Serveur d'exploration MERS

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A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome

Identifieur interne : 001149 ( Pmc/Checkpoint ); précédent : 001148; suivant : 001150

A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome

Auteurs : Md Mahmudul Hasan [États-Unis] ; Rozina Akter [États-Unis] ; Md. Shahin Ullah [Bangladesh] ; Md. Jaynul Abedin [Bangladesh] ; G. M. Ahsan Ullah [Bangladesh] ; Md. Zakir Hossain [États-Unis]

Source :

RBID : PMC:4283225

Abstract

The new epidemic Middle East Respiratory Syndrome (MERS) is caused by a type of human coronavirus called MERS-CoV which has global fatality rate of about 30%. We are investigating potential antiviral therapeutics against MERS-CoV by using host microRNAs (miRNAs) which may downregulate viral gene expression to quell viral replication. We computationally predicted potential 13 cellular miRNAs from 11 potential hairpin sequences of MERS-CoV genome. Our study provided an interesting hypothesis that those miRNAs, that is, hsa-miR-628-5p, hsa-miR-6804-3p, hsa-miR-4289, hsa-miR-208a-3p, hsa-miR-510-3p, hsa-miR-18a-3p, hsa-miR-329-3p, hsa-miR-548ax, hsa-miR-3934-5p, hsa-miR-4474-5p, hsa-miR-7974, hsa-miR-6865-5p, and hsa-miR-342-3p, would be antiviral therapeutics against MERS-CoV infection.


Url:
DOI: 10.1155/2014/967946
PubMed: 25610462
PubMed Central: 4283225


Affiliations:


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PMC:4283225

Le document en format XML

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<p>The new epidemic Middle East Respiratory Syndrome (MERS) is caused by a type of human coronavirus called MERS-CoV which has global fatality rate of about 30%. We are investigating potential antiviral therapeutics against MERS-CoV by using host microRNAs (miRNAs) which may downregulate viral gene expression to quell viral replication. We computationally predicted potential 13 cellular miRNAs from 11 potential hairpin sequences of MERS-CoV genome. Our study provided an interesting hypothesis that those miRNAs, that is, hsa-miR-628-5p, hsa-miR-6804-3p, hsa-miR-4289, hsa-miR-208a-3p, hsa-miR-510-3p, hsa-miR-18a-3p, hsa-miR-329-3p, hsa-miR-548ax, hsa-miR-3934-5p, hsa-miR-4474-5p, hsa-miR-7974, hsa-miR-6865-5p, and hsa-miR-342-3p, would be antiviral therapeutics against MERS-CoV infection.</p>
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</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Adv Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">Adv Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">ABI</journal-id>
<journal-title-group>
<journal-title>Advances in Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1687-8027</issn>
<issn pub-type="epub">1687-8035</issn>
<publisher>
<publisher-name>Hindawi Publishing Corporation</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">25610462</article-id>
<article-id pub-id-type="pmc">4283225</article-id>
<article-id pub-id-type="doi">10.1155/2014/967946</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>A Computational Approach for Predicting Role of Human MicroRNAs in MERS-CoV Genome</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Hasan</surname>
<given-names>Md Mahmudul</given-names>
</name>
<xref ref-type="aff" rid="I1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Akter</surname>
<given-names>Rozina</given-names>
</name>
<xref ref-type="aff" rid="I2">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ullah</surname>
<given-names>Md. Shahin</given-names>
</name>
<xref ref-type="aff" rid="I3">
<sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Abedin</surname>
<given-names>Md. Jaynul</given-names>
</name>
<xref ref-type="aff" rid="I4">
<sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ullah</surname>
<given-names>G. M. Ahsan</given-names>
</name>
<xref ref-type="aff" rid="I5">
<sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-3679-612X</contrib-id>
<name>
<surname>Hossain</surname>
<given-names>Md. Zakir</given-names>
</name>
<xref ref-type="aff" rid="I2">
<sup>2</sup>
</xref>
<xref ref-type="corresp" rid="cor1">
<sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="I1">
<sup>1</sup>
Institute of Biomedical Studies, Baylor University, Waco, TX 76706, USA</aff>
<aff id="I2">
<sup>2</sup>
BioMedNanoTech, Inc., 500 South University Avenue Suite 319, Little Rock, AR 72205, USA</aff>
<aff id="I3">
<sup>3</sup>
Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna 9208, Bangladesh</aff>
<aff id="I4">
<sup>4</sup>
Civil Engineering Department, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh</aff>
<aff id="I5">
<sup>5</sup>
Environment Science Discipline, Khulna University, Khulna 9208, Bangladesh</aff>
<author-notes>
<corresp id="cor1">*Md. Zakir Hossain:
<email>mzh.ceo@biomednanotech.com</email>
</corresp>
<fn fn-type="other">
<p>Academic Editor: Huixiao Hong</p>
</fn>
</author-notes>
<pub-date pub-type="ppub">
<year>2014</year>
</pub-date>
<pub-date pub-type="epub">
<day>23</day>
<month>12</month>
<year>2014</year>
</pub-date>
<volume>2014</volume>
<elocation-id>967946</elocation-id>
<history>
<date date-type="received">
<day>27</day>
<month>6</month>
<year>2014</year>
</date>
<date date-type="rev-recd">
<day>24</day>
<month>9</month>
<year>2014</year>
</date>
<date date-type="accepted">
<day>27</day>
<month>9</month>
<year>2014</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright © 2014 Md Mahmudul Hasan et al.</copyright-statement>
<copyright-year>2014</copyright-year>
<license xlink:href="https://creativecommons.org/licenses/by/3.0/">
<license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract>
<p>The new epidemic Middle East Respiratory Syndrome (MERS) is caused by a type of human coronavirus called MERS-CoV which has global fatality rate of about 30%. We are investigating potential antiviral therapeutics against MERS-CoV by using host microRNAs (miRNAs) which may downregulate viral gene expression to quell viral replication. We computationally predicted potential 13 cellular miRNAs from 11 potential hairpin sequences of MERS-CoV genome. Our study provided an interesting hypothesis that those miRNAs, that is, hsa-miR-628-5p, hsa-miR-6804-3p, hsa-miR-4289, hsa-miR-208a-3p, hsa-miR-510-3p, hsa-miR-18a-3p, hsa-miR-329-3p, hsa-miR-548ax, hsa-miR-3934-5p, hsa-miR-4474-5p, hsa-miR-7974, hsa-miR-6865-5p, and hsa-miR-342-3p, would be antiviral therapeutics against MERS-CoV infection.</p>
</abstract>
</article-meta>
</front>
<floats-group>
<fig id="fig1" orientation="portrait" position="float">
<label>Figure 1</label>
<caption>
<p>Schematic representation of human miRNA prediction on MERS-CoV viral genome [
<xref rid="B27" ref-type="bibr">27</xref>
].</p>
</caption>
<graphic xlink:href="ABI2014-967946.001"></graphic>
</fig>
<fig id="fig2" orientation="portrait" position="float">
<label>Figure 2</label>
<caption>
<p>Graphical view of VMir analysis of the MERS-CoV genome. (a) All hairpins of pre-miRNAs were shown using default settings. The hairpin is plotted according to the positions of the viral genome. (b) Customized view of predicted pre-miRNA after filtering (minimum hairpin size: 60 nt, maximum hairpin size: 120 nt, minimum hairpin score: 115, and minimum window count: 25).</p>
</caption>
<graphic xlink:href="ABI2014-967946.002"></graphic>
</fig>
<fig id="fig3" orientation="portrait" position="float">
<label>Figure 3</label>
<caption>
<p>Mounting plot of predicted secondary structure of precursor miRNA hairpin. Here, hairpin MR268 was shown as an example. Red line, green line, and blue line were used to show the minimum free energy (MFE), the thermodynamic ensemble of RNA (pf), and the centroid structures, respectively.</p>
</caption>
<graphic xlink:href="ABI2014-967946.003"></graphic>
</fig>
<fig id="fig4" orientation="portrait" position="float">
<label>Figure 4</label>
<caption>
<p>Predicated secondary structure of potential hairpins candidate of MERS-CoV. Only centroid structures were depicted.</p>
</caption>
<graphic xlink:href="ABI2014-967946.004"></graphic>
</fig>
<fig id="figbox1" orientation="portrait" position="float">
<label>Box 1</label>
<caption>
<p>Hybridization between microRNA and viral RNA using RNA hybrid program. The program finds the energetically most favorable hybridization sites of a miRNA in a large hairpin of viral RNA.</p>
</caption>
<graphic xlink:href="ABI2014-967946.figbox.001"></graphic>
</fig>
<table-wrap id="tab1" orientation="portrait" position="float">
<label>Table 1</label>
<caption>
<p>Alignments of precursor miRNAs hairpin sequences with human miRNAs.</p>
</caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" rowspan="1" colspan="1">S. number</th>
<th align="center" rowspan="1" colspan="1">Hairpin</th>
<th align="center" rowspan="1" colspan="1">Score</th>
<th align="center" colspan="4" rowspan="1">Alignments between human microRNA and MERS CoV</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" rowspan="2" colspan="1">1</td>
<td align="center" rowspan="2" colspan="1">MD5</td>
<td align="center" rowspan="2" colspan="1">151.6</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">37</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i001.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">17</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-628-5p</td>
<td align="center" rowspan="1" colspan="1">1</td>
<td align="left" rowspan="1" colspan="1">21</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">2</td>
<td align="center" rowspan="2" colspan="1">MD17</td>
<td align="center" rowspan="2" colspan="1">140</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">61</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i002.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">41</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1">hsa-miR-6804-3p</td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">22</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="4" colspan="1">3</td>
<td align="center" rowspan="4" colspan="1">MD110</td>
<td align="center" rowspan="4" colspan="1">181.1</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">44</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i003.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">61</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-3934-5p </td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">19</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> UserSeq </td>
<td align="center" rowspan="1" colspan="1">71</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i004.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">52</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-4474-5p</td>
<td align="center" rowspan="1" colspan="1">1</td>
<td align="left" rowspan="1" colspan="1">20</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">4</td>
<td align="center" rowspan="2" colspan="1">MD157</td>
<td align="center" rowspan="2" colspan="1">151.6</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">38</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i005.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">56</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-4289</td>
<td align="center" rowspan="1" colspan="1"> 1</td>
<td align="left" rowspan="1" colspan="1">19</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="4" colspan="1">5</td>
<td align="center" rowspan="4" colspan="1">MD186</td>
<td align="center" rowspan="4" colspan="1">151.1</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">52</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i006.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">32</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-7974 </td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">22</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> UserSeq </td>
<td align="center" rowspan="1" colspan="1">59</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i007.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">41</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-6856-5p</td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">20</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">6</td>
<td align="center" rowspan="2" colspan="1">MD244</td>
<td align="center" rowspan="2" colspan="1">127.3</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">1</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i008.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">20</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-208a-3p</td>
<td align="center" rowspan="1" colspan="1">1</td>
<td align="left" rowspan="1" colspan="1">20</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">7</td>
<td align="center" rowspan="2" colspan="1">MD366</td>
<td align="center" rowspan="2" colspan="1">156.4</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">60</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i009.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">41</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-510-3p</td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">21</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">8</td>
<td align="center" rowspan="2" colspan="1">MR175</td>
<td align="center" rowspan="2" colspan="1">140.9</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">5</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i010.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">27</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-18a-3p</td>
<td align="center" rowspan="1" colspan="1">1</td>
<td align="left" rowspan="1" colspan="1">23</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">9</td>
<td align="center" rowspan="2" colspan="1">MR201</td>
<td align="center" rowspan="2" colspan="1">148.8</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">31</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i011.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">11</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-329-3p</td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">22</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">10</td>
<td align="center" rowspan="2" colspan="1">MR268</td>
<td align="center" rowspan="2" colspan="1">137</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">41</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i012.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">21</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-548ax</td>
<td align="center" rowspan="1" colspan="1">2</td>
<td align="left" rowspan="1" colspan="1">22</td>
</tr>
<tr>
<td align="center" colspan="7" rowspan="1">
<hr></hr>
</td>
</tr>
<tr>
<td align="left" rowspan="2" colspan="1">11</td>
<td align="center" rowspan="2" colspan="1">MR282</td>
<td align="center" rowspan="2" colspan="1">163.6</td>
<td align="center" rowspan="1" colspan="1">UserSeq </td>
<td align="center" rowspan="1" colspan="1">50</td>
<td align="left" rowspan="2" colspan="1">
<inline-graphic xlink:href="ABI2014-967946.tab1.i013.jpg"></inline-graphic>
</td>
<td align="left" rowspan="1" colspan="1">28</td>
</tr>
<tr>
<td align="center" rowspan="1" colspan="1"> hsa-miR-342-3p</td>
<td align="center" rowspan="1" colspan="1">1</td>
<td align="left" rowspan="1" colspan="1">23</td>
</tr>
</tbody>
</table>
</table-wrap>
</floats-group>
</pmc>
<affiliations>
<list>
<country>
<li>Bangladesh</li>
<li>États-Unis</li>
</country>
<region>
<li>Arkansas</li>
<li>Texas</li>
</region>
</list>
<tree>
<country name="États-Unis">
<region name="Texas">
<name sortKey="Hasan, Md Mahmudul" sort="Hasan, Md Mahmudul" uniqKey="Hasan M" first="Md Mahmudul" last="Hasan">Md Mahmudul Hasan</name>
</region>
<name sortKey="Akter, Rozina" sort="Akter, Rozina" uniqKey="Akter R" first="Rozina" last="Akter">Rozina Akter</name>
<name sortKey="Hossain, Md Zakir" sort="Hossain, Md Zakir" uniqKey="Hossain M" first="Md. Zakir" last="Hossain">Md. Zakir Hossain</name>
</country>
<country name="Bangladesh">
<noRegion>
<name sortKey="Ullah, Md Shahin" sort="Ullah, Md Shahin" uniqKey="Ullah M" first="Md. Shahin" last="Ullah">Md. Shahin Ullah</name>
</noRegion>
<name sortKey="Abedin, Md Jaynul" sort="Abedin, Md Jaynul" uniqKey="Abedin M" first="Md. Jaynul" last="Abedin">Md. Jaynul Abedin</name>
<name sortKey="Ullah, G M Ahsan" sort="Ullah, G M Ahsan" uniqKey="Ullah G" first="G. M. Ahsan" last="Ullah">G. M. Ahsan Ullah</name>
</country>
</tree>
</affiliations>
</record>

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