Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagation

References

• Chen L-L. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol. 2016;17:205–211.
   PubMed Web of Science ®Google Scholar
• Holdt LM, Kohlmaier A, Teupser D. Molecular roles and function of circular RNAs in eukaryotic cells. Cell Mol Life Sci. 2018;75(6):1071–1098.
   PubMed Web of Science ®Google Scholar
• Zhang XO, Dong R, Zhang Y, et al. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26(9):1277–1287.
   PubMed Web of Science ®Google Scholar
• Lasda E, Parker R. Circular RNAs: diversity of form and function. Rna. 2014;20(12):1829–1842.
   PubMed Web of Science ®Google Scholar
• Lopez-Jimenez E, Rojas AM, Andres-Leon E. RNA sequencing and prediction tools for Circular RNAs analysis. Adv Exp Med Biol. 2018;1087:17–33.
   PubMed Web of Science ®Google Scholar
• Hansen TB, Dong R, Zhang Y, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–388.
   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(3):353–358.
   PubMed Web of Science ®Google Scholar
• Shi JD, Hu N, Li J, et al. Unique expression signatures of circular RNAs in response to DNA tumor virus SV40 infection. Oncotarget. 2017;8(58):98609–98622.
   PubMedGoogle Scholar
• Wang ZY, Guo ZD, Li JM, et al. Genome-wide search for competing endogenous RNAs responsible for the effects induced by Ebola virus replication and transcription using a trVLP system. Front Cell Infect Microbiol. 2017;7:479.
   PubMed Web of Science ®Google Scholar
• Zhang XH, Yan Y, Lei X, et al. Circular RNA alterations are involved in resistance to avian leukosis virus subgroup-J-induced tumor formation in chickens. Oncotarget. 2017;8(21):34961–34970.
   PubMedGoogle Scholar
• Cui SC, Qian Z, Chen Y, et al. Screening of up- and downregulation of circRNAs in HBV-related hepatocellular carcinoma by microarray. Oncol Lett. 2018;15(1):423–432.
   PubMed Web of Science ®Google Scholar
• Tagawa T, Gao S, Koparde VN, et al. Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA. Proc Natl Acad Sci USA. 2018;115(50):12805–12810.
   PubMed Web of Science ®Google Scholar
• Chen JN, Wang H, Jin L, et al. Profile analysis of circRNAs induced by porcine endemic diarrhea virus infection in porcine intestinal epithelial cells. Virology. 2019;527:169–179.
   PubMed Web of Science ®Google Scholar
• Tao P, Ning Z, Hao X, et al. Comparative analysis of whole-transcriptome RNA expression in MDCK cells infected With the H3N2 and H5N1 canine influenza viruses. Front Cell Infect Microbiol. 2019;9:76.
   PubMed Web of Science ®Google Scholar
• Ma X, Zhao X, Zhang Z, et al. Differentially expressed non-coding RNAs induced by transmissible gastroenteritis virus potentially regulate inflammation and NF-kappaB pathway in porcine intestinal epithelial cell line. BMC Genomics. 2018;19(1):747.
   PubMed Web of Science ®Google Scholar
• Yu TQ, Ding Y, Zhang Y, et al. Circular RNA GATAD2A promotes H1N1 replication through inhibiting autophagy. Vet Microbiol. 2019;231:238–245.
   PubMed Web of Science ®Google Scholar
• Chan JFW, Li KSM, To KKW, et al. Is the discovery of the novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) the beginning of another SARS-like pandemic? J Infect. 2012;65(6):477–489.
   PubMed Web of Science ®Google Scholar
• Chan JFW, Lau SKP, To KKW, et al. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin Microbiol Rev. 2015;28(2):465–522.
   PubMed Web of Science ®Google Scholar
• WHO. Middle East respiratory syndrome coronavirus (MERS-CoV). 2019. Available from: https://www.who.int/emergencies/mers-cov/en/.
   Google Scholar
• Zumla A, Chan JFW, Azhar EI, et al. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov. 2016;15(5):327–347.
   PubMed Web of Science ®Google Scholar
• Zaki AM, van Boheemen S, Bestebroer TM, et al. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367(19):1814–1820.
   PubMed Web of Science ®Google Scholar
• Yuan SF, Chu H, Chan JFW, et al. SREBP-dependent lipidomic reprogramming as a broad-spectrum antiviral target. Nat Commun. 2019;10(1):120.
   PubMed Web of Science ®Google Scholar
• Yeung ML, Yao Y, Jia L, et al. MERS coronavirus induces apoptosis in kidney and lung by upregulating Smad7 and FGF2. Nat Microbiol. 2016;1:16004.
   PubMed Web of Science ®Google Scholar
• Chan JF, Chan K-H, Choi GK-Y, et al. Differential cell line susceptibility to the emerging novel human betacoronavirus 2c EMC/2012: implications for disease pathogenesis and clinical manifestation. J Infect Dis. 2013;207(11):1743–1752.
   PubMed Web of Science ®Google Scholar
• Chan JF, Chan K-H, Kao RYT, et al. Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus. J Infect. 2013;67(6):606–616.
   PubMed Web of Science ®Google Scholar
• Chu H, Chan C-M, Zhang X, et al. Middle East respiratory syndrome coronavirus and bat coronavirus HKU9 both can utilize GRP78 for attachment onto host cells. J Biol Chem. 2018;293(30):11709–11726.
   PubMed Web of Science ®Google Scholar
• Chen SF, Zhou Y, Chen Y, et al., Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890.
   PubMed Web of Science ®Google Scholar
• Gao Y, Zhang JY, Zhao FQ. Circular RNA identification based on multiple seed matching. Brief Bioinformatics. 2018;19(5):803–810.
   PubMed Web of Science ®Google Scholar
• Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–338.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
   PubMed Web of Science ®Google Scholar
• Enright AJ, John B, Gaul U, et al. MicroRNA targets in drosophila. Genome Biol. 2003;5(1):R1.
   PubMed Web of Science ®Google Scholar
• Dudekulay DB, Panda AC, Grammatikakis I, et al. Circinteractome: a web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biol. 2016;13(1):34–42.
   PubMed Web of Science ®Google Scholar
• Chu H, Zhou J, Ho-Yin Wong B, et al. Productive replication of Middle East respiratory syndrome coronavirus in monocyte-derived dendritic cells modulates innate immune response. Virology. 2014;454-455:197–205.
   PubMed Web of Science ®Google Scholar
• Chu H, Zhou J, Wong BH-Y, et al. Middle East respiratory syndrome coronavirus efficiently infects human primary T Lymphocytes and activates the extrinsic and intrinsic apoptosis pathways. J Infect Dis. 2016;213(6):904–914.
   PubMed Web of Science ®Google Scholar
• Chan CM, Chu H, Wang Y, et al. Carcinoembryonic antigen-related cell adhesion molecule 5 is an important surface attachment factor that facilitates entry of Middle East respiratory syndrome coronavirus. J Virol. 2016;90(20):9114–9127.
   PubMed Web of Science ®Google Scholar
• Chan JF, Zhu Z, Chu H, et al. The celecoxib derivative kinase inhibitor AR-12 (OSU-03012) inhibits Zika virus via down-regulation of the PI3 K/Akt pathway and protects Zika virus-infected A129 mice: a host-targeting treatment strategy. Antiviral Res. 2018;160:38–47.
   PubMed Web of Science ®Google Scholar
• Chan JF, Zhang AJ, Chan CC-S, et al. Zika virus infection in dexamethasone-immunosuppressed mice demonstrating disseminated infection with multi-organ involvement including orchitis effectively treated by recombinant type I interferons. EBioMedicine. 2016;14:112–122.
   PubMed Web of Science ®Google Scholar
• Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58(5):870–885.
   PubMed Web of Science ®Google Scholar
• Li S, Ma Y, Tan Y, et al. Profiling and functional analysis of circular RNAs in acute promyelocytic leukemia and their dynamic regulation during all-trans retinoic acid treatment. Cell Death Dis. 2018;9(6):651.
   PubMed Web of Science ®Google Scholar
• Chen BJ, Mills JD, Takenaka K, et al. Characterization of circular RNAs landscape in multiple system atrophy brain. J Neurochem. 2016;139(3):485–496.
   PubMed Web of Science ®Google Scholar
• Flavell JR, Baumforth KRN, Wood VHJ, et al. Down-regulation of the TGF-beta target gene, PTPRK, by the Epstein-Barr virus-encoded EBNA1 contributes to the growth and survival of Hodgkin lymphoma cells. Blood. 2008;111(1):292–301.
   PubMed Web of Science ®Google Scholar
• Golebiewski L, Liu H, Javier RT, et al. The avian influenza virus NS1 ESEV PDZ binding motif associates with Dlg1 and scribble to disrupt cellular tight junctions. J Virol. 2011;85(20):10639–10648.
   PubMed Web of Science ®Google Scholar
• Yoshimatsu Y, Nakahara T, Tanaka K, et al. Roles of the PDZ-binding motif of HPV 16 E6 protein in oncogenic transformation of human cervical keratinocytes. Cancer Sci. 2017;108(7):1303–1309.
   PubMed Web of Science ®Google Scholar
• Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9(9):e1003777.
   PubMed Web of Science ®Google Scholar
• Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol. 2014;32(5):453–461.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
   PubMed Web of Science ®Google Scholar
• Winter J, Jung S, Keller S, et al. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol. 2009;11(3):228–234.
   PubMed Web of Science ®Google Scholar
• Thomas LF, Saetrom P. Circular RNAs are depleted of polymorphisms at microRNA binding sites. Bioinformatics. 2014;30(16):2243–2246.
   PubMed Web of Science ®Google Scholar
• Bernier A, Sagan SM. The diverse roles of microRNAs at the host(-)virus interface. Viruses. 2018;10(8):440.
   PubMed Web of Science ®Google Scholar
• Cullen BR. Viruses and microRNAs. Nat Genet. 2006;38(Suppl):S25–S30.
   PubMed Web of Science ®Google Scholar
• Bailey-Elkin BA, Knaap RCM, Johnson GG, et al. Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression. J Biol Chem. 2014;289(50):34667–34682.
   PubMed Web of Science ®Google Scholar
• Ratia K, Saikatendu KS, Santarsiero BD, et al. Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci USA. 2006;103(15):5717–5722.
   PubMed Web of Science ®Google Scholar
• Qi M, Elion EA. MAP kinase pathways. J Cell Sci. 2005;118(Pt 16):3569–3572.
   PubMed Web of Science ®Google Scholar
• Kindrachuk J, Ork B, Hart BJ, et al. Antiviral potential of ERK/MAPK and PI3 K/AKT/mTOR signaling modulation for Middle East respiratory syndrome coronavirus infection as identified by temporal kinome analysis. Antimicrob Agents Chemother. 2015;59(2):1088–1099.
   PubMed Web of Science ®Google Scholar
• Pauli EK, Chan YK, Davis ME, et al. The ubiquitin-specific protease USP15 promotes RIG-I-mediated antiviral signaling by deubiquitylating TRIM25. Sci Signal. 2014;7(307):ra3.
   PubMed Web of Science ®Google Scholar
• Pyeon D, Timani KA, Gulraiz F, et al. Function of ubiquitin (Ub) specific protease 15 (USP15) in HIV-1 replication and viral protein degradation. Virus Res. 2016;223:161–169.
   PubMed Web of Science ®Google Scholar
• Chiang C, Pauli EK, Biryukov J, et al. The human papillomavirus E6 Oncoprotein targets USP15 and TRIM25 to suppress RIG-I-mediated innate immune signaling. J Virol. 2018;92(6): e01737-17.
   Web of Science ®Google Scholar
• Kusakabe S, Suzuki T, Sugiyama Y, et al. USP15 participates in hepatitis C virus propagation through regulation of viral RNA translation and lipid droplet formation. J Virol. 2019;93(6): e01708-18.
   PubMed Web of Science ®Google Scholar
• Wang C, Jiang S, Zhang L, et al. TAF family proteins and MEF2C are essential for epstein-barr virus super-enhancer activity. J Virol. 2019;93(16): e00513-19.
   Web of Science ®Google Scholar