-
Barriocanal, M., Prats-Mari, L., Razquin, N., Prior, C., Unfried, J.P., Fortes, P., 2022. ISR8/IRF1-AS1 is relevant for IFNalpha and NF-kappaB responses. Front. Immunol. 13, 829335.
-
Batista, P.J., Chang, H.Y., 2013. Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298–1307.
-
Carnero, E., Barriocanal, M., Prior, C., Pablo Unfried, J., Segura, V., Guruceaga, E., Enguita, M., Smerdou, C., Gastaminza, P., Fortes, P., 2016. Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication. EMBO Rep. 17, 1013–1028.
-
Carpenter, S., Aiello, D., Atianand, M.K., Ricci, E.P., Gandhi, P., Hall, L.L., Byron, M., Monks, B., Henry-Bezy, M., Lawrence, J.B., O'neill, L.A., Moore, M.J., Caffrey, D.R., Fitzgerald, K.A., 2013. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341, 789–792.
-
Chen, S., Huang, X., Xie, Q., Liu, Q., Zhu, H., 2022. The role of long noncoding RNA BST2-2 in the innate immune response to viral infection. J. Virol. 96, e0020722.
-
Chiu, H.P., Chiu, H., Yang, C.F., Lee, Y.L., Chiu, F.L., Kuo, H.C., Lin, R.J., Lin, Y.L., 2018. Inhibition of Japanese encephalitis virus infection by the host zinc-finger antiviral protein. PLoS Pathog. 14, e1007166.
-
Covarrubias, S., Robinson, E.K., Shapleigh, B., Vollmers, A., Katzman, S., Hanley, N., Fong, N., Mcmanus, M.T., Carpenter, S., 2017. CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-kappaB reporter. J. Biol. Chem. 292, 20911–20920.
-
Djebali, S., Davis, C.A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G.K., Khatun, J., Williams, B.A., Zaleski, C., Rozowsky, J., Roder, M., Kokocinski, F., Abdelhamid, R.F., Alioto, T., Antoshechkin, I., Baer, M.T., Bar, N.S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M.J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O.J., Park, E., Persaud, K., Preall, J.B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L.H., Shahab, A., Skancke, J., Suzuki, A.M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S.E., Hannon, G., Giddings, M.C., Ruan, Y., Wold, B., Carninci, P., Guigo, R., Gingeras, T.R., 2012.Landscape of transcription in human cells. Nature 489, 101–108.
-
Etebari, K., Hegde, S., Saldana, M.A., Widen, S.G., Wood, T.G., Asgari, S., Hughes, G.L., 2017. Global transcriptome analysis of Aedes aegypti Mosquitoes in response to zika virus infection. mSphere 2 e00456-17.
-
Ghafouri-Fard, S., Hussen, B.M., Jamal, H.H., Taheri, M., Sharifi, G., 2022. The emerging role of non-coding RNAs in the regulation of virus replication and resultant cellular pathologies. Int. J. Mol. Sci. 23, 815.
-
Gomez, J.A., Wapinski, O.L., Yang, Y.W., Bureau, J.F., Gopinath, S., Monack, D.M., Chang, H.Y., Brahic, M., Kirkegaard, K., 2013. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 152, 743–754.
-
Hu, B., Huo, Y., Yang, L., Chen, G., Luo, M., Yang, J., Zhou, J., 2017. ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells. Virol. J. 14, 217.
-
Huang, Y., Lin, Q., Huo, Z., Chen, C., Zhou, S., Ma, X., Gao, H., Lin, Y., Li, X., He, J., Zhang, P., Liu, C., 2020. Inositol-requiring enzyme 1alpha promotes zika virus infection through regulation of stearoyl coenzyme A desaturase 1-mediated lipid metabolism. J. Virol. 94, e01229–20.
-
Huppertz, I., Attig, J., D'ambrogio, A., Easton, L.E., Sibley, C.R., Sugimoto, Y., Tajnik, M., Konig, J., Ule, J., 2014. iCLIP: protein-RNA interactions at nucleotide resolution. Methods 65, 274–287.
-
Imamura, K., Imamachi, N., Akizuki, G., Kumakura, M., Kawaguchi, A., Nagata, K., Kato, A., Kawaguchi, Y., Sato, H., Yoneda, M., Kai, C., Yada, T., Suzuki, Y., Yamada, T., Ozawa, T., Kaneki, K., Inoue, T., Kobayashi, M., Kodama, T., Wada, Y., Sekimizu, K., Akimitsu, N., 2014. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol. Cell. 53, 393–406.
-
Jiang, M., Zhang, S., Yang, Z., Lin, H., Zhu, J., Liu, L., Wang, W., Liu, S., Liu, W., Ma, Y., Zhang, L., Cao, X., 2018. Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response. Cell 173, 906–919.e913.
-
Kambara, H., Niazi, F., Kostadinova, L., Moonka, D.K., Siegel, C.T., Post, A.B., Carnero, E., Barriocanal, M., Fortes, P., Anthony, D.D., Valadkhan, S., 2014. Negative regulation of the interferon response by an interferon-induced long non-coding RNA. Nucleic Acids Res. 42, 10668–10680.
-
Kino, T., Hurt, D.E., Ichijo, T., Nader, N., Chrousos, G.P., 2010. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci.Signal. 3, ra8.
-
Lee, L.J., Komarasamy, T.V., Adnan, N.A.A., James, W., Balasubramaniam, V.R., 2021. Hide and Seek: The Interplay Between Zika Virus and the Host Immune Response. Front Immunol 12, 750365.
-
Li, J., Chen, C., Ma, X., Geng, G., Liu, B., Zhang, Y., Zhang, S., Zhong, F., Liu, C., Yin, Y., Cai, W., Zhang, H., 2016. Long noncoding RNA NRON contributes to HIV-1 latency by specifically inducing tat protein degradation. Nat. Commun. 7, 11730.
-
Li, J., Li, M., Wang, X., Sun, M., Ma, C., Liang, W., Gao, X., Wei, L., 2020. Long noncoding RNA NRAV promotes respiratory syncytial virus replication by targeting the MicroRNA miR-509-3p/rab5c Axis to regulate vesicle transportation. J. Virol. 94, e00113–e00120.
-
Liu, S., Liu, X., Li, J., Zhou, H., Carr, M.J., Zhang, Z., Shi, W., 2019. Long noncoding RNAs:novel regulators of virus-host interactions. Rev. Med. Virol. 29, e2046.
-
Ma, H., Han, P., Ye, W., Chen, H., Zheng, X., Cheng, L., Zhang, L., Yu, L., Wu, X., Xu, Z., Lei, Y., Zhang, F., 2017. The long noncoding RNA NEAT1 exerts antihantaviral effects by acting as positive feedback for RIG-I signaling. J. Virol. 91, e02250–16.
-
Ma, X., Luo, X., Zhou, S., Huang, Y., Chen, C., Huang, C., Shen, L., Zhang, P., Liu, C., 2019. Hydroxycarboxylic acid receptor 2 is a zika virus restriction factor that can Be induced by zika virus infection through the IRE1-XBP1 pathway. Front. Cell. Infect. Microbiol. 9, 480.
-
Ouyang, J., Zhu, X., Chen, Y., Wei, H., Chen, Q., Chi, X., Qi, B., Zhang, L., Zhao, Y., Gao, G.F., Wang, G., Chen, J.L., 2014. NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription. Cell Host Microbe 16, 616–626.
-
Penkala, I., Wang, J., Syrett, C.M., Goetzl, L., Lopez, C.B., Anguera, M.C., 2016. lncRHOXF1, a long noncoding RNA from the X chromosome that suppresses viral response genes during development of the early human placenta. Mol. Cell Biol. 36, 1764–1775.
-
Pierson, T.C., Diamond, M.S., 2018. The emergence of Zika virus and its new clinical syndromes. Nature 560, 573–581.
-
Pierson, T.C., Diamond, M.S., 2020. The continued threat of emerging flaviviruses. Nat. Microbiol. 5, 796–812.
-
Qiu, L., Wang, T., Tang, Q., Li, G., Wu, P., Chen, K., 2018. Long non-coding RNAs:regulators of viral infection and the interferon antiviral response. Front. Microbiol. 9, 1621.
-
Ran, F.A., Hsu, P.D., Wright, J., Agarwala, V., Scott, D.A., Zhang, F., 2013. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281–2308.
-
Rapicavoli, N.A., Qu, K., Zhang, J., Mikhail, M., Laberge, R.M., Chang, H.Y., 2013. A mammalian pseudogene lncRNA at the interface of inflammation and antiinflammatory therapeutics. Elife 2, e00762.
-
Schneider, W.M., Chevillotte, M.D., Rice, C.M., 2014. Interferon-stimulated genes: a complex web of host defenses. Annu. Rev. Immunol. 32, 513–545.
-
Seal, R.L., Chen, L.L., Griffiths-Jones, S., Lowe, T.M., Mathews, M.B., O'reilly, D., Pierce, A.J., Stadler, P.F., Ulitsky, I., Wolin, S.L., Bruford, E.A., 2020. A guide to naming human non-coding RNA genes. EMBO J. 39, e103777.
-
Wang, P., Luo, M.L., Song, E., Zhou, Z., Ma, T., Wang, J., Jia, N., Wang, G., Nie, S., Liu, Y., Hou, F., 2018. Long noncoding RNA lnc-TSI inhibits renal fibrogenesis by negatively regulating the TGF-beta/Smad3 pathway. Sci. Transl. Med. 10, eaat2039.
-
Wang, P., Xu, J., Wang, Y., Cao, X., 2017. An interferon-independent lncRNA promotes viral replication by modulating cellular metabolism. Science 358, 1051–1055.
-
Wang, J., Zhang, Y., Li, Q., Zhao, J., Yi, D., Ding, J., Zhao, F., Hu, S., Zhou, J., Deng, T., Li, X., Guo, F., Liang, C., Cen, S., 2019a. Influenza virus exploits an interferonindependent lncRNA to preserve viral RNA synthesis through stabilizing viral RNA polymerase PB1. Cell Rep. 27, 3295–3304 e3294.
-
Wang, Y., Chen, X., Xie, J., Zhou, S., Huang, Y., Li, Y.P., Li, X., Liu, C., He, J., Zhang, P., 2019b. RNA helicase A is an important host factor involved in dengue virus replication. J. Virol. 93, e01306–e01318.
-
Wang, Y., Huo, Z., Lin, Q., Lin, Y., Chen, C., Huang, Y., Huang, C., Zhang, J., He, J., Liu, C., Zhang, P., 2021. 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. 13, 179–193.
-
Xie, Q., Chen, S., Tian, R., Huang, X., Deng, R., Xue, B., Qin, Y., Xu, Y., Wang, J., Guo, M., Chen, J., Tang, S., Li, G., Zhu, H., 2018. Long noncoding RNA ITPRIP-1 positively regulates the innate immune response through promotion of oligomerization and activation of MDA5. J. Virol. 92, e00507–e00518.
-
Xue, Z., Zhang, Z., Liu, H., Li, W., Guo, X., Zhang, Z., Liu, Y., Jia, L., Li, Y., Ren, Y., Yang, H., Zhang, L., Zhang, Q., Da, Y., Hao, J., Yao, Z., Zhang, R., 2019. lincRNACox2 regulates NLRP3 inflammasome and autophagy mediated neuroinflammation. Cell Death Differ. 26, 130–145.
-
Yang, W., Wu, Y.H., Liu, S.Q., Sheng, Z.Y., Zhen, Z.D., Gao, R.Q., Cui, X.Y., Fan, D.Y., Qin, Z.H., Zheng, A.H., Wang, P.G., An, J., 2020. S100A4+ macrophages facilitate zika virus invasion and persistence in the seminiferous tubules via interferon-gamma mediation. PLoS. Pathog. 16, e1009019.
-
Yin, X., Gao, J., Liu, Z., Han, M., Ji, X., Wang, Z., Li, Y., He, D., Zhang, F., Liu, Q., Xin, T., 2022. Mechanisms of long non-coding RNAs in biological phenotypes and ferroptosis of glioma. Front. Oncol. 12, 941327.
-
Zhang, Q., Chen, C.Y., Yedavalli, V.S., Jeang, K.T., 2013. NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. mBio 4, e00596–512.
-
Zhang, X., Li, G., Chen, G., Zhu, N., Wu, D., Wu, Y., James, T.D., 2021. Recent progresses and remaining challenges for the detection of Zika virus. Med. Res. Rev. 41, 2039–2108.
-
Zheng, H., Chen, C., Luo, Y., Yu, M., He, W., An, M., Gao, B., Kong, Y., Ya, Y., Lin, Y., Li, Y., Xie, K., Huang, J., Lin, T., 2021. Tumor-derived exosomal BCYRN1 activates WNT5A/VEGF-C/VEGFR3 feedforward loop to drive lymphatic metastasis of bladder cancer. Clin. Transl. Med. 11, e497.
-
Zhou, S., Yang, C., Zhao, F., Huang, Y., Lin, Y., Huang, C., Ma, X., Du, J., Wang, Y., Long, G., He, J., Liu, C., Zhang, P., 2019. Double-stranded RNA deaminase ADAR1 promotes the Zika virus replication by inhibiting the activation of protein kinase PKR. J. Biol. Chem. 294, 18168–18180.