PoplarV1, Main, Exploration, bibRecord, 002E62

Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.

Identifieur interne : 002E62 ( Main/Exploration ); précédent : 002E61; suivant : 002E63

Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.

Auteurs : Meng Zhou [République populaire de Chine] ; Jie Sun ; Qiang-Hu Wang ; Li-Qun Song ; Guang Zhao ; Hong-Zhi Wang ; Hai-Xiu Yang ; Xia Li

Source :

The FEBS journal [ 1742-4658 ] ; 2011.

RBID : pubmed:21223508

Descripteurs français

English descriptors

KwdEn :
- Arabidopsis (genetics), Base Sequence (MeSH), Cluster Analysis (MeSH), Consensus Sequence (MeSH), Genes, Plant (MeSH), Genome, Plant (genetics), Genome-Wide Association Study (MeSH), MicroRNAs (genetics), Oryza (genetics), Populus (genetics), Promoter Regions, Genetic (MeSH), RNA, Plant (genetics), Sorghum (genetics).
MESH :
- chemical , genetics : MicroRNAs, RNA, Plant.
- genetics : Arabidopsis, Genome, Plant, Oryza, Populus, Sorghum.
- Base Sequence, Cluster Analysis, Consensus Sequence, Genes, Plant, Genome-Wide Association Study, Promoter Regions, Genetic.

Abstract

MicroRNAs (miRNAs) have been proven to play important roles at the post-transcriptional level in animals and plants. To investigate clustering patterns and specific sequence characteristics in the flanking regions of plant miRNA genes, we performed genome-wide analyses of Arabidopsis thaliana, Populus trichocarpa, Oryza sativa and Sorghum bicolor. Our results showed that miRNA pair distances were significantly higher than would have been expected to occur at random and that the number of miRNA gene pairs separated by very short distances of < 1 kb was higher than of protein-coding gene pairs. Analysis of the promoter architecture of different miRNA genes in plants revealed significant differences in the number and distribution of core promoters between intergenic miRNAs and intragenic miRNAs, and between highly conserved miRNAs and low conserved or nonconserved miRNAs. We applied two motif-finding algorithms to search for over-represented, statistically significant sequence motifs, and discovered six species-specific motifs across the four plant species studied. Moreover, we also identified, for the first time, several significantly over-represented motifs that were associated with conserved miRNAs, and these motifs may be useful for understanding the mechanism of origin of new plant miRNAs. The results presented provide a new insight into the transcriptional regulation and processing of plant miRNAs.

DOI: 10.1111/j.1742-4658.2011.08008.x
PubMed: 21223508

Affiliations:

République populaire de Chine

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 002F54
to stream Main, to step Curation: 002F54

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.</title>
<author><name sortKey="Zhou, Meng" sort="Zhou, Meng" uniqKey="Zhou M" first="Meng" last="Zhou">Meng Zhou</name>
<affiliation wicri:level="1"><nlm:affiliation>College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Bioinformatics Science and Technology, Harbin Medical University, Harbin</wicri:regionArea>
<wicri:noRegion>Harbin</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Sun, Jie" sort="Sun, Jie" uniqKey="Sun J" first="Jie" last="Sun">Jie Sun</name>
</author>
<author><name sortKey="Wang, Qiang Hu" sort="Wang, Qiang Hu" uniqKey="Wang Q" first="Qiang-Hu" last="Wang">Qiang-Hu Wang</name>
</author>
<author><name sortKey="Song, Li Qun" sort="Song, Li Qun" uniqKey="Song L" first="Li-Qun" last="Song">Li-Qun Song</name>
</author>
<author><name sortKey="Zhao, Guang" sort="Zhao, Guang" uniqKey="Zhao G" first="Guang" last="Zhao">Guang Zhao</name>
</author>
<author><name sortKey="Wang, Hong Zhi" sort="Wang, Hong Zhi" uniqKey="Wang H" first="Hong-Zhi" last="Wang">Hong-Zhi Wang</name>
</author>
<author><name sortKey="Yang, Hai Xiu" sort="Yang, Hai Xiu" uniqKey="Yang H" first="Hai-Xiu" last="Yang">Hai-Xiu Yang</name>
</author>
<author><name sortKey="Li, Xia" sort="Li, Xia" uniqKey="Li X" first="Xia" last="Li">Xia Li</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2011">2011</date>
<idno type="RBID">pubmed:21223508</idno>
<idno type="pmid">21223508</idno>
<idno type="doi">10.1111/j.1742-4658.2011.08008.x</idno>
<idno type="wicri:Area/Main/Corpus">002F54</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002F54</idno>
<idno type="wicri:Area/Main/Curation">002F54</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002F54</idno>
<idno type="wicri:Area/Main/Exploration">002F54</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.</title>
<author><name sortKey="Zhou, Meng" sort="Zhou, Meng" uniqKey="Zhou M" first="Meng" last="Zhou">Meng Zhou</name>
<affiliation wicri:level="1"><nlm:affiliation>College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Bioinformatics Science and Technology, Harbin Medical University, Harbin</wicri:regionArea>
<wicri:noRegion>Harbin</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Sun, Jie" sort="Sun, Jie" uniqKey="Sun J" first="Jie" last="Sun">Jie Sun</name>
</author>
<author><name sortKey="Wang, Qiang Hu" sort="Wang, Qiang Hu" uniqKey="Wang Q" first="Qiang-Hu" last="Wang">Qiang-Hu Wang</name>
</author>
<author><name sortKey="Song, Li Qun" sort="Song, Li Qun" uniqKey="Song L" first="Li-Qun" last="Song">Li-Qun Song</name>
</author>
<author><name sortKey="Zhao, Guang" sort="Zhao, Guang" uniqKey="Zhao G" first="Guang" last="Zhao">Guang Zhao</name>
</author>
<author><name sortKey="Wang, Hong Zhi" sort="Wang, Hong Zhi" uniqKey="Wang H" first="Hong-Zhi" last="Wang">Hong-Zhi Wang</name>
</author>
<author><name sortKey="Yang, Hai Xiu" sort="Yang, Hai Xiu" uniqKey="Yang H" first="Hai-Xiu" last="Yang">Hai-Xiu Yang</name>
</author>
<author><name sortKey="Li, Xia" sort="Li, Xia" uniqKey="Li X" first="Xia" last="Li">Xia Li</name>
</author>
</analytic>
<series><title level="j">The FEBS journal</title>
<idno type="eISSN">1742-4658</idno>
<imprint><date when="2011" type="published">2011</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term>
<term>Base Sequence (MeSH)</term>
<term>Cluster Analysis (MeSH)</term>
<term>Consensus Sequence (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genome, Plant (genetics)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>MicroRNAs (genetics)</term>
<term>Oryza (genetics)</term>
<term>Populus (genetics)</term>
<term>Promoter Regions, Genetic (MeSH)</term>
<term>RNA, Plant (genetics)</term>
<term>Sorghum (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term>
<term>Analyse de regroupements (MeSH)</term>
<term>Arabidopsis (génétique)</term>
<term>Gènes de plante (MeSH)</term>
<term>Génome végétal (génétique)</term>
<term>Oryza (génétique)</term>
<term>Populus (génétique)</term>
<term>Régions promotrices (génétique) (MeSH)</term>
<term>Sorghum (génétique)</term>
<term>Séquence consensus (MeSH)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>microARN (génétique)</term>
<term>Étude d'association pangénomique (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term>
<term>RNA, Plant</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Genome, Plant</term>
<term>Oryza</term>
<term>Populus</term>
<term>Sorghum</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term>
<term>Arabidopsis</term>
<term>Génome végétal</term>
<term>Oryza</term>
<term>Populus</term>
<term>Sorghum</term>
<term>microARN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Cluster Analysis</term>
<term>Consensus Sequence</term>
<term>Genes, Plant</term>
<term>Genome-Wide Association Study</term>
<term>Promoter Regions, Genetic</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term>
<term>Gènes de plante</term>
<term>Régions promotrices (génétique)</term>
<term>Séquence consensus</term>
<term>Séquence nucléotidique</term>
<term>Étude d'association pangénomique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">MicroRNAs (miRNAs) have been proven to play important roles at the post-transcriptional level in animals and plants. To investigate clustering patterns and specific sequence characteristics in the flanking regions of plant miRNA genes, we performed genome-wide analyses of Arabidopsis thaliana, Populus trichocarpa, Oryza sativa and Sorghum bicolor. Our results showed that miRNA pair distances were significantly higher than would have been expected to occur at random and that the number of miRNA gene pairs separated by very short distances of < 1 kb was higher than of protein-coding gene pairs. Analysis of the promoter architecture of different miRNA genes in plants revealed significant differences in the number and distribution of core promoters between intergenic miRNAs and intragenic miRNAs, and between highly conserved miRNAs and low conserved or nonconserved miRNAs. We applied two motif-finding algorithms to search for over-represented, statistically significant sequence motifs, and discovered six species-specific motifs across the four plant species studied. Moreover, we also identified, for the first time, several significantly over-represented motifs that were associated with conserved miRNAs, and these motifs may be useful for understanding the mechanism of origin of new plant miRNAs. The results presented provide a new insight into the transcriptional regulation and processing of plant miRNAs.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21223508</PMID>
<DateCompleted><Year>2011</Year>
<Month>05</Month>
<Day>09</Day>
</DateCompleted>
<DateRevised><Year>2015</Year>
<Month>11</Month>
<Day>19</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1742-4658</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>278</Volume>
<Issue>6</Issue>
<PubDate><Year>2011</Year>
<Month>Apr</Month>
</PubDate>
</JournalIssue>
<Title>The FEBS journal</Title>
<ISOAbbreviation>FEBS J</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.</ArticleTitle>
<Pagination><MedlinePgn>929-40</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1742-4658.2011.08008.x</ELocationID>
<Abstract><AbstractText>MicroRNAs (miRNAs) have been proven to play important roles at the post-transcriptional level in animals and plants. To investigate clustering patterns and specific sequence characteristics in the flanking regions of plant miRNA genes, we performed genome-wide analyses of Arabidopsis thaliana, Populus trichocarpa, Oryza sativa and Sorghum bicolor. Our results showed that miRNA pair distances were significantly higher than would have been expected to occur at random and that the number of miRNA gene pairs separated by very short distances of < 1 kb was higher than of protein-coding gene pairs. Analysis of the promoter architecture of different miRNA genes in plants revealed significant differences in the number and distribution of core promoters between intergenic miRNAs and intragenic miRNAs, and between highly conserved miRNAs and low conserved or nonconserved miRNAs. We applied two motif-finding algorithms to search for over-represented, statistically significant sequence motifs, and discovered six species-specific motifs across the four plant species studied. Moreover, we also identified, for the first time, several significantly over-represented motifs that were associated with conserved miRNAs, and these motifs may be useful for understanding the mechanism of origin of new plant miRNAs. The results presented provide a new insight into the transcriptional regulation and processing of plant miRNAs.</AbstractText>
<CopyrightInformation>© 2011 The Authors Journal compilation © 2011 FEBS.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhou</LastName>
<ForeName>Meng</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Sun</LastName>
<ForeName>Jie</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Qiang-Hu</ForeName>
<Initials>QH</Initials>
</Author>
<Author ValidYN="Y"><LastName>Song</LastName>
<ForeName>Li-Qun</ForeName>
<Initials>LQ</Initials>
</Author>
<Author ValidYN="Y"><LastName>Zhao</LastName>
<ForeName>Guang</ForeName>
<Initials>G</Initials>
</Author>
<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Hong-Zhi</ForeName>
<Initials>HZ</Initials>
</Author>
<Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Hai-Xiu</ForeName>
<Initials>HX</Initials>
</Author>
<Author ValidYN="Y"><LastName>Li</LastName>
<ForeName>Xia</ForeName>
<Initials>X</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2011</Year>
<Month>02</Month>
<Day>05</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>FEBS J</MedlineTA>
<NlmUniqueID>101229646</NlmUniqueID>
<ISSNLinking>1742-464X</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016384" MajorTopicYN="N">Consensus Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045868" MajorTopicYN="N">Sorghum</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2011</Year>
<Month>1</Month>
<Day>13</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2011</Year>
<Month>1</Month>
<Day>13</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2011</Year>
<Month>5</Month>
<Day>10</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">21223508</ArticleId>
<ArticleId IdType="doi">10.1111/j.1742-4658.2011.08008.x</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
</list>
<tree><noCountry><name sortKey="Li, Xia" sort="Li, Xia" uniqKey="Li X" first="Xia" last="Li">Xia Li</name>
<name sortKey="Song, Li Qun" sort="Song, Li Qun" uniqKey="Song L" first="Li-Qun" last="Song">Li-Qun Song</name>
<name sortKey="Sun, Jie" sort="Sun, Jie" uniqKey="Sun J" first="Jie" last="Sun">Jie Sun</name>
<name sortKey="Wang, Hong Zhi" sort="Wang, Hong Zhi" uniqKey="Wang H" first="Hong-Zhi" last="Wang">Hong-Zhi Wang</name>
<name sortKey="Wang, Qiang Hu" sort="Wang, Qiang Hu" uniqKey="Wang Q" first="Qiang-Hu" last="Wang">Qiang-Hu Wang</name>
<name sortKey="Yang, Hai Xiu" sort="Yang, Hai Xiu" uniqKey="Yang H" first="Hai-Xiu" last="Yang">Hai-Xiu Yang</name>
<name sortKey="Zhao, Guang" sort="Zhao, Guang" uniqKey="Zhao G" first="Guang" last="Zhao">Guang Zhao</name>
</noCountry>
<country name="République populaire de Chine"><noRegion><name sortKey="Zhou, Meng" sort="Zhou, Meng" uniqKey="Zhou M" first="Meng" last="Zhou">Meng Zhou</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002E62 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002E62 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Bois
   |area=    PoplarV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:21223508
   |texte=   Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:21223508" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a PoplarV1

This area was generated with Dilib version V0.6.37.
Data generation: Wed Nov 18 12:07:19 2020. Site generation: Wed Nov 18 12:16:31 2020

	Serveur d'exploration sur le peuplier
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration sur le peuplier

Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.

Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki