Involvement of paraspeckle components in viral infections

References

• Fox AH, Lam YW, Leung AK, et al. Paraspeckles: a novel nuclear domain. Curr Biol. 2002;12(1):13–12. doi: 10.1016/S0960-9822(01)00632-7
   PubMed Web of Science ®Google Scholar
• Hirose T, Yamazaki T, Nakagawa S. Molecular anatomy of the architectural NEAT1 noncoding RNA: the domains, interactors, and biogenesis pathway required to build phase-separated nuclear paraspeckles. Wiley Interdiscip Rev RNA. 2019;10(6):e1545. doi: 10.1002/wrna.1545
   PubMed Web of Science ®Google Scholar
• McCluggage F, Fox AH. Paraspeckle nuclear condensates: global sensors of cell stress? BioEssays. 2021;43(5):2000245. doi: 10.1002/bies.202000245
   Web of Science ®Google Scholar
• Knott GJ, Bond CS, Fox AH. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res. 2016;44(9):3989–4004. doi: 10.1093/nar/gkw271
   PubMed Web of Science ®Google Scholar
• Shav-Tal Y, Zipori D. PSF and p54nrb/NonO – multi‐functional nuclear proteins. FEBS Lett. 2002;531(2):109–114. doi: 10.1016/S0014-5793(02)03447-6
   PubMed Web of Science ®Google Scholar
• Dong P, Xiong Y, Yue J, et al. Long non-coding RNA NEAT1: a novel target for diagnosis and therapy in human tumors. Front Genet. 2018;9. doi: 10.3389/fgene.2018.00471
   Web of Science ®Google Scholar
• Klec C, Prinz F, Pichler M. Involvement of the long noncoding RNA NEAT 1 in carcinogenesis. Mol Oncol. 2019;13(1):46–60. doi: 10.1002/1878-0261.12404
   PubMed Web of Science ®Google Scholar
• Wang Y, Hu S-B, Wang M-R, et al. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria. Nat Cell Biol. 2018;20(10):1145–1158. doi: 10.1038/s41556-018-0204-2
   PubMed Web of Science ®Google Scholar
• Azam S, Armijo KS, Weindel CG, et al. The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle. Proc Nat Acad Sci. 2024;121(9). doi: 10.1073/pnas.2312587121
   PubMedGoogle Scholar
• Chen LL, Carmichael GG. Altered nuclear retention of mRnas containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell. 2009;35(4):467–478. doi: 10.1016/j.molcel.2009.06.027
   PubMed Web of Science ®Google Scholar
• Prasanth KV, Prasanth SG, Xuan Z, et al. Regulating gene expression through RNA nuclear retention. Cell. 2005;123(2):249–263. doi: 10.1016/j.cell.2005.08.033
   PubMed Web of Science ®Google Scholar
• Zhang Z, Carmichael GG. The fate of dsRNA in the nucleus: a p54nrb-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell. 2001;106(4):465–476. doi: 10.1016/S0092-8674(01)00466-4
   PubMed Web of Science ®Google Scholar
• Chen LL, JN D, Carmichael GG. Alu element-mediated gene silencing. Embo J. 2008;27(12):1694–1705. doi: 10.1038/emboj.2008.94
   PubMed Web of Science ®Google Scholar
• Fortes P, Morris KV. Long noncoding RNAs in viral infections. Virus Res. 2016;212:1–11. doi: 10.1016/j.virusres.2015.10.002
   PubMed Web of Science ®Google Scholar
• Ghafouri-Fard S, Hussen BM, Jamal HH, et al. The emerging role of non-coding RNAs in the regulation of virus replication and resultant cellular pathologies. Int J Mol Sci. 2022;23(2):815. doi: 10.3390/ijms23020815
   PubMed Web of Science ®Google Scholar
• Damas ND, Fossat N, Scheel TKH. Functional interplay between RNA viruses and non-coding RNA in mammals. Noncoding RNA. 2019;5(1):7. doi: 10.3390/ncrna5010007
   PubMed Web of Science ®Google Scholar
• Liu S, Liu X, Li J, et al. Long noncoding RNAs: novel regulators of virus-host interactions. Rev Med Virol. 2019;29(4):e2046. doi: 10.1002/rmv.2046
   PubMed Web of Science ®Google Scholar
• Wang P. The opening of Pandora’s box: an emerging role of long noncoding RNA in viral infections. Front Immunol. 2018;9:3138. doi: 10.3389/fimmu.2018.03138
   PubMed Web of Science ®Google Scholar
• Orly J, Yul BJ-F, Gopinath S, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell. 2013;152(4):743–754. doi: 10.1016/j.cell.2013.01.015
   PubMed Web of Science ®Google Scholar
• 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. doi: 10.1038/srep08639
   PubMedGoogle Scholar
• Romanchikova N, Ivanova V, Scheller C, et al. NFAT transcription factors control HIV-1 expression through a binding site downstream of TAR region. Immunobiology. 2003;208(4):361–365. doi: 10.1078/0171-2985-00283
   PubMed Web of Science ®Google Scholar
• Saha S, Murthy S, Rangarajan PN. Identification and characterization of a virus-inducible non-coding RNA in mouse brain. J Gen Virol. 2006;87(7):1991–1995. doi: 10.1099/vir.0.81768-0
   PubMedGoogle Scholar
• Naganuma T, Hirose T. Paraspeckle formation during the biogenesis of long non-coding RNAs. RNA Biol. 2013;10(3):456–461. doi: 10.4161/rna.23547
   PubMed Web of Science ®Google Scholar
• Sunwoo H, Dinger ME, Wilusz JE, et al. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2009;19(3):347–359. doi: 10.1101/gr.087775.108
   PubMed Web of Science ®Google Scholar
• Naganuma T, Nakagawa S, Tanigawa A, et al. Alternative 3’-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. Embo J. 2012;31(20):4020–4034. doi: 10.1038/emboj.2012.251
   PubMed Web of Science ®Google Scholar
• Sasaki YT, Ideue T, Sano M, et al. Menepsilon/Beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A. 2009;106(8):2525–2530. doi: 10.1073/pnas.0807899106
   PubMed Web of Science ®Google Scholar
• Chujo T, Yamazaki T, Kawaguchi T, et al. Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. Embo J. 2017;36(10):1447–1462. doi: 10.15252/embj.201695848
   PubMed Web of Science ®Google Scholar
• West JA, Mito M, Kurosaka S, et al. Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization. J Cell Biol. 2016;214(7):817–830. doi: 10.1083/jcb.201601071
   PubMed Web of Science ®Google Scholar
• Dettwiler S, Aringhieri C, Cardinale S, et al. Distinct sequence motifs within the 68-kDa subunit of cleavage factor im mediate RNA binding, protein-protein interactions, and subcellular localization. J Biol Chem. 2004;279(34):35788–35797. doi: 10.1074/jbc.M403927200
   PubMed Web of Science ®Google Scholar
• Hirose T, Virnicchi G, Tanigawa A, et al. NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol Biol Cell. 2014;25(1):169–183. doi: 10.1091/mbc.e13-09-0558
   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. Molecular Cell. 2014;53(3):393–406. doi: 10.1016/j.molcel.2014.01.009
   PubMed Web of Science ®Google Scholar
• Ahmed ASI, Dong K, Liu J, et al. Long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1) is critical for phenotypic switching of vascular smooth muscle cells. Proc Natl Acad Sci U S A. 2018;115(37):E8660–e7. doi: 10.1073/pnas.1803725115
   PubMed Web of Science ®Google Scholar
• Koyama S, Ishii KJ, Coban C, et al. Innate immune response to viral infection. Cytokine. 2008;43(3):336–341. doi: 10.1016/j.cyto.2008.07.009
   PubMed Web of Science ®Google Scholar
• Zhou B, Wu F, Han J, et al. Exploitation of nuclear protein SFPQ by the encephalomyocarditis virus to facilitate its replication. Biochem Biophys Res Commun. 2019;510(1):65–71. doi: 10.1016/j.bbrc.2019.01.032
   PubMed Web of Science ®Google Scholar
• Lenarcic EM, Landry DM, Greco TM, et al. Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification. J Virol. 2013;87(15):8697–8712. doi: 10.1128/JVI.00950-13
   PubMed Web of Science ®Google Scholar
• Dave P, George B, Sharma DK, et al. Polypyrimidine tract-binding protein (PTB) and PTB-associated splicing factor in CVB3 infection: an ITAF for an ITAF. Nucleic Acids Res. 2017;45(15):9068–9084. doi: 10.1093/nar/gkx519
   PubMed Web of Science ®Google Scholar
• Flather D, Nguyen JHC, Semler BL, et al. Exploitation of nuclear functions by human rhinovirus, a cytoplasmic RNA virus. PLOS Pathog. 2018;14(8):e1007277. doi: 10.1371/journal.ppat.1007277
   PubMed Web of Science ®Google Scholar
• Pandey AD, Goswami S, Shukla S, et al. Correlation of altered expression of a long non-coding RNA, NEAT1, in peripheral blood mononuclear cells with dengue disease progression. J Infect. 2017;75(6):541–554. doi: 10.1016/j.jinf.2017.09.016
   PubMed Web of Science ®Google Scholar
• Ramaiah A, Contreras D, Gangalapudi V, et al. Dysregulation of long non-coding RNA (lncRNA) genes and predicted lncRNA-protein interactions during zika virus infection. bioRxiv. 2016;061788. doi: 10.1101/061788
   Google Scholar
• Labeau A, Fery-Simonian L, Lefevre-Utile A, et al. Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep. 2022;39(4):110744. doi: 10.1016/j.celrep.2022.110744
   PubMed Web of Science ®Google Scholar
• Girardi E, Messmer M, Lopez P, et al. Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in sindbis virus infection. RNA. 2023;29(3):361–375. doi: 10.1261/rna.079270.122
   PubMed Web of Science ®Google Scholar
• Landeras-Bueno S, Jorba N, Pérez-Cidoncha M, et al. The splicing factor proline-glutamine rich (SFPQ/PSF) is involved in influenza virus transcription. PLOS Pathog. 2011;7(11):e1002397. doi: 10.1371/journal.ppat.1002397
   PubMed Web of Science ®Google Scholar
• Beyleveld G, Chin DJ, Moreno Del Olmo E, et al. Nucleolar relocalization of RBM14 by influenza a virus NS1 protein. mSphere. 2018;3(6). doi: 10.1128/mSphereDirect.00549-18
   PubMed 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(9):JVI.02250–16. doi: 10.1128/JVI.02250-16
   Web of Science ®Google Scholar
• Beeharry Y, Goodrum G, Imperiale CJ, et al. The hepatitis delta virus accumulation requires paraspeckle components and affects NEAT1 level and PSP1 localization. Sci Rep. 2018;8(1). doi: 10.1038/s41598-018-24500-1
   Google Scholar
• Greco-Stewart VS, Thibault CS, Pelchat M. Binding of the polypyrimidine tract-binding protein-associated splicing factor (PSF) to the hepatitis delta virus RNA. Virology. 2006;356(1–2):35–44. doi: 10.1016/j.virol.2006.06.040
   PubMed Web of Science ®Google Scholar
• Sikora D, Greco-Stewart VS, Miron P, et al. The hepatitis delta virus RNA genome interacts with eEF1A1, p54(nrb), hnRNP-L, GAPDH and ASF/SF2. Virology. 2009;390(1):71–78. doi: 10.1016/j.virol.2009.04.022
   PubMed Web of Science ®Google Scholar
• Greco-Stewart VS, Miron P, Abrahem A, et al. The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome. Virology. 2007;357(1):68–78. doi: 10.1016/j.virol.2006.08.010
   PubMed Web of Science ®Google Scholar
• Shadrina OA, Kikhay TF, Agapkina YY, et al. SFPQ and NONO Proteins and long non-coding NEAT1 RNA: cellular functions and role in the HIV-1 life cycle. Mol Biol. 2022;56(2):196–209. doi: 10.1134/S0026893322020133
   Web of Science ®Google Scholar
• Wang Z, Fan P, Zhao Y, et al. NEAT1 modulates herpes simplex virus-1 replication by regulating viral gene transcription. Cell Mol Life Sci. 2017;74(6):1117–1131. doi: 10.1007/s00018-016-2398-4
   PubMed Web of Science ®Google Scholar
• Lee N, Yario TA, Gao JS, Steitz JA. EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression. 2016. p. 3221–3226. Proc Natl Acad Sci. 113(12).
   PubMed Web of Science ®Google Scholar
• Jiang D, Jiang C, Sui C, et al. Swine NONO is an essential factor to inhibit pseudorabies virus infection. Vet Microbiol. 2022;275:109582. doi: 10.1016/j.vetmic.2022.109582
   PubMed Web of Science ®Google Scholar
• Oshiumi H, Miyashita M, Okamoto M, et al. DDX60 Is involved in RIG-I-Dependent and Independent antiviral responses, and its function Is attenuated by virus-induced EGFR activation. Cell Rep. 2015;11(8):1193–1207. doi: 10.1016/j.celrep.2015.04.047
   PubMed Web of Science ®Google Scholar
• Godet A-C, David F, Hantelys F, et al. IRES trans-acting factors, key actors of the stress response. Int J Mol Sci. 2019;20(4):924. doi: 10.3390/ijms20040924
   PubMed Web of Science ®Google Scholar
• Ho B-C, Yu S-L, Chen JJW, et al. Enterovirus-induced miR-141 contributes to shutoff of host protein translation by targeting the translation initiation factor eIF4E. Cell Host Microbe. 2011;9(1):58–69. doi: 10.1016/j.chom.2010.12.001
   PubMed Web of Science ®Google Scholar
• Pilipenko EV, Pestova TV, Kolupaeva VG, et al. A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes Dev. 2000;14(16):2028–2045. doi: 10.1101/gad.14.16.2028
   PubMed Web of Science ®Google Scholar
• Mitchell SA, Spriggs KA, Bushell M, et al. Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. Genes Dev. 2005;19(13):1556–1571. doi: 10.1101/gad.339105
   PubMed Web of Science ®Google Scholar
• Lizcano-Perret B, Lardinois C, Wavreil F, et al. Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic. PLOS Pathog. 2022;18(12):e1011042. doi: 10.1371/journal.ppat.1011042
   PubMed Web of Science ®Google Scholar
• Lizcano-Perret B, Michiels T. Nucleocytoplasmic trafficking perturbation induced by Picornaviruses. Viruses. 2021;13(7):1210. doi: 10.3390/v13071210
   PubMed Web of Science ®Google Scholar
• Hanson PJ, Hossain AR, Qiu Y, et al. Cleavage and sub-cellular redistribution of nuclear pore protein 98 by coxsackievirus B3 protease 2A impairs cardioprotection. Front Cell Infect Microbiol. 2019;9. doi: 10.3389/fcimb.2019.00265
   PubMed Web of Science ®Google Scholar
• Jorba N, Juarez S, Torreira E, et al. Analysis of the interaction of influenza virus polymerase complex with human cell factors. Proteomics. 2008;8(10):2077–2088. doi: 10.1002/pmic.200700508
   PubMed Web of Science ®Google Scholar
• Li X, Palese P. Characterization of the polyadenylation signal of influenza virus RNA. J Virol. 1994;68(2):1245–1249. doi: 10.1128/jvi.68.2.1245-1249.1994
   PubMed Web of Science ®Google Scholar
• Lee N, Therese W, Joan. EBV noncoding RNA binds nascent RNA to drive Host PAX5 to viral DNA. Cell. 2015;160(4):607–618. doi: 10.1016/j.cell.2015.01.015
   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. Molecular Cell. 2017;67(3):387–99.e5. doi: 10.1016/j.molcel.2017.06.020
   PubMed Web of Science ®Google Scholar
• Viollet C, Davis DA, Tekeste SS, et al. RNA sequencing reveals that Kaposi sarcoma-associated herpesvirus infection mimics hypoxia gene expression signature. PLOS Pathog. 2017;13(1):e1006143. doi: 10.1371/journal.ppat.1006143
   PubMed Web of Science ®Google Scholar
• An H, Tan JT, Shelkovnikova TA. Stress granules regulate stress-induced paraspeckle assembly. J Cell Bio. 2019;218(12):4127–4140. doi: 10.1083/jcb.201904098
   PubMed Web of Science ®Google Scholar
• Tayel SI, EA E-M, Abdelaal GA, et al. Interplay of LncRNAs NEAT1 and TUG1 in incidence of cytokine storm in appraisal of COVID-19 infection. Int J Biol Sci. 2022;18(13):4901–4913. doi: 10.7150/ijbs.72318
   PubMed Web of Science ®Google Scholar
• Huang K, Wang C, Vagts C, et al. Long non-coding RNAs (lncRnas) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: an integrated single-cell analysis. PLOS ONE. 2022;17(1):e0261242. doi: 10.1371/journal.pone.0261242
   PubMed Web of Science ®Google Scholar
• Meydan C, Madrer N, Soreq H. The neat dance of COVID-19: NEAT1, DANCR, and Co-modulated cholinergic RNAs link to inflammation. Front Immunol. 2020;11:11. doi: 10.3389/fimmu.2020.590870
   PubMed Web of Science ®Google Scholar