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Review
. 2024 May 18;16(5):804.
doi: 10.3390/v16050804.

Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus

Clara Isabel Bermudez-Santana  1 , Juan Carlos Gallego-Gómez  2
Affiliations
Review

Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus

Clara Isabel Bermudez-Santana et al. Viruses. .

Abstract

In recent years, the function of noncoding RNAs (ncRNAs) as regulatory molecules of cell physiology has begun to be better understood. Advances in viral molecular biology have shown that host ncRNAs, cellular factors, and virus-derived ncRNAs and their interplay are strongly disturbed during viral infections. Nevertheless, the folding of RNA virus genomes has also been identified as a critical factor in regulating canonical and non-canonical functions. Due to the influence of host ncRNAs and the structure of RNA viral genomes, complex molecular and cellular processes in infections are modulated. We propose three main categories to organize the current information about RNA-RNA interactions in some well-known human viruses. The first category shows examples of host ncRNAs associated with the immune response triggered in viral infections. Even though miRNAs introduce a standpoint, they are briefly presented to keep researchers moving forward in uncovering other RNAs. The second category outlines interactions between virus-host ncRNAs, while the third describes how the structure of the RNA viral genome serves as a scaffold for processing virus-derived RNAs. Our grouping may provide a comprehensive framework to classify ncRNA-host-cell interactions for emerging viruses and diseases. In this sense, we introduced them to organize DENV-host-cell interactions.

Keywords: DENV; immune response; microRNAs; ncRNAs; sfRNAs; virus–host cell interactions.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Schematic of three different possible scenarios for processing miRNAs, miRNA-type, and ncRNAs for viruses and host cells. Canonical cell miRNA biogenesis is schematized. Independently of miRNA locus activation, in (A), the main steps of this canonical processing in a generic host cell are shown based on Shapiro’s description [83]. Once RNApol-II transcribes the miRNA locus, its product is a precursor of miRNAs (pri-miRNA) that DROSHA will process into a pre-miRNA, as exported by exportin to the cytoplasm, to further proceed and be processed as a duplex RNA by the cytoplasmic endonuclease DICER. AGO will later recognize the mature miRNA to guide miRISC to a target messenger RNA. The processing of small RNAs from DNA genome viruses is presented in (B). There, VA RNAs are shown as precursors of v-miRNAs [10]. (C) Canonical processing of sfRNAs to produce small RNAs in RNA viruses with cytoplasmic replication, as in flaviviruses [84,85,86,87]. In (D), the possible biosynthesis of ncRNAs for retroviruses is shown. TAR RNAs are confirmed by [88], as well as BLV-miRNAs with activity in the RISC complex [89].
Figure 2
Figure 2
The major regions of the DENV genome are shown. At the top, we observed the projected zoom at the UTR regions. There, SLA, SLB, cHP, and domains I, II, and III fold into shapes with increased complexity on the UTR in 3D as described previously [169,170]. They were revealed using computational and experimental techniques, including folding prediction, probe analysis, and RNA interaction groups by mutational profiling (RING-maP). These UTR regions may be potential precursors for the processing of vsRNA-like miRNAs. RNA structures in the 3′ UTR are also resistant to Xrn1. The polyprotein is then plotted and the coding regions that encode the viral proteins are shown in their order. The signal for the peptidase, Golgi and NS3 proteases is also indicated by an arrow. The corresponding names are organized on the bottom boxes for both the RNA and protein parts of the DENV genome.
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References

    1. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermüller J., Hofacker I.L., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316:1484–1488. doi: 10.1126/science.1138341. - DOI - PubMed
    1. Josset L., Tisoncik-Go J., Katze M.G. MicroRNAs and Other Non-Coding RNAs in Inflammation. Springer; Berlin/Heidelberg, Germany: 2015. Non-coding RNA expression during viral infection: The long and the short of it; pp. 107–137.
    1. Suleiman A.A., Al-Chalabi R., Shaban S.A. Integrative role of small non-coding RNAs in viral immune response: A systematic review. Mol. Biol. Rep. 2024;51:107. doi: 10.1007/s11033-023-09141-6. - DOI - PubMed
    1. Dexheimer P.J., Cochella L. MicroRNAs: From Mechanism to Organism. Front. Cell Dev. Biol. 2020;8:409. doi: 10.3389/fcell.2020.00409. - DOI - PMC - PubMed
    1. Mehta A., Baltimore D. MicroRNAs as regulatory elements in immune system logic. Nat. Rev. Immunol. 2016;16:279–294. doi: 10.1038/nri.2016.40. - DOI - PubMed

Grants and funding

This research was funded by Universidad Nacional de Colombia and Universidad de Antioquia, which granted time to authors to write this review.

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