AustralieFrV1, PubMed, Checkpoint, bibRecord, 000165

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.

Identifieur interne : 000165 ( PubMed/Checkpoint ); précédent : 000164; suivant : 000166

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.

Auteurs : Valérie Cognat [France] ; Geoffrey Morelle [France] ; Cyrille Megel [France] ; Stéphanie Lalande [France] ; Jean Molinier [France] ; Timothée Vincent [France] ; Ian Small [Australie] ; Anne-Marie Duchêne [France] ; Laurence Maréchal-Drouard [France]

Source :

Nucleic acids research [ 1362-4962 ] ; 2017.

RBID : pubmed:27899576

Descripteurs français

English descriptors

KwdEn :
- Arabidopsis (genetics), Arabidopsis (metabolism), Arabidopsis Proteins (metabolism), Argonaute Proteins (metabolism), Cell Nucleus (genetics), Cell Nucleus (metabolism), Plant Leaves (genetics), Plant Leaves (metabolism), Plant Roots (genetics), Plant Roots (metabolism), Plastids (metabolism), RNA (metabolism), RNA, Chloroplast (metabolism), RNA, Transfer (chemistry), RNA, Transfer (metabolism), RNA, Untranslated (chemistry), RNA, Untranslated (metabolism), Stress, Physiological.
MESH :
- chemical , chemistry : RNA, Transfer, RNA, Untranslated.
- chemical , metabolism : Arabidopsis Proteins, Argonaute Proteins, RNA, RNA, Chloroplast, RNA, Transfer, RNA, Untranslated.
- genetics : Arabidopsis, Cell Nucleus, Plant Leaves, Plant Roots.
- metabolism : Arabidopsis, Cell Nucleus, Plant Leaves, Plant Roots, Plastids.
- Stress, Physiological.

Abstract

In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.

DOI: 10.1093/nar/gkw1122
PubMed: 27899576

Affiliations:

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<front><div type="abstract" xml:lang="en">In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.</div>
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<Abstract><AbstractText>In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.</AbstractText>
<CopyrightInformation>© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cognat</LastName>
<ForeName>Valérie</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Morelle</LastName>
<ForeName>Geoffrey</ForeName>
<Initials>G</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Megel</LastName>
<ForeName>Cyrille</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lalande</LastName>
<ForeName>Stéphanie</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Molinier</LastName>
<ForeName>Jean</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Vincent</LastName>
<ForeName>Timothée</ForeName>
<Initials>T</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Small</LastName>
<ForeName>Ian</ForeName>
<Initials>I</Initials>
<AffiliationInfo><Affiliation>Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Duchêne</LastName>
<ForeName>Anne-Marie</ForeName>
<Initials>AM</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Maréchal-Drouard</LastName>
<ForeName>Laurence</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Nucleic Acids Res</MedlineTA>
<NlmUniqueID>0411011</NlmUniqueID>
<ISSNLinking>0305-1048</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C117457">AGO1 protein, Arabidopsis</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D029681">Arabidopsis Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D060565">Argonaute Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018747">RNA, Chloroplast</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D022661">RNA, Untranslated</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C040111">RNA, mitochondrial</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>63231-63-0</RegistryNumber>
<NameOfSubstance UI="D012313">RNA</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>9014-25-9</RegistryNumber>
<NameOfSubstance UI="D012343">RNA, Transfer</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D029681" MajorTopicYN="N">Arabidopsis Proteins</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D060565" MajorTopicYN="N">Argonaute Proteins</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002467" MajorTopicYN="N">Cell Nucleus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018087" MajorTopicYN="N">Plastids</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018747" MajorTopicYN="N">RNA, Chloroplast</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012343" MajorTopicYN="N">RNA, Transfer</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D022661" MajorTopicYN="N">RNA, Untranslated</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013312" MajorTopicYN="N">Stress, Physiological</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year>
<Month>05</Month>
<Day>06</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2016</Year>
<Month>10</Month>
<Day>27</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2016</Year>
<Month>12</Month>
<Day>3</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2017</Year>
<Month>8</Month>
<Day>15</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2016</Year>
<Month>12</Month>
<Day>1</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">27899576</ArticleId>
<ArticleId IdType="pii">gkw1122</ArticleId>
<ArticleId IdType="doi">10.1093/nar/gkw1122</ArticleId>
<ArticleId IdType="pmc">PMC5389709</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>Australie</li>
<li>France</li>
</country>
<region><li>Alsace (région administrative)</li>
<li>Grand Est</li>
</region>
<settlement><li>Strasbourg</li>
</settlement>
</list>
<tree><country name="France"><region name="Grand Est"><name sortKey="Cognat, Valerie" sort="Cognat, Valerie" uniqKey="Cognat V" first="Valérie" last="Cognat">Valérie Cognat</name>
</region>
<name sortKey="Duchene, Anne Marie" sort="Duchene, Anne Marie" uniqKey="Duchene A" first="Anne-Marie" last="Duchêne">Anne-Marie Duchêne</name>
<name sortKey="Lalande, Stephanie" sort="Lalande, Stephanie" uniqKey="Lalande S" first="Stéphanie" last="Lalande">Stéphanie Lalande</name>
<name sortKey="Marechal Drouard, Laurence" sort="Marechal Drouard, Laurence" uniqKey="Marechal Drouard L" first="Laurence" last="Maréchal-Drouard">Laurence Maréchal-Drouard</name>
<name sortKey="Megel, Cyrille" sort="Megel, Cyrille" uniqKey="Megel C" first="Cyrille" last="Megel">Cyrille Megel</name>
<name sortKey="Molinier, Jean" sort="Molinier, Jean" uniqKey="Molinier J" first="Jean" last="Molinier">Jean Molinier</name>
<name sortKey="Morelle, Geoffrey" sort="Morelle, Geoffrey" uniqKey="Morelle G" first="Geoffrey" last="Morelle">Geoffrey Morelle</name>
<name sortKey="Vincent, Timothee" sort="Vincent, Timothee" uniqKey="Vincent T" first="Timothée" last="Vincent">Timothée Vincent</name>
</country>
<country name="Australie"><noRegion><name sortKey="Small, Ian" sort="Small, Ian" uniqKey="Small I" first="Ian" last="Small">Ian Small</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.

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