Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans
Identifieur interne : 002982 ( Main/Exploration ); précédent : 002981; suivant : 002983Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans
Auteurs : Suvi Asikainen [Finlande] ; Liisa Heikkinen [Finlande] ; Garry Wong [Finlande] ; Markus Storvik [Finlande]Source :
- BMC Genomics [ 1471-2164 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Small Interfering.
- genetics : Caenorhabditis elegans, Genome, Helminth.
- Animals, Base Sequence, Conserved Sequence, Gene Library, Molecular Sequence Data.
Abstract
Small interfering RNA (siRNA) molecules mediate sequence specific silencing in RNA interference (RNAi), a gene regulatory phenomenon observed in almost all organisms. Large scale sequencing of small RNA libraries obtained from
Systematic trends in categorization of target genes according to the specific length of siRNA sequences were observed: 18- to 22-mer siRNAs were associated with genes required for embryonic development; 23-mers were associated uniquely with post-embryonic development; 24–26-mers were associated with phosphorus metabolism or protein modification. Moreover, we observe that some argonaute related genes associate with siRNAs with multiple reads. Sequence frequency graphs suggest that different lengths of siRNAs share similarities in overall sequence structure: the 5' end begins with G, while the body predominates with U and C.
These results suggest that the lengths of endogenous siRNA molecules are consequential to their biological functions since the gene ontology categories for their cognate mRNA targets vary depending upon their lengths.
Url:
DOI: 10.1186/1471-2164-9-270
PubMed: 18522735
PubMed Central: 2440555
Affiliations:
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Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Department of Neurobiology, A. I. Virtanen Institute, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Neurobiology, A. I. Virtanen Institute, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation></author><author><name sortKey="Heikkinen, Liisa" sort="Heikkinen, Liisa" uniqKey="Heikkinen L" first="Liisa" last="Heikkinen">Liisa Heikkinen</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Department of Neurobiology, A. I. Virtanen Institute, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Neurobiology, A. I. Virtanen Institute, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation></author><author><name sortKey="Wong, Garry" sort="Wong, Garry" uniqKey="Wong G" first="Garry" last="Wong">Garry Wong</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Department of Neurobiology, A. I. Virtanen Institute, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Neurobiology, A. I. Virtanen Institute, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation></author><author><name sortKey="Storvik, Markus" sort="Storvik, Markus" uniqKey="Storvik M" first="Markus" last="Storvik">Markus Storvik</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Biosciences, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Pharmacology and Toxicology, University of Kuopio, P.O. Box 1627, Kuopio 70211, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Pharmacology and Toxicology, University of Kuopio, P.O. Box 1627, Kuopio 70211</wicri:regionArea><wicri:noRegion>Kuopio 70211</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Caenorhabditis elegans (genetics)</term><term>Conserved Sequence</term><term>Gene Library</term><term>Genome, Helminth (genetics)</term><term>Molecular Sequence Data</term><term>RNA, Small Interfering (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Banque de gènes</term><term>Caenorhabditis elegans (génétique)</term><term>Données de séquences moléculaires</term><term>Génome d'helminthe (génétique)</term><term>Petit ARN interférent (génétique)</term><term>Séquence conservée</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Small Interfering</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Caenorhabditis elegans</term><term>Genome, Helminth</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Caenorhabditis elegans</term><term>Génome d'helminthe</term><term>Petit ARN interférent</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Conserved Sequence</term><term>Gene Library</term><term>Molecular Sequence Data</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Banque de gènes</term><term>Données de séquences moléculaires</term><term>Séquence conservée</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Small interfering RNA (siRNA) molecules mediate sequence specific silencing in RNA interference (RNAi), a gene regulatory phenomenon observed in almost all organisms. Large scale sequencing of small RNA libraries obtained from <italic>C. elegans </italic>has revealed that a broad spectrum of siRNAs is endogenously transcribed from genomic sequences. The biological role and molecular diversity of <italic>C. elegans </italic>endogenous siRNA (endo-siRNA) molecules, nonetheless, remain poorly understood. In order to gain insight into their biological function, we annotated two large libraries of endo-siRNA sequences, identified their cognate targets, and performed gene ontology analysis to identify enriched functional categories.</p></sec><sec><title>Results</title><p>Systematic trends in categorization of target genes according to the specific length of siRNA sequences were observed: 18- to 22-mer siRNAs were associated with genes required for embryonic development; 23-mers were associated uniquely with post-embryonic development; 24–26-mers were associated with phosphorus metabolism or protein modification. Moreover, we observe that some argonaute related genes associate with siRNAs with multiple reads. Sequence frequency graphs suggest that different lengths of siRNAs share similarities in overall sequence structure: the 5' end begins with G, while the body predominates with U and C.</p></sec><sec><title>Conclusion</title><p>These results suggest that the lengths of endogenous siRNA molecules are consequential to their biological functions since the gene ontology categories for their cognate mRNA targets vary depending upon their lengths.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Finlande</li></country></list><tree><country name="Finlande"><noRegion><name sortKey="Asikainen, Suvi" sort="Asikainen, Suvi" uniqKey="Asikainen S" first="Suvi" last="Asikainen">Suvi Asikainen</name></noRegion><name sortKey="Asikainen, Suvi" sort="Asikainen, Suvi" uniqKey="Asikainen S" first="Suvi" last="Asikainen">Suvi Asikainen</name><name sortKey="Heikkinen, Liisa" sort="Heikkinen, Liisa" uniqKey="Heikkinen L" first="Liisa" last="Heikkinen">Liisa Heikkinen</name><name sortKey="Heikkinen, Liisa" sort="Heikkinen, Liisa" uniqKey="Heikkinen L" first="Liisa" last="Heikkinen">Liisa Heikkinen</name><name sortKey="Storvik, Markus" sort="Storvik, Markus" uniqKey="Storvik M" first="Markus" last="Storvik">Markus Storvik</name><name sortKey="Storvik, Markus" sort="Storvik, Markus" uniqKey="Storvik M" first="Markus" last="Storvik">Markus Storvik</name><name sortKey="Wong, Garry" sort="Wong, Garry" uniqKey="Wong G" first="Garry" last="Wong">Garry Wong</name><name sortKey="Wong, Garry" sort="Wong, Garry" uniqKey="Wong G" first="Garry" last="Wong">Garry Wong</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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