Conserved generation of short products at piRNA loci
Identifieur interne : 000152 ( France/Analysis ); précédent : 000151; suivant : 000153Conserved generation of short products at piRNA loci
Auteurs : Philipp Berninger [Suisse, France] ; Lukasz Jaskiewicz [Suisse] ; Mohsen Khorshid [Suisse] ; Mihaela Zavolan [Suisse]Source :
- BMC Genomics [ 1471-2164 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Petit ARN interférent, Platypus, Rétroéléments.
- Animaux, Mâle, Rats, Souris.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Small Interfering, Retroelements.
- genetics : Platypus.
- Animals, Male, Mice, Rats.
Abstract
The piRNA pathway operates in animal germ lines to ensure genome integrity through retrotransposon silencing. The Piwi protein-associated small RNAs (piRNAs) guide Piwi proteins to retrotransposon transcripts, which are degraded and thereby post-transcriptionally silenced through a ping-pong amplification process. Cleavage of the retrotransposon transcript defines at the same time the 5' end of a secondary piRNA that will in turn guide a Piwi protein to a primary piRNA precursor, thereby amplifying primary piRNAs. Although several studies provided evidence that this mechanism is conserved among metazoa, how the process is initiated and what enzymatic activities are responsible for generating the primary and secondary piRNAs are not entirely clear.
Here we analyzed small RNAs from three mammalian species, seeking to gain further insight into the mechanisms responsible for the piRNA amplification loop. We found that in all these species piRNA-directed targeting is accompanied by the generation of short sequences that have a very precisely defined length, 19 nucleotides, and a specific spatial relationship with the guide piRNAs.
This suggests that the processing of the 5' product of piRNA-guided cleavage occurs while the piRNA target is engaged by the Piwi protein. Although they are not stabilized through methylation of their 3' ends, the 19-mers are abundant not only in testes lysates but also in immunoprecipitates of Miwi and Mili proteins. They will enable more accurate identification of piRNA loci in deep sequencing data sets.
Url:
DOI: 10.1186/1471-2164-12-46
PubMed: 21247452
PubMed Central: 3037900
Affiliations:
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PMC:3037900Le document en format XML
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xml:lang="fr">Suisse</country><wicri:regionArea>Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel</wicri:regionArea><wicri:noRegion>4056 Basel</wicri:noRegion></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">EMBL Grenoble, 6 rue Jules Horowitz, 38042 Grenoble, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>EMBL Grenoble, 6 rue Jules Horowitz, 38042 Grenoble</wicri:regionArea><placeName><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Jaskiewicz, Lukasz" sort="Jaskiewicz, Lukasz" uniqKey="Jaskiewicz L" first="Lukasz" last="Jaskiewicz">Lukasz Jaskiewicz</name><affiliation wicri:level="1"><nlm:aff id="I1">Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel</wicri:regionArea><wicri:noRegion>4056 Basel</wicri:noRegion></affiliation></author><author><name sortKey="Khorshid, Mohsen" sort="Khorshid, Mohsen" uniqKey="Khorshid M" first="Mohsen" last="Khorshid">Mohsen Khorshid</name><affiliation wicri:level="1"><nlm:aff id="I1">Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel</wicri:regionArea><wicri:noRegion>4056 Basel</wicri:noRegion></affiliation></author><author><name sortKey="Zavolan, Mihaela" sort="Zavolan, Mihaela" uniqKey="Zavolan M" first="Mihaela" last="Zavolan">Mihaela Zavolan</name><affiliation wicri:level="1"><nlm:aff id="I1">Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel</wicri:regionArea><wicri:noRegion>4056 Basel</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Male</term><term>Mice</term><term>Platypus (genetics)</term><term>RNA, Small Interfering (genetics)</term><term>Rats</term><term>Retroelements (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Mâle</term><term>Petit ARN interférent (génétique)</term><term>Platypus (génétique)</term><term>Rats</term><term>Rétroéléments (génétique)</term><term>Souris</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Small Interfering</term><term>Retroelements</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Platypus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Petit ARN interférent</term><term>Platypus</term><term>Rétroéléments</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Male</term><term>Mice</term><term>Rats</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Mâle</term><term>Rats</term><term>Souris</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The piRNA pathway operates in animal germ lines to ensure genome integrity through retrotransposon silencing. The Piwi protein-associated small RNAs (piRNAs) guide Piwi proteins to retrotransposon transcripts, which are degraded and thereby post-transcriptionally silenced through a ping-pong amplification process. Cleavage of the retrotransposon transcript defines at the same time the 5' end of a secondary piRNA that will in turn guide a Piwi protein to a primary piRNA precursor, thereby amplifying primary piRNAs. Although several studies provided evidence that this mechanism is conserved among metazoa, how the process is initiated and what enzymatic activities are responsible for generating the primary and secondary piRNAs are not entirely clear.</p></sec><sec><title>Results</title><p>Here we analyzed small RNAs from three mammalian species, seeking to gain further insight into the mechanisms responsible for the piRNA amplification loop. We found that in all these species piRNA-directed targeting is accompanied by the generation of short sequences that have a very precisely defined length, 19 nucleotides, and a specific spatial relationship with the guide piRNAs.</p></sec><sec><title>Conclusions</title><p>This suggests that the processing of the 5' product of piRNA-guided cleavage occurs while the piRNA target is engaged by the Piwi protein. Although they are not stabilized through methylation of their 3' ends, the 19-mers are abundant not only in testes lysates but also in immunoprecipitates of Miwi and Mili proteins. They will enable more accurate identification of piRNA loci in deep sequencing data sets.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Vagin, Vv" uniqKey="Vagin V">VV Vagin</name></author><author><name sortKey="Sigova, A" uniqKey="Sigova A">A Sigova</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author><author><name sortKey="Seitz, H" uniqKey="Seitz H">H Seitz</name></author><author><name sortKey="Gvozdev, V" uniqKey="Gvozdev V">V Gvozdev</name></author><author><name sortKey="Zamore, Pd D" uniqKey="Zamore P">PD D Zamore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saito, K" uniqKey="Saito K">K Saito</name></author><author><name sortKey="Nishida, Km" uniqKey="Nishida K">KM Nishida</name></author><author><name sortKey="Mori, T" uniqKey="Mori T">T Mori</name></author><author><name sortKey="Kawamura, Y" uniqKey="Kawamura Y">Y 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Zavolan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olsen, Aj" uniqKey="Olsen A">AJ Olsen</name></author><author><name sortKey="Brennecke, J" uniqKey="Brennecke J">J Brennecke</name></author><author><name sortKey="Aravin, Aa" uniqKey="Aravin A">AA Aravin</name></author><author><name sortKey="Hannon, Gj" uniqKey="Hannon G">GJ Hannon</name></author><author><name sortKey="Sachidanandam, R" uniqKey="Sachidanandam R">R Sachidanandam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hafner, M" uniqKey="Hafner M">M Hafner</name></author><author><name sortKey="Landgraf, P" uniqKey="Landgraf P">P Landgraf</name></author><author><name sortKey="Ludwig, J" uniqKey="Ludwig J">J Ludwig</name></author><author><name sortKey="Rice, A" uniqKey="Rice A">A Rice</name></author><author><name sortKey="Ojo, T" uniqKey="Ojo T">T Ojo</name></author><author><name sortKey="Lin, C" uniqKey="Lin C">C Lin</name></author><author><name sortKey="Holoch, D" uniqKey="Holoch D">D Holoch</name></author><author><name sortKey="Lim, C" uniqKey="Lim C">C Lim</name></author><author><name sortKey="Tuschl, T" uniqKey="Tuschl T">T Tuschl</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>Suisse</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Rhône-Alpes</li></region><settlement><li>Grenoble</li></settlement></list><tree><country name="Suisse"><noRegion><name sortKey="Berninger, Philipp" sort="Berninger, Philipp" uniqKey="Berninger P" first="Philipp" last="Berninger">Philipp Berninger</name></noRegion><name sortKey="Jaskiewicz, Lukasz" sort="Jaskiewicz, Lukasz" uniqKey="Jaskiewicz L" first="Lukasz" last="Jaskiewicz">Lukasz Jaskiewicz</name><name sortKey="Khorshid, Mohsen" sort="Khorshid, Mohsen" uniqKey="Khorshid M" first="Mohsen" last="Khorshid">Mohsen Khorshid</name><name sortKey="Zavolan, Mihaela" sort="Zavolan, Mihaela" uniqKey="Zavolan M" first="Mihaela" last="Zavolan">Mihaela Zavolan</name></country><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Berninger, Philipp" sort="Berninger, Philipp" uniqKey="Berninger P" first="Philipp" last="Berninger">Philipp Berninger</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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