):511–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR. Methods. 2001;25(4):402–8.
Article
CAS
PubMed
Google Scholar
Liu LB, Xiao QH, Gilbert ER, Cui ZF, Zhao XL, Wang Y, Yin HD, Li DY, Zhang HH, Zhu Q. Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis. Sci Rep. 2018;8(1):7231.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lyu KX, Li Y, Xu Y, Yue HJ, Wen YH, Liu TS, Chen SY, Liu QH, Yang WQ, Zhu XL. Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in laryngeal squamous cell carcinoma. RNA Biol. 2020;17(7):977–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Steinfeld I, Navon R, Creech ML, Yakhini Z, Tsalenko A. ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types. Bioinformatics. 2015;31(10):1683–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504.
Article
CAS
PubMed
PubMed Central
Google Scholar