The role of lncRNAs in innate immunity and inflammation

References

• Kagan JC, Barton GM. Emerging principles governing signal transduction by pattern-recognition receptors. Cold Spring Harb Perspect Biol. 2014;7:a016253.
   PubMed Web of Science ®Google Scholar
• Iwasaki A, Medzhitov R. Regulation of adaptive immunity by the innate immune system. Science. 2010;327:291–295.
   PubMed Web of Science ®Google Scholar
• Liu T, Zhang L, Joo D, et al. NF-kappaB signaling in inflammation. Signal Transduct Target Ther. 2017;2. DOI:10.1038/sigtrans.2017.23
   Web of Science ®Google Scholar
• Marchese FP, Raimondi I, Huarte M. The multidimensional mechanisms of long noncoding RNA function. Genome Biol. 2017;18:206.
   PubMed Web of Science ®Google Scholar
• Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012;81:145–166.
   PubMed Web of Science ®Google Scholar
• Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet. 2015;16:421–433.
   PubMed Web of Science ®Google Scholar
• Mehta A, Baltimore D. MicroRNAs as regulatory elements in immune system logic. Nat Rev Immunol. 2016;16:279–294.
   PubMed Web of Science ®Google Scholar
• O’Connell RM, Taganov KD, Boldin MP, et al. MicroRNA-155 is induced during the macrophage inflammatory response. Proc Natl Acad Sci USA. 2007;104:1604–1609.
   PubMed Web of Science ®Google Scholar
• Taganov KD, Boldin MP, Chang KJ, et al. NF-kappa B-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci USA. 2006;103:12481–12486.
   PubMed Web of Science ®Google Scholar
• Schulte LN, Westermann AJ, Vogel J. Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing. Nucleic Acids Res. 2013;41:542–553.
   PubMed Web of Science ®Google Scholar
• Janga H, Aznaourova M, Boldt F, et al. Cas9-mediated excision of proximal DNaseI/H3K4me3 signatures confers robust silencing of microRNA and long non-coding RNA genes. PloS One. 2018;13:e0193066.
   PubMed Web of Science ®Google Scholar
• Schulte LN, Eulalio A, Mollenkopf HJ, et al. Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family. Embo J. 2011;30:1977–1989.
   PubMed Web of Science ®Google Scholar
• Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22:1775–1789.
   PubMed Web of Science ®Google Scholar
• Hon CC, Ramilowski JA, Harshbarger J, et al. An atlas of human long non-coding RNAs with accurate 5ʹ ends. Nature. 2017;543:199–204.
   PubMed Web of Science ®Google Scholar
• Giral H, Landmesser U, Kratzer A. Into the wild: GWAS exploration of Non-coding RNAs. Front Cardiovasc Med. 2018;5:181.
   PubMed Web of Science ®Google Scholar
• Castellanos-Rubio A, Ghosh S. Disease-associated SNPs in inflammation-related lncRNAs. Front Immunol. 2019;10:420.
   PubMed Web of Science ®Google Scholar
• Carlevaro-Fita J, Johnson R. Global positioning system: understanding long noncoding RNAs through subcellular localization. Mol Cell. 2019;73:869–883.
   PubMed Web of Science ®Google Scholar
• Krawczyk M, Emerson BM. p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes. Elife. 2014;3:e01776.
   PubMed Web of Science ®Google Scholar
• Rinn JL, Kertesz M, Wang JK, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007;129:1311–1323.
   PubMed Web of Science ®Google Scholar
• Zhao J, Sun BK, Erwin JA, et al. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science. 2008;322:750–756.
   PubMed Web of Science ®Google Scholar
• Tsai MC, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010;329:689–693.
   PubMed Web of Science ®Google Scholar
• Chen LL. Linking long noncoding RNA localization and function. Trends Biochem Sci. 2016;41:761–772.
   PubMed Web of Science ®Google Scholar
• Fox AH, Nakagawa S, Hirose T, et al. Paraspeckles: where long noncoding RNA meets phase separation. Trends Biochem Sci. 2018;43:124–135.
   PubMed Web of Science ®Google Scholar
• Thapa P, Shanmugam N, Pokrzywa W. Ubiquitin signaling regulates RNA biogenesis, processing, and metabolism. BioEssays. 2020;42:e1900171.
   PubMed Web of Science ®Google Scholar
• Chen J, Brunner AD, Cogan JZ, et al. Pervasive functional translation of noncanonical human open reading frames. Science. 2020;367:1140–1146.
   PubMed Web of Science ®Google Scholar
• Jackson R, Kroehling L, Khitun A, et al. The translation of non-canonical open reading frames controls mucosal immunity. Nature. 2018;564:434–438.
   PubMed Web of Science ®Google Scholar
• Aznaourova M, Janga H, Sefried S, et al. Noncoding RNA MaIL1 is an integral component of the TLR4-TRIF pathway. Proc Natl Acad Sci USA. 2020;117:9042–9053.
   PubMed Web of Science ®Google Scholar
• van Heesch S, van Iterson M, Jacobi J, et al. Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome Biol. 2014;15:R6.
   PubMed Web of Science ®Google Scholar
• Carlevaro-Fita J, Rahim A, Guigo R, et al. Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. Rna. 2016;22:867–882.
   PubMed Web of Science ®Google Scholar
• Wang HV, Chekanova JA. An overview of methodologies in studying lncRNAs in the high-throughput era: when acronyms ATTACK!. Methods Mol Biol. 2019;1933:1–30.
   PubMedGoogle Scholar
• Gonzalez-Moro I, Olazagoitia-Garmendia A, Colli ML, et al. The T1D-associated lncRNA Lnc13 modulates human pancreatic beta cell inflammation by allele-specific stabilization of STAT1 mRNA. Proc Natl Acad Sci USA. 2020;117:9022–9031.
   PubMed Web of Science ®Google Scholar
• Atianand MK, Hu W, Satpathy AT, et al. A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation. Cell. 2016;165:1672–1685.
   PubMed Web of Science ®Google Scholar
• Takeuchi O, Akira S. Pattern recognition receptors and inflammation. Cell. 2010;140:805–820.
   PubMed Web of Science ®Google Scholar
• Motwani M, Pesiridis S, Fitzgerald KA. DNA sensing by the cGAS-STING pathway in health and disease. Nat Rev Genet. 2019;20:657–674.
   PubMed Web of Science ®Google Scholar
• Trinchieri G. Type I interferon: friend or foe? J Exp Med. 2010;207:2053–2063.
   PubMed Web of Science ®Google Scholar
• Schneider WM, Chevillotte MD, Rice CM. Interferon-stimulated genes: a complex web of host defenses. Annu Rev Immunol. 2014;32:513–545.
   PubMed Web of Science ®Google Scholar
• Shi JH, Sun SC. Tumor necrosis factor receptor-associated factor regulation of nuclear factor kappaB and mitogen-activated protein kinase pathways. Front Immunol. 2018;9:1849.
   PubMed Web of Science ®Google Scholar
• Turner MD, Nedjai B, Hurst T, et al. Cytokines and chemokines: at the crossroads of cell signalling and inflammatory disease. Biochim Biophys Acta. 2014;1843:2563–2582.
   PubMed Web of Science ®Google Scholar
• Narumiya S, Furuyashiki T. Fever, inflammation, pain and beyond: prostanoid receptor research during these 25 years. Faseb J. 2011;25:813–818.
   PubMed Web of Science ®Google Scholar
• Tanaka T, Narazaki M, Kishimoto T. IL-6 in inflammation, immunity, and disease. Cold Spring Harb Perspect Biol. 2014;6:a016295.
   PubMed Web of Science ®Google Scholar
• Swiecki M, Colonna M. Type I interferons: diversity of sources, production pathways and effects on immune responses. Curr Opin Virol. 2011;1:463–475.
   PubMed Web of Science ®Google Scholar
• Cai B, Cai JP, Luo YL, et al. The specific roles of JAK/STAT signaling pathway in sepsis. Inflammation. 2015;38:1599–1608.
   PubMed Web of Science ®Google Scholar
• Rawlings JS, Rosler KM, Harrison DA. The JAK/STAT signaling pathway. J Cell Sci. 2004;117:1281–1283.
   PubMed Web of Science ®Google Scholar
• Schroder K, Hertzog PJ, Ravasi T, et al. Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol. 2004;75:163–189.
   PubMed Web of Science ®Google Scholar
• Schoggins JW, Rice CM. Interferon-stimulated genes and their antiviral effector functions. Curr Opin Virol. 2011;1:519–525.
   PubMed Web of Science ®Google Scholar
• Gabay C. Interleukin-6 and chronic inflammation. Arthritis Res Ther. 2006;8(Suppl 2):S3.
   PubMed Web of Science ®Google Scholar
• Bhattacharya J, Westphalen K. Macrophage-epithelial interactions in pulmonary alveoli. Semin Immunopathol. 2016;38:461–469.
   PubMed Web of Science ®Google Scholar
• Guilliams M, Thierry GR, Bonnardel J, et al. Establishment and maintenance of the macrophage niche. Immunity. 2020;52:434–451.
   PubMed Web of Science ®Google Scholar
• Schulte LN, Schweinlin M, Westermann AJ, et al. An advanced human intestinal coculture model reveals compartmentalized host and pathogen strategies during salmonella infection. mBio. 2020;11:e03348–19.
   PubMed Web of Science ®Google Scholar
• Roux BT, Heward JA, Donnelly LE, et al. Catalog of differentially expressed long non-coding RNA following activation of human and mouse innate immune response. Front Immunol. 2017;8:1038.
   PubMed Web of Science ®Google Scholar
• Mariotti B, Servaas NH, Rossato M, et al. The long non-coding RNA NRIR drives IFN-response in monocytes: implication for systemic sclerosis. Front Immunol. 2019;10:100.
   PubMed Web of Science ®Google Scholar
• Lin H, Jiang M, Liu L, et al. The long noncoding RNA Lnczc3h7a promotes a TRIM25-mediated RIG-I antiviral innate immune response. Nat Immunol. 2019;20:812–823.
   Web of Science ®Google Scholar
• Zhou Y, Li M, Xue Y, et al. Interferon-inducible cytoplasmic lncLrrc55-AS promotes antiviral innate responses by strengthening IRF3 phosphorylation. Cell Res. 2019;29:641–654.
   PubMed Web of Science ®Google Scholar
• Jiang M, Zhang S, Yang Z, et al. Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response. Cell. 2018;173:906–19 e13.
   PubMed Web of Science ®Google Scholar
• Zhang K, Shi Z, Zhang M, et al. Silencing lncRNA Lfar1 alleviates the classical activation and pyoptosis of macrophage in hepatic fibrosis. Cell Death Dis. 2020;11:132.
   PubMed Web of Science ®Google Scholar
• NE II, Heward JA, Roux B, et al. Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun. 2014;5:3979.
   PubMed Web of Science ®Google Scholar
• Castellanos-Rubio A, Kratchmarov R, Sebastian M, et al. Cytoplasmic form of Carlr lncRNA facilitates inflammatory gene expression upon NF-kappaB activation. J Iimmunol. 2017;199:581–588.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Chao TC, Patil VS, et al. The long noncoding RNA ROCKI regulates inflammatory gene expression. Embo J. 2019;38. DOI:10.15252/embj.2018100041.
   Web of Science ®Google Scholar
• Liu X, Lu Y, Zhu J, et al. A long noncoding RNA, antisense IL-7, promotes inflammatory gene transcription through facilitating histone acetylation and switch/sucrose nonfermentable chromatin remodeling. J Iimmunol. 2019;203:1548–1559.
   Web of Science ®Google Scholar
• Ma S, Ming Z, Gong AY, et al. A long noncoding RNA, lincRNA-Tnfaip3, acts as a coregulator of NF-kappaB to modulate inflammatory gene transcription in mouse macrophages. Faseb J. 2017;31:1215–1225.
   PubMed Web of Science ®Google Scholar
• Zhou B, Qi F, Wu F, et al. Endogenous retrovirus-derived long noncoding RNA enhances innate immune responses via derepressing RELA expression. mBio. 2019;10. DOI:10.1128/mBio.00937-19.
   Web of Science ®Google Scholar
• Covarrubias S, Robinson EK, Shapleigh B, et al. CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-kappaB reporter. J Biol Chem. 2017;292:20911–20920.
   PubMed Web of Science ®Google Scholar
• Carpenter S, Aiello D, Atianand MK, et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science. 2013;341:789–792.
   PubMed Web of Science ®Google Scholar
• Hu G, Gong AY, Wang Y, et al. LincRNA-Cox2 promotes late inflammatory gene transcription in macrophages through modulating SWI/SNF-mediated chromatin remodeling. J Iimmunol. 2016;196:2799–2808.
   PubMed Web of Science ®Google Scholar
• Chan J, Atianand M, Jiang Z, et al. Cutting edge: a natural antisense transcript, AS-IL1alpha, controls inducible transcription of the proinflammatory cytokine IL-1alpha. J Iimmunol. 2015;195:1359–1363.
   PubMed Web of Science ®Google Scholar
• Lu Y, Liu X, Xie M, et al. The NF-kappaB-responsive long noncoding RNA FIRRE regulates posttranscriptional regulation of inflammatory gene expression through interacting with hnRNPU. J Iimmunol. 2017;199:3571–3582.
   PubMed Web of Science ®Google Scholar
• Lewandowski JP, Lee JC, Hwang T, et al. The firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun. 2019;10:5137.
   PubMed Web of Science ®Google Scholar
• Jia Y, Li Z, Cai W, et al. SIRT1 regulates inflammation response of macrophages in sepsis mediated by long noncoding RNA. Biochimica Et Biophysica Acta Mol Basis Dis. 2018;1864:784–792.
   PubMed Web of Science ®Google Scholar
• Agliano F, Fitzgerald KA, Vella AT, et al. Long non-coding RNA LincRNA-EPS inhibits host defense against listeria monocytogenes infection. Front Cell Infect Microbiol. 2019;9:481.
   PubMed Web of Science ®Google Scholar
• Castellanos-Rubio A, Fernandez-Jimenez N, Kratchmarov R, et al. A long noncoding RNA associated with susceptibility to celiac disease. Science. 2016;352:91–95.
   PubMed Web of Science ®Google Scholar
• Li Z, Chao TC, Chang KY, et al. The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. 2014;111:1002–1007.
   PubMed Web of Science ®Google Scholar
• Du M, Yuan L, Tan X, et al. The LPS-inducible lncRNA Mirt2 is a negative regulator of inflammation. Nat Commun. 2017;8:2049.
   PubMed Web of Science ®Google Scholar
• Lu J, Wu X, Hong M, et al. A potential suppressive effect of natural antisense IL-1beta RNA on lipopolysaccharide-induced IL-1beta expression. J Iimmunol. 2013;190:6570–6578.
   PubMed Web of Science ®Google Scholar
• Stratigi K, Kapsetaki M, Aivaliotis M, et al. Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression. Proc Natl Acad Sci USA. 2015;112:E1577–86.
   PubMed Web of Science ®Google Scholar
• Stathopoulou C, Kapsetaki M, Stratigi K, et al. Long non-coding RNA SeT and miR-155 regulate the Tnfalpha gene allelic expression profile. PloS One. 2017;12:e0184788.
   PubMed Web of Science ®Google Scholar
• Thapa B, Lee K. Metabolic influence on macrophage polarization and pathogenesis. BMB Rep. 2019;52:360–372.
   PubMed Web of Science ®Google Scholar
• Nakayama Y, Fujiu K, Yuki R, et al. A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation. Proc Natl Acad Sci USA. 2020;117:14365–14375.
   PubMed Web of Science ®Google Scholar
• Washietl S, Kellis M, Garber M. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res. 2014;24:616–628.
   PubMed Web of Science ®Google Scholar
• Zhang X, Lian Z, Padden C, et al. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood. 2009;113:2526–2534.
   PubMed Web of Science ®Google Scholar
• Wei S, Zhao M, Wang X, et al. PU.1 controls the expression of long noncoding RNA HOTAIRM1 during granulocytic differentiation. J Hematol Oncol. 2016;9:44.
   PubMed Web of Science ®Google Scholar
• Panopoulos AD, Bartos D, Zhang L, et al. Control of myeloid-specific integrin alpha Mbeta 2 (CD11b/CD18) expression by cytokines is regulated by Stat3-dependent activation of PU.1. J Biol Chem. 2002;277:19001–19007.
   PubMed Web of Science ®Google Scholar
• Kotzin JJ, Spencer SP, McCright SJ, et al. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature. 2016;537:239–243.
   PubMed Web of Science ®Google Scholar
• Wagner LA, Christensen CJ, Dunn DM, et al. EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood. 2007;109:5191–5198.
   PubMed Web of Science ®Google Scholar
• Wang P, Xue Y, Han Y, et al. The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science. 2014;344:310–313.
   PubMed Web of Science ®Google Scholar
• Zhang M, Zheng Y, Sun Y, et al. Knockdown of NEAT1 induces tolerogenic phenotype in dendritic cells by inhibiting activation of NLRP3 inflammasome. Theranostics. 2019;9:3425–3442.
   PubMed Web of Science ®Google Scholar
• Atri C, Guerfali FZ, Laouini D. Role of human macrophage polarization in inflammation during infectious diseases. Int J Mol Sci. 2018;19:1801.
   Web of Science ®Google Scholar
• Chen Y, Li H, Ding T, et al. Lnc-M2 controls M2 macrophage differentiation via the PKA/CREB pathway. Mol Immunol. 2020;124:142–152.
   PubMed Web of Science ®Google Scholar
• Pei W, Zhang Y, Li X, et al. LncRNA AK085865 depletion ameliorates asthmatic airway inflammation by modulating macrophage polarization. Int Immunopharmacol. 2020;83:106450.
   PubMed Web of Science ®Google Scholar
• Kotredes KP, Thomas B, Gamero AM. The protective role of type I interferons in the gastrointestinal tract. Front Immunol. 2017;8:410.
   PubMed Web of Science ®Google Scholar
• Morchikh M, Cribier A, Raffel R, et al. HEXIM1 and NEAT1 long non-coding RNA form a multi-subunit complex that regulates DNA-mediated innate immune response. Mol Cell. 2017;67:387–99 e5.
   PubMed Web of Science ®Google Scholar
• Ahn J, Barber GN. STING signaling and host defense against microbial infection. Exp Mol Med. 2019;51:1–10.
   Web of Science ®Google Scholar
• Ma H, Han P, Ye W, et al. The long noncoding RNA NEAT1 exerts antihantaviral effects by acting as positive feedback for RIG-I signaling. J Virol. 2017;91:e02250–16.
   Web of Science ®Google Scholar
• Zhao L, Xia M, Wang K, et al. A long non-coding RNA IVRPIE promotes host antiviral immune responses through regulating interferon beta1 and ISG expression. Front Microbiol. 2020;11:260.
   PubMed Web of Science ®Google Scholar
• 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;16:616–626.
   PubMed Web of Science ®Google Scholar
• Wang P, Xu J, Wang Y, et al. An interferon-independent lncRNA promotes viral replication by modulating cellular metabolism. Science. 2017;358:1051–1055.
   PubMed Web of Science ®Google Scholar
• Wang J, Cen S. Roles of lncRNAs in influenza virus infection. Emerg Microbes Infect. 2020;9:1407–1414.
   PubMed Web of Science ®Google Scholar
• Xie Q, Chen S, Tian R, et al. Long noncoding RNA ITPRIP-1 positively regulates the innate immune response through promotion of oligomerization and activation of MDA5. J Virol. 2018;92. DOI:10.1128/JVI.00507-18.
   Web of Science ®Google Scholar
• Wang Q, Zhang D, Feng W, et al. Long noncoding RNA TSPOAP1 antisense RNA 1 negatively modulates type I IFN signaling to facilitate influenza A virus replication. J Med Virol. 2019:1–10.
   Google Scholar
• Li X, Guo G, Lu M, et al. Long noncoding RNA Lnc-MxA inhibits beta interferon transcription by forming RNA-DNA triplexes at its promoter. J Virol. 2019;93. DOI:10.1128/JVI.00786-19.
   Web of Science ®Google Scholar
• Fan J, Cheng M, Chi X, et al. A human long non-coding RNA LncATV promotes virus replication through restricting RIG-I-mediated innate immunity. Front Immunol. 2019;10:1711.
   PubMed Web of Science ®Google Scholar
• Carnero E, Barriocanal M, Prior C, et al. Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication. EMBO Rep. 2016;17:1013–1028.
   PubMed Web of Science ®Google Scholar
• Kambara H, Niazi F, Kostadinova L, et al. Negative regulation of the interferon response by an interferon-induced long non-coding RNA. Nucleic Acids Res. 2014;42:10668–10680.
   PubMed Web of Science ®Google Scholar
• Nishitsuji H, Ujino S, Yoshio S, et al. Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc Natl Acad Sci USA. 2016;113:10388–10393.
   PubMed Web of Science ®Google Scholar
• Lentsch AB, Ward PA. Regulation of inflammatory vascular damage. J Pathol. 2000;190:343–348.
   PubMed Web of Science ®Google Scholar
• Luissint AC, Parkos CA, Nusrat A. Inflammation and the intestinal barrier: leukocyte-epithelial cell interactions, cell junction remodeling, and mucosal repair. Gastroenterology. 2016;151:616–632.
   PubMed Web of Science ®Google Scholar
• 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;53:393–406.
   PubMed Web of Science ®Google Scholar
• Imamura K, Takaya A, Ishida YI, et al. Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs. Embo J. 2018;37:e97723.
   Web of Science ®Google Scholar
• Taniguchi K, Karin M. NF-kappa B, inflammation, immunity and cancer: coming of age. Nat Rev Immunol. 2018;18:309–324.
   PubMed Web of Science ®Google Scholar
• Liu B, Sun L, Liu Q, et al. A cytoplasmic NF-kappaB interacting long noncoding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis. Cancer Cell. 2015;27:370–381.
   PubMed Web of Science ®Google Scholar
• Ye M, Xie M, Zhu J, et al. LPS-inducible lncRNA TMC3-AS1 negatively regulates the expression of IL-10. Front Immunol. 2020;11:1418.
   PubMed Web of Science ®Google Scholar
• Cui H, Xie N, Tan Z, et al. The human long noncoding RNA lnc-IL7R regulates the inflammatory response. Eur J Immunol. 2014;44:2085–2095.
   PubMed Web of Science ®Google Scholar
• Rapicavoli NA, Qu K, Zhang J, et al. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife. 2013;2:e00762.
   PubMed Web of Science ®Google Scholar
• Tong Q, Gong AY, Zhang XT, et al. LincRNA-Cox2 modulates TNF-alpha-induced transcription of Il12b gene in intestinal epithelial cells through regulation of Mi-2/NuRD-mediated epigenetic histone modifications. Faseb J. 2016;30:1187–1197.
   PubMed Web of Science ®Google Scholar
• Rahman A, Tiwari A, Narula J, et al. Importance of feedback and feedforward loops to adaptive immune response modeling. CPT Pharmacometrics Syst Pharmacol. 2018;7:621–628.
   PubMedGoogle Scholar
• Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol. 2020. DOI:10.1080/15476286.2020.1838783
   PubMed Web of Science ®Google Scholar
• Kaiko GE, Horvat JC, Beagley KW, et al. Immunological decision-making: how does the immune system decide to mount a helper T-cell response? Immunology. 2008;123:326–338.
   PubMed Web of Science ®Google Scholar
• Hogan PG. Calcium-NFAT transcriptional signalling in T cell activation and T cell exhaustion. Cell Calcium. 2017;63:66–69.
   PubMed Web of Science ®Google Scholar
• Willingham AT, Orth AP, Batalov S, et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science. 2005;309:1570–1573.
   PubMed Web of Science ®Google Scholar
• Sharma S, Findlay GM, Bandukwala HS, et al. Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex. Proc Natl Acad Sci USA. 2011;108:11381–11386.
   PubMed Web of Science ®Google Scholar
• Huang D, Chen J, Yang L, et al. NKILA lncRNA promotes tumor immune evasion by sensitizing T cells to activation-induced cell death. Nat Immunol. 2018;19:1112–1125.
   PubMed Web of Science ®Google Scholar
• Ivashkiv LB. IFNgamma: signalling, epigenetics and roles in immunity, metabolism, disease and cancer immunotherapy. Nat Rev Immunol. 2018;18:545–558.
   PubMed Web of Science ®Google Scholar
• Vigneau S, Rohrlich PS, Brahic M, et al. Tmevpg1, a candidate gene for the control of Theiler’s virus persistence, could be implicated in the regulation of gamma interferon. J Virol. 2003;77:5632–5638.
   PubMed Web of Science ®Google Scholar
• Padua D, Mahurkar-Joshi S, Law IK, et al. A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation. Am J Physiol Gastrointest Liver Physiol. 2016;311:G446–57.
   PubMed Web of Science ®Google Scholar
• Collier SP, Collins PL, Williams CL, et al. Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. J Iimmunol. 2012;189:2084–2088.
   PubMed Web of Science ®Google Scholar
• Petermann F, Pekowska A, Johnson CA, et al. The magnitude of IFN-gamma responses is fine-tuned by DNA architecture and the non-coding transcript of Ifng-as1. Mol Cell. 2019;75:1229–42 e5.
   PubMed Web of Science ®Google Scholar
• Gomez JA, Wapinski OL, Yang YW, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell. 2013;152:743–754.
   PubMed Web of Science ®Google Scholar
• Mirza AH, Berthelsen CH, Seemann SE, et al. Transcriptomic landscape of lncRNAs in inflammatory bowel disease. Genome Med. 2015;7:39.
   PubMed Web of Science ®Google Scholar
• Stein N, Berhani O, Schmiedel D, et al. IFNG-AS1 enhances interferon gamma production in human natural killer cells. iScience. 2019;11:466–473.
   PubMed Web of Science ®Google Scholar
• Kotzin JJ, Iseka F, Wright J, et al. The long noncoding RNA Morrbid regulates CD8 T cells in response to viral infection. Proc Natl Acad Sci U S A. 2019;116:11916–11925.
   PubMed Web of Science ®Google Scholar
• Caligiuri MA. Human natural killer cells. Blood. 2008;112:461–469.
   PubMed Web of Science ®Google Scholar
• Lo Nigro C, Macagno M, Sangiolo D, et al. NK-mediated antibody-dependent cell-mediated cytotoxicity in solid tumors: biological evidence and clinical perspectives. Ann Transl Med. 2019;7:105.
   PubMed Web of Science ®Google Scholar
• Zhang R, Ni F, Fu B, et al. A long noncoding RNA positively regulates CD56 in human natural killer cells. Oncotarget. 2016;7:72546–72558.
   PubMedGoogle Scholar
• Cooper GM, Brown CD. Qualifying the relationship between sequence conservation and molecular function. Genome Res. 2008;18:201–205.
   PubMed Web of Science ®Google Scholar
• Kapusta A, Feschotte C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet. 2014;30:439–452.
   PubMed Web of Science ®Google Scholar
• Enard D, Cai L, Gwennap C, et al. Viruses are a dominant driver of protein adaptation in mammals. Elife. 2016;5. DOI:10.7554/eLife.12469
   PubMed Web of Science ®Google Scholar
• Walter Costa MB, Honer Z, Siederdissen C, et al. SSS-test: a novel test for detecting positive selection on RNA secondary structure. Bmc Bioinformatics. 2019;20:151.
   PubMed Web of Science ®Google Scholar
• Doris SM, Smith DR, Beamesderfer JN, et al. Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics. Rna. 2015;21:1719–1730.
   PubMed Web of Science ®Google Scholar
• Diederichs S. The four dimensions of noncoding RNA conservation. Trends Genet. 2014;30:121–123.
   PubMed Web of Science ®Google Scholar
• Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915–1927.
   PubMed Web of Science ®Google Scholar
• Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146:353–358.
   PubMed Web of Science ®Google Scholar
• Seiler J, Breinig M, Caudron-Herger M, et al. The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance. Nucleic Acids Res. 2017;45:5458–5469.
   PubMed Web of Science ®Google Scholar
• Tan Y, Kagan JC. Innate immune signaling organelles display natural and programmable signaling flexibility. Cell. 2019;177:384–98 e11.
   PubMed Web of Science ®Google Scholar
• Smirnov A, Forstner KU, Holmqvist E, et al. Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proc Natl Acad Sci USA. 2016;113:11591–11596.
   PubMed Web of Science ®Google Scholar
• McHugh CA, Guttman M. RAP-MS: a method to identify proteins that interact directly with a specific RNA molecule in cells. Methods Mol Biol. 2018;1649:473–488.
   PubMedGoogle Scholar
• Yi W, Li J, Zhu X, et al. CRISPR-assisted detection of RNA-protein interactions in living cells. Nat Methods. 2020;17:685–688.
   PubMed Web of Science ®Google Scholar
• Consortium EP, Moore JE, Purcaro MJ, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020;583:699–710.
   PubMed Web of Science ®Google Scholar