The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs
Identifieur interne : 001B73 ( Ncbi/Checkpoint ); précédent : 001B72; suivant : 001B74The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs
Auteurs : Hongtao Hu [États-Unis] ; Aaron M. Rashotte [États-Unis] ; Narendra K. Singh [États-Unis] ; David B. Weaver [États-Unis] ; Leslie R. Goertzen [États-Unis] ; Shree R. Singh [États-Unis] ; Robert D. Locy [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
MicroRNAs (miRNAs) and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs) are two distinct subfamilies of small RNAs (sRNAs) that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs) are processed from longer RNA precursors by DICER-LIKE proteins (DCLs).
Url:
DOI: 10.1371/journal.pone.0127468
PubMed: 26070200
PubMed Central: 4466472
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by <italic>In Silico</italic> Analysis of <italic>Gossypium arboreum</italic> L. Leaf, Flower and Boll Small Regulatory RNAs</title><author><name sortKey="Hu, Hongtao" sort="Hu, Hongtao" uniqKey="Hu H" first="Hongtao" last="Hu">Hongtao Hu</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104</wicri:regionArea><wicri:noRegion>AL 33104</wicri:noRegion></affiliation></author><author><name sortKey="Rashotte, Aaron M" sort="Rashotte, Aaron M" uniqKey="Rashotte A" first="Aaron M." last="Rashotte">Aaron M. Rashotte</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Narendra K" sort="Singh, Narendra K" uniqKey="Singh N" first="Narendra K." last="Singh">Narendra K. Singh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Weaver, David B" sort="Weaver, David B" uniqKey="Weaver D" first="David B." last="Weaver">David B. Weaver</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Goertzen, Leslie R" sort="Goertzen, Leslie R" uniqKey="Goertzen L" first="Leslie R." last="Goertzen">Leslie R. Goertzen</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Shree R" sort="Singh, Shree R" uniqKey="Singh S" first="Shree R." last="Singh">Shree R. Singh</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104</wicri:regionArea><wicri:noRegion>AL 33104</wicri:noRegion></affiliation></author><author><name sortKey="Locy, Robert D" sort="Locy, Robert D" uniqKey="Locy R" first="Robert D." last="Locy">Robert D. Locy</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26070200</idno><idno type="pmc">4466472</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466472</idno><idno type="RBID">PMC:4466472</idno><idno type="doi">10.1371/journal.pone.0127468</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000154</idno><idno type="wicri:Area/Pmc/Curation">000154</idno><idno type="wicri:Area/Pmc/Checkpoint">000337</idno><idno type="wicri:Area/Ncbi/Merge">001B73</idno><idno type="wicri:Area/Ncbi/Curation">001B73</idno><idno type="wicri:Area/Ncbi/Checkpoint">001B73</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by <italic>In Silico</italic> Analysis of <italic>Gossypium arboreum</italic> L. Leaf, Flower and Boll Small Regulatory RNAs</title><author><name sortKey="Hu, Hongtao" sort="Hu, Hongtao" uniqKey="Hu H" first="Hongtao" last="Hu">Hongtao Hu</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104</wicri:regionArea><wicri:noRegion>AL 33104</wicri:noRegion></affiliation></author><author><name sortKey="Rashotte, Aaron M" sort="Rashotte, Aaron M" uniqKey="Rashotte A" first="Aaron M." last="Rashotte">Aaron M. Rashotte</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Narendra K" sort="Singh, Narendra K" uniqKey="Singh N" first="Narendra K." last="Singh">Narendra K. Singh</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Weaver, David B" sort="Weaver, David B" uniqKey="Weaver D" first="David B." last="Weaver">David B. Weaver</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Crop, Soil & Environmental Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Goertzen, Leslie R" sort="Goertzen, Leslie R" uniqKey="Goertzen L" first="Leslie R." last="Goertzen">Leslie R. Goertzen</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Shree R" sort="Singh, Shree R" uniqKey="Singh S" first="Shree R." last="Singh">Shree R. Singh</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Nano Biotechnology Research, Alabama State University, Montgomery, AL 33104</wicri:regionArea><wicri:noRegion>AL 33104</wicri:noRegion></affiliation></author><author><name sortKey="Locy, Robert D" sort="Locy, Robert D" uniqKey="Locy R" first="Robert D." last="Locy">Robert D. Locy</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Department of Biological Sciences, Auburn University, Auburn, AL 36849, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Auburn University, Auburn, AL 36849</wicri:regionArea><wicri:noRegion>AL 36849</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>MicroRNAs (miRNAs) and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs) are two distinct subfamilies of small RNAs (sRNAs) that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs) are processed from longer RNA precursors by DICER-LIKE proteins (DCLs). <italic>Gossypium arboreum</italic> L., also known as tree cotton or Asian cotton, is a diploid, possibly ancestral relative of tetraploid <italic>Gossypium hirsutum</italic> L., the predominant type of commercially grown cotton worldwide known as upland cotton. To understand the biological significance of these gene regulators in <italic>G</italic>. <italic>arboreum</italic>, a bioinformatics analysis was performed on <italic>G</italic>. <italic>arboreum</italic> small RNAs produced from <italic>G</italic>. <italic>arboreum</italic> leaf, flower, and boll tissues. Consequently, 263 miRNAs derived from 353 precursors, including 155 conserved miRNAs (cs-miRNAs) and 108 novel lineage-specific miRNAs (ls-miRNAs). Along with miRNAs, 2,033 miRNA variants (isomiRNAs) were identified as well. Those isomiRNAs with variation at the 3’-miRNA end were expressed at the highest levels, compared to other types of variants. In addition, 755 pha-siRNAs derived 319 pha-siRNA gene transcripts (PGTs) were identified, and the potential pha-siRNA initiators were predicted. Also, 2,251 non-phased siRNAs were found as well, of which 1,088 appeared to be produced by so-called <italic>cis</italic>- or <italic>trans</italic>-cleavage of the PGTs observed at positions differing from pha-siRNAs. Of those sRNAs, 148 miRNAs/isomiRNAs and 274 phased/non-phased siRNAs were differentially expressed in one or more pairs of tissues examined. Target analysis revealed that target genes for both miRNAs and pha-siRNAs are involved a broad range of metabolic and enzymatic activities. We demonstrate that secondary siRNA production could result from initial cleavage of precursors by both miRNAs or isomiRNAs, and that subsequently produced phased and unphased siRNAs could result that also serve as triggers of a second round of both <italic>cis</italic>- and <italic>trans</italic>-cleavage of additional siRNAs, leading to the formation of complex sRNA regulatory networks mediating posttranscriptional gene silencing. Results from this study extended our knowledge on <italic>G</italic>. <italic>arboreum</italic> sRNAs and their biological importance, which would facilitate future studies on regulatory mechanism of tissue development in cotton and other plant species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Khraiwesh, B" uniqKey="Khraiwesh B">B Khraiwesh</name></author><author><name sortKey="Zhu, Jk" uniqKey="Zhu J">JK Zhu</name></author><author><name sortKey="Zhu, J" uniqKey="Zhu J">J Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, C" uniqKey="Zhang C">C Zhang</name></author><author><name sortKey="Li, G" uniqKey="Li G">G Li</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Zhu, S" uniqKey="Zhu S">S Zhu</name></author><author><name sortKey="Li, H" uniqKey="Li H">H Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cho, Sh" uniqKey="Cho S">SH Cho</name></author><author><name sortKey="Coruh, C" uniqKey="Coruh C">C Coruh</name></author><author><name sortKey="Axtell, Mj" uniqKey="Axtell M">MJ Axtell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Axtell, Mj" uniqKey="Axtell M">MJ Axtell</name></author><author><name sortKey="Jan, C" uniqKey="Jan C">C Jan</name></author><author><name sortKey="Rajagopalan, R" uniqKey="Rajagopalan R">R Rajagopalan</name></author><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fei, Q" uniqKey="Fei Q">Q Fei</name></author><author><name sortKey="Xia, R" uniqKey="Xia R">R Xia</name></author><author><name sortKey="Meyers, Bc" uniqKey="Meyers B">BC Meyers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Visser, M" uniqKey="Visser M">M Visser</name></author><author><name sortKey="Van Der Walt, Ap" uniqKey="Van Der Walt A">AP van der Walt</name></author><author><name sortKey="Maree, Hj" uniqKey="Maree H">HJ Maree</name></author><author><name sortKey="Rees, Dj" uniqKey="Rees D">DJ Rees</name></author><author><name sortKey="Burger, Jt" uniqKey="Burger J">JT Burger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Xia, J" uniqKey="Xia J">J Xia</name></author><author><name sortKey="Lii, Ye" uniqKey="Lii Y">YE Lii</name></author><author><name sortKey="Barrera Figueroa, Be" uniqKey="Barrera Figueroa B">BE Barrera-Figueroa</name></author><author><name sortKey="Zhou, X" uniqKey="Zhou X">X Zhou</name></author><author><name sortKey="Gao, S" uniqKey="Gao S">S. 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uniqKey="Xu H">H Xu</name></author><author><name sortKey="Llewellyn, D" uniqKey="Llewellyn D">D Llewellyn</name></author><author><name sortKey="Wilson, I" uniqKey="Wilson I">I Wilson</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Hu, Hongtao" sort="Hu, Hongtao" uniqKey="Hu H" first="Hongtao" last="Hu">Hongtao Hu</name></noRegion><name sortKey="Goertzen, Leslie R" sort="Goertzen, Leslie R" uniqKey="Goertzen L" first="Leslie R." last="Goertzen">Leslie R. Goertzen</name><name sortKey="Hu, Hongtao" sort="Hu, Hongtao" uniqKey="Hu H" first="Hongtao" last="Hu">Hongtao Hu</name><name sortKey="Locy, Robert D" sort="Locy, Robert D" uniqKey="Locy R" first="Robert D." last="Locy">Robert D. Locy</name><name sortKey="Rashotte, Aaron M" sort="Rashotte, Aaron M" uniqKey="Rashotte A" first="Aaron M." last="Rashotte">Aaron M. Rashotte</name><name sortKey="Singh, Narendra K" sort="Singh, Narendra K" uniqKey="Singh N" first="Narendra K." last="Singh">Narendra K. Singh</name><name sortKey="Singh, Shree R" sort="Singh, Shree R" uniqKey="Singh S" first="Shree R." last="Singh">Shree R. Singh</name><name sortKey="Weaver, David B" sort="Weaver, David B" uniqKey="Weaver D" first="David B." last="Weaver">David B. Weaver</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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