Computational analysis revealed miRNAs produced by Chikungunya virus target genes associated with antiviral immune responses and cell cycle regulation

Computational Biology and Chemistry - Tập 92 - Trang 107462 - 2021
Md. Sajedul Islam1, Md. Abdullah-Al-Kamran Khan2
1Department of Biochemistry & Biotechnology, University of Barishal, Barishal, 8254, Bangladesh
2Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh

Tài liệu tham khảo

Abere, 2012, Proteomic analysis of chikungunya virus infected microgial cells, PLoS One, 7, 10.1371/journal.pone.0034800 Abraham, 2013, Induction of cytopathogenicity in human glioblastoma cells by chikungunya virus, PLoS One, 8, 10.1371/journal.pone.0075854 Ahmad, 2018, Autophagy-virus interplay: from cell biology to human disease, Front. Cell Dev. Biol., 6, 10.3389/fcell.2018.00155 Barber, 2001, Host defense, viruses and apoptosis, Cell Death Differ., 8, 113, 10.1038/sj.cdd.4400823 Barrett, 2013, NCBI GEO: archive for functional genomics data sets--update, Nucleic Acids Res., 41, D991, 10.1093/nar/gks1193 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc.: Ser. B (Methodol.), 57, 289 Brandstadter, 2011, Natural killer cell responses to viral infection, J. Innate Immun., 3, 274, 10.1159/000324176 Chan, 2015, RIG-I-like receptor regulation in virus infection and immunity, Curr. Opin. Virol., 12, 7, 10.1016/j.coviro.2015.01.004 Chen, 2016, iMiRNA-SSF: improving the Identification of MicroRNA precursors by combining negative sets with different distributions, Sci. Rep., 6, 19062, 10.1038/srep19062 Cho, 2007, OncomiRs: the discovery and progress of microRNAs in cancers, Mol. Cancer, 6, 10.1186/1476-4598-6-60 Couderc, 2008, A mouse model for Chikungunya: young age and inefficient type-I interferon signaling are risk factors for severe disease, PLoS Pathog., 4, e29, 10.1371/journal.ppat.0040029 Dai, 2018, X. psRNATarget: a plant small RNA target analysis server (2017 release), Nucleic Acids Res., 46, W49, 10.1093/nar/gky316 Dhanwani, 2012, Characterization of Chikungunya virus infection in human neuroblastoma SH-SY5Y cells: role of apoptosis in neuronal cell death, Virus Res., 163, 563, 10.1016/j.virusres.2011.12.009 Ding, 2007, Antiviral immunity directed by small RNAs, Cell, 130, 413, 10.1016/j.cell.2007.07.039 2015, Gene Ontology Consortium: going forward, Nucleic Acids Res., 43, D1049, 10.1093/nar/gku1179 Ghosh, 2009, Cellular versus viral microRNAs in host–virus interaction, Nucleic Acids Res., 37, 1035, 10.1093/nar/gkn1004 Gkirtzou, 2010, MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors, PLoS One, 5, 10.1371/journal.pone.0011843 Grundhoff, 2011, Virus-encoded microRNAs, Virology, 411, 325, 10.1016/j.virol.2011.01.002 Hariharan, 2005, Targets for human encoded microRNAs in HIV genes, Biochem. Biophys. Res. Commun., 337, 1214, 10.1016/j.bbrc.2005.09.183 Hoarau, 2010, Persistent chronic inflammation and infection by Chikungunya arthritogenic alphavirus in spite of a robust host immune response, J. Immunol. (Baltimore, Md. : 1950), 184, 5914 Hussain, 2014, MicroRNA-like viral small RNA from dengue virus 2 autoregulates its replication in mosquito cells, Proc. Natl. Acad. Sci., 111, 2746, 10.1073/pnas.1320123111 Islam, 2019, In silico analysis revealed Zika virus miRNAs associated with viral pathogenesis through alteration of host genes involved in immune response and neurological functions, J. Med. Virol., 91, 1584, 10.1002/jmv.25505 Kanehisa, 2016, KEGG as a reference resource for gene and protein annotation, Nucleic Acids Res., 44, D457, 10.1093/nar/gkv1070 Kincaid, 2012, Virus-encoded microRNAs: an overview and a look to the future, PLoS Pathog., 8, 10.1371/journal.ppat.1003018 Kinsella, 2011, Ensembl BioMarts: a hub for data retrieval across taxonomic space, Database, 2011, 10.1093/database/bar030 Kohl, 2011, Cytoscape: software for visualization and analysis of biological networks, Methods Mol. Biol. (Clifton, N.J.), 696, 291, 10.1007/978-1-60761-987-1_18 Kruger, 2006, RNAhybrid: microRNA target prediction easy, fast and flexible, Nucleic Acids Res., 34, W451, 10.1093/nar/gkl243 Lester, 2014, Toll-liK.e receptors in antiviral innate immunity, J. Mol. Biol., 426, 1246, 10.1016/j.jmb.2013.11.024 Li, 2019, An overview of RNA virus-encoded microRNAs, ExRNA, 1, 37, 10.1186/s41544-019-0037-6 Lim, 2003, Vertebrate microRNA genes, Science, 299, 10.1126/science.1080372 Lu, 2009, MicroRNA in the immune system, microRNA as an immune system, Immunology, 127, 291, 10.1111/j.1365-2567.2009.03092.x Mann, 2017, IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions, Nucleic Acids Res., 45, W435, 10.1093/nar/gkx279 Manni, 2009, The microRNA miR-92 increases proliferation of myeloid cells and by targeting p63 modulates the abundance of its isoforms, FASEB J., 23, 3957, 10.1096/fj.09-131847 Matusali, 2019, Tropism of the Chikungunya virus, Viruses, 11, 10.3390/v11020175 Mishra, 2020, The interplay between viral-derived miRNAs and host immunity during infection, Front. Immunol., 10, 10.3389/fimmu.2019.03079 Mogensen, 2001, Molecular pathways in virus-induced cytokine production, Microbiol. Mol. Biol. Rev., 65, 131, 10.1128/MMBR.65.1.131-150.2001 Mohanta, 2020, Molecular insights into the MAPK cascade during viral infection: potential crosstalk between HCQ and HCQ analogues, Biomed Res. Int., 10.1155/2020/8827752 Nukui, 2014, A human herpesvirus 6A encoded miRNA: a role in viral lytic replication, J. Virol. Perez-Llamas, 2011, Gitools: analysis and visualisation of genomic data using interactive heat-maps, PLoS One, 6, 10.1371/journal.pone.0019541 Pruitt, 2001, RefSeq and LocusLink: NCBI gene-centered resources, Nucleic Acids Res., 29, 10.1093/nar/29.1.137 Ritchie, 2015, Limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res., 43, e47, 10.1093/nar/gkv007 Ross, 1956, The Newala epidemic: III. The virus: isolation, pathogenic properties and relationship to the epidemic, J. Hyg., 54, 177, 10.1017/S0022172400044442 Rougeron, 2015, Chikungunya, a paradigm of neglected tropical disease that emerged to be a new health global risk, J. Clin. Virol., 64, 144, 10.1016/j.jcv.2014.08.032 Saxena, 2013, Combined miRNA and mRNA signature identifies key molecular players and pathways involved in chikungunya virus infection in human cells, PLoS One, 8, 10.1371/journal.pone.0079886 Shen, 2012, MicroRNA prediction using a fixed-order markov model based on the secondary structure pattern, PLoS One, 7, 10.1371/journal.pone.0048236 Skalsky, 2010, Viruses, microRNAs, and host interactions, Annu. Rev. Microbiol., 64, 123, 10.1146/annurev.micro.112408.134243 Stern-Ginossar, 2007, Host immune system gene targeting by a viral miRNA, Science (New York, N.Y.), 317, 376, 10.1126/science.1140956 Tav, 2016, miRNAFold: a web server for fast miRNA precursor prediction in genomes, Nucleic Acids Res., 44, W181, 10.1093/nar/gkw459 Tempel, 2012, A fast ab-initio method for predicting miRNA precursors in genomes, Nucleic Acids Res., 40, 10.1093/nar/gks146 Thiberville, 2013, Chikungunya fever: epidemiology, clinical syndrome, pathogenesis and therapy, Antiviral Res., 99, 345, 10.1016/j.antiviral.2013.06.009 Wang, 2009, MicroRNA and cancer – focus on apoptosis, J. Cell. Mol. Med., 13, 12, 10.1111/j.1582-4934.2008.00510.x Wen-Tsai, 2008, PI3K-Akt signaling and viral infection, Recent Pat. Biotechnol., 2, 218, 10.2174/187220808786241042 Wienholds, 2003, The microRNA-producing enzyme Dicer1 is essential for zebrafish development, Nat. Genet., 35, 217, 10.1038/ng1251 Xue, 2005, Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine, BMC Bioinformatics, 6, 310, 10.1186/1471-2105-6-310 Zhang, 2018, Differences in genome characters and cell tropisms between two chikungunya isolates of Asian lineage and Indian Ocean lineage, Virol. J., 15, 130, 10.1186/s12985-018-1024-5