High-throughput analysis of the interactions between viral proteins and host cell RNAs

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dc.authoridFarzad Kiani / 0000-0002-0354-9344
dc.authorscopusidFarzad Kiani / 36662461100
dc.authorwosidFarzad Kiani / O-3363-2013
dc.contributor.authorLanjanian, Hossein
dc.contributor.authorNematzadeh, Sajjad
dc.contributor.authorHosseini, Shadi
dc.contributor.authorTorkamanian-Afshar, Mahsa
dc.contributor.authorKiani, Farzad
dc.contributor.authorMoazzam-Jazi, Maryam
dc.contributor.authorAydin, Nizamettin
dc.contributor.authorMasoudi-Nejad, Ali
dc.date.accessioned2021-07-13T06:55:51Z
dc.date.available2021-07-13T06:55:51Z
dc.date.issued2021en_US
dc.departmentİstinye Üniversitesi, Mühendislik ve Doğa Bilimleri Fakültesi, Yazılım Mühendisliği Bölümüen_US
dc.description.abstractIndexed keywords Abstract RNA-protein interactions of a virus play a major role in the replication of RNA viruses. The replication and transcription of these viruses take place in the cytoplasm of the host cell; hence, there is a probability for the host RNA-viral protein and viral RNA-host protein interactions. The current study applies a high-throughput computational approach, including feature extraction and machine learning methods, to predict the affinity of protein sequences of ten viruses to three categories of RNA sequences. These categories include RNAs involved in the protein-RNA complexes stored in the RCSB database, the human miRNAs deposited at the mirBase database, and the lncRNA deposited in the LNCipedia database. The results show that evolution not only tries to conserve key viral proteins involved in the replication and transcription but also prunes their interaction capability. These proteins with specific interactions do not perturb the host cell through undesired interactions. On the other hand, the hypermutation rate of NSP3 is related to its affinity to host cell RNAs. The Gene Ontology (GO) analysis of the miRNA with affiliation to NSP3 suggests that these miRNAs show strongly significantly enriched GO terms related to the known symptoms of COVID-19. Docking and MD simulation study of the obtained miRNA through high-throughput analysis suggest a non-coding RNA (an RNA antitoxin, ToxI) as a natural aptamer drug candidate for NSP5 inhibition. Finally, a significant interplay of the host RNA-viral protein in the host cell can disrupt the host cell's system by influencing the RNA-dependent processes of the host cells, such as a differential expression in RNA. Furthermore, our results are useful to identify the side effects of mRNA-based vaccines, many of which are caused by the off-label interactions with the human lncRNAs.en_US
dc.identifier.citationLanjanian, H., Nematzadeh, S., Hosseini, S., Torkamanian-Afshar, M., Kiani, F., Moazzam-Jazi, M., ... & Masoudi-Nejad, A. (2021). High-Throughput Analysis of the Interactions between Viral Proteins and Host Cell RNAs. Computers in Biology and Medicine, 104611.en_US
dc.identifier.doi10.1016/j.compbiomed.2021.104611en_US
dc.identifier.endpage48en_US
dc.identifier.issn0010-4825en_US
dc.identifier.pmid34246161en_US
dc.identifier.scopus2-s2.0-85109169432en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1016/j.compbiomed.2021.104611
dc.identifier.urihttps://hdl.handle.net/20.500.12713/1915
dc.identifier.volume135en_US
dc.identifier.wosWOS:000687882400009en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorKiani, Farzad
dc.language.isoenen_US
dc.publisherElsevier Ltden_US
dc.relation.ispartofComputers in Biology and Medicineen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectCOVID-19en_US
dc.subjectHost Cell RNAen_US
dc.subjectRNA-Protein Affinityen_US
dc.subjectRPINBASEen_US
dc.subjectViral Nonstructural Proteins (NSP)en_US
dc.titleHigh-throughput analysis of the interactions between viral proteins and host cell RNAsen_US
dc.typeArticleen_US

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