Computational Identification of Dengue Virus MicroRNA-Like Structures and Their Cellular Targets

Ospina-Bedoya, Maicol; Campillo-Pedroza, Natalia; Franco-Salazar, Juan P.; Gallego-Gómez, Juan Carlos

doi:10.4137/bbi.s13649

Cited by 17 publications

(17 citation statements)

References 28 publications

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“…The program slides a window of defined size across the entire sequence of interest, advancing each window by a given step size . The parameters of window and step sizes were set at 500 and 1 nt, respectively, as described in other literature . The secondary structures of the RNAs corresponding to each window were predicted using the RNAFold algorithm .…”

Section: Methodsmentioning

confidence: 99%

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Computational identification of hepatitis E virus‐encoded microRNAs and their targets in human

Baruah

Bose

2019

Journal of Medical Virology

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microRNAs (miRNAs) are small, noncoding RNAs which regulate eukaryotic gene expression via RNA interference pathway. Recently, miRNAs have been identified in a number of viruses with current evidence suggesting that they regulate gene expression in both virus and host. This makes viral miRNAs potential targets of clinical intervention, with the possibility of inhibiting aberrant host gene expression associated with the disease. In this study, computational approaches were taken to scan the hepatitis E virus (HEV) genome for putative pre-miRNA molecules, which were then analyzed for the presence of mature miRNAs. The 3′untranslated region (3′-UTR) and 5′-UTR sequences targeted by these miRNAs were identified using Miranda computational tool, followed by the functional annotation of the associated messenger RNAs (mRNAs) using Gene Ontology terms and Kyoto Encyclopaedia of Genes and Genomes pathway analysis. We identified a total of nine viral encoded miRNAs in HEV. After functional annotation, the majority of the viral miRNA targets were found to be associated with cell cycle, cell differentiation, nitrogen compound metabolism, transmembrane transport, and chromosome organization. This in-silico study identified putative viral miRNAs encoded by HEV and their potential human mRNAs targets.These viral miRNAs have the potential to affect host gene expression as well as viral life cycle and pathogenesis and can, therefore, serve as potential therapeutic targets during HEV infection. K E Y W O R D S hepatitis E, microRNA, messenger RNA, RNA interference 1 | BACKGROUND microRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression in eukaryotes. The 60 to 80-nucleotide (nt) precursor miRNA (pre-miRNA) is of intronic origin and is cleaved in the cytoplasm by the RNAse III enzyme Dicer to yield the 21 to 23-nt long miRNA. These miRNAs interact with the multiprotein RNA-induced silencing complex and can bind specific cellular mRNAs based on sequence complementarity. Depending on the extent of complementarity, the translation of the messenger RNA (mRNA) may be reduced or completely silenced, with the mRNA being marked for destruction. 1 While the regulatory function of miRNAs is well documented in eukaryotes, there have not been many reports on virally encoded miRNAs, with preliminary reports identifying miRNAs in herpes simplex virus type 1, human adenovirus, dengue virus, West Nile virus, porcine reproductive and respiratory syndrome virus, and human cytomegalovirus. 2-8 J Med Virol. 2019;91:1545-1552. wileyonlinelibrary.com/journal/jmv

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Section: Methodsmentioning

confidence: 99%

“…While the regulatory function of miRNAs is well documented in eukaryotes, there have not been many reports on virally encoded miRNAs, with preliminary reports identifying miRNAs in herpes simplex virus type 1, human adenovirus, dengue virus, West Nile virus, porcine reproductive and respiratory syndrome virus, and human cytomegalovirus …”

Section: Introductionmentioning

confidence: 99%

Computational identification of hepatitis E virus‐encoded microRNAs and their targets in human

Baruah

Bose

2019

Journal of Medical Virology

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“…The geographical location of KFDV is not just limited to India, genome analysis studies has shown that it has more than 90 % sequence identity with Alkhurma hemorrhagic fever virus (AHFV), which is isolated in 1994 from blood of hemorrhagic fever patients in Makkah, Saudi Arabia and thought to be transferred by migratory birds from India [15,16]. Many members of Flaviviridae family such as Dengue [17], Japanese Encephalitis [18], and recently Zika virus [19] were predicted to have encoded miRNAs. It is also evident in past that viral miRNAs can down regulate host genes expression [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Genome Wide Computational Prediction of miRNAs in Kyasanur Forest Disease Virus and their Targeted Genes in Human

Saini¹,

Thakur²,

Kumar³

2016

Preprint

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RNAs are versatile biomolecules and can be coding or non-coding. Among the non-coding RNAs, miRNAs are small endogenous molecules that play important role in posttranscriptional gene regulation. miRNAs are identified in viruses too and involved in down regulation of host genes. Flavivirus family members are classified in to two groups: mosquito-borne flaviviruses (MBFV) and tick-borne flaviviruses (TBFV). Kyasanur forest disease virus (KFDV) found in India in 1957 (Karnataka) relates to TBFV. Virus has been diffuse to new areas in India and needs attention as it can cause severe hemorrhagic fever. Here in this study, we scanned the virus genome for prediction of miRNAs that can inhibit host target genes. VMir, tool was used for extraction of pre-miRNAs. A total of four miRNAs were found and submitted to ViralMir for classification in to real or pseudo. Interestingly, all four pre-miRNAs were classified as real.Eight mature miRNAs were located in pre-miRNAs by Mature Bayes. A total of 539 human target genes has been identified by using miRDB but ANGPT1 (angiopoietin 1) and TFRC (transferrin receptor) genes were screened to play role in hemorrhagic fever and neurological problems. GO analysis of target genes also supported the evidences.

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“…To date, RNA virus-encoded miRNAs have been identified in Hepatitis C virus [15], Human Immunodeficiency virus (HIV) [16], Bovine Leukemia virus (BLV) [17], West Nile virus (WNV) [18], Dengue virus(DENV) [19] and Middle East Respiratory Syndrome (MERS) coronavirus [20]. Very recent studies revealed that the antigenome of another cytoplasmic RNA virus, Hepatitis A virus (HAV), could be processed into miRNA-like small RNAs by the cellular miRNA processing machinery, similar to virus genomes [21].…”

Section: Introductionmentioning

confidence: 99%

Identification of MicroRNA-Like Molecules Derived from the Antigenome RNA of Hepatitis C Virus: A Bioinformatics Approach

Cristina¹,

Recarey²

2016

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MicroRNAs (miRNAs) are small, noncoding RNA molecules that play important roles in the regulation of gene expression of the cell. Recent studies have described cytoplasmic RNA virus genomederived miRNAs. Moreover, miRNAs have also been encountered in the reverse strand of the viral mRNA, revealing the presence of miRNAs in replication intermediaries. In order to get insight into the possible role of Hepatitis C Virus (HCV) antigenome in relation to miRNA coding, we computationally identified potential miRNAs on the antigenome of HCV reference strain H77. By utilizing a series of bioinformatics tools, we identified a miRNA present in the antigenomeof HCV H77 strain. This miRNA maps in the 5'non-translated region (5'UTR) of the HCV genome and is found to be conserved among HCV genotypes and sub-types. In silico target prediction generated 17 cellular genes. These potential targets are involved in apoptosis as well as immune response pathways, suggesting that they could play a role in the pathogenesis caused by viral infection. The results of these studies revealed the presence of a viral miRNA in the negative-sense RNA strand used as a replication template for the HCV genome, as observed for other RNA viruses.

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Computational Identification of Dengue Virus MicroRNA-Like Structures and Their Cellular Targets

Cited by 17 publications

References 28 publications

Computational identification of hepatitis E virus‐encoded microRNAs and their targets in human

Computational identification of hepatitis E virus‐encoded microRNAs and their targets in human

Genome Wide Computational Prediction of miRNAs in Kyasanur Forest Disease Virus and their Targeted Genes in Human

Identification of MicroRNA-Like Molecules Derived from the Antigenome RNA of Hepatitis C Virus: A Bioinformatics Approach

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