Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa.
Identifieur interne : 002203 ( Main/Exploration ); précédent : 002202; suivant : 002204Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa.
Auteurs : Peng Shuai [République populaire de Chine] ; Dan Liang [République populaire de Chine] ; Sha Tang [République populaire de Chine] ; Zhoujia Zhang [République populaire de Chine] ; Chu-Yu Ye [République populaire de Chine] ; Yanyan Su [République populaire de Chine] ; Xinli Xia ; Weilun YinSource :
- Journal of experimental botany [ 1460-2431 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN long non codant (génétique), ARN long non codant (métabolisme), Populus (génétique), Populus (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Sécheresses (MeSH), Séquence nucléotidique (MeSH), Séquençage nucléotidique à haut débit (MeSH), Transcriptome (MeSH), microARN (génétique).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : MicroRNAs, RNA, Long Noncoding.
- genetics : Populus.
- metabolism : Populus, RNA, Long Noncoding.
- Base Sequence, Droughts, Gene Expression Regulation, Plant, High-Throughput Nucleotide Sequencing, Transcriptome.
Abstract
Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa (P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis.
DOI: 10.1093/jxb/eru256
PubMed: 24948679
PubMed Central: PMC4144774
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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China.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Ye, Chu Yu" sort="Ye, Chu Yu" uniqKey="Ye C" first="Chu-Yu" last="Ye">Chu-Yu Ye</name><affiliation wicri:level="1"><nlm:affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. 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China.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><affiliation><nlm:affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China xiaxl@bjfu.edu.cn yinwl@bjfu.edu.cn.</nlm:affiliation><wicri:noCountry code="subField">P.R.</wicri:noCountry></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name><affiliation><nlm:affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China xiaxl@bjfu.edu.cn yinwl@bjfu.edu.cn.</nlm:affiliation><wicri:noCountry code="subField">P.R.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Journal of experimental botany</title><idno type="eISSN">1460-2431</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Droughts (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>MicroRNAs (genetics)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>RNA, Long Noncoding (genetics)</term><term>RNA, Long Noncoding (metabolism)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN long non codant (génétique)</term><term>ARN long non codant (métabolisme)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Sécheresses (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Transcriptome (MeSH)</term><term>microARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN long non codant</term><term>Populus</term><term>microARN</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Populus</term><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN long non codant</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Droughts</term><term>Gene Expression Regulation, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Régulation de l'expression des gènes végétaux</term><term>Sécheresses</term><term>Séquence nucléotidique</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa (P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24948679</PMID><DateCompleted><Year>2015</Year><Month>05</Month><Day>28</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1460-2431</ISSN><JournalIssue CitedMedium="Internet"><Volume>65</Volume><Issue>17</Issue><PubDate><Year>2014</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Journal of experimental botany</Title><ISOAbbreviation>J Exp Bot</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>4975-83</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/jxb/eru256</ELocationID><Abstract><AbstractText>Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa (P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis. </AbstractText><CopyrightInformation>© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shuai</LastName><ForeName>Peng</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liang</LastName><ForeName>Dan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Sha</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhoujia</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Chu-Yu</ForeName><Initials>CY</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Yanyan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xia</LastName><ForeName>Xinli</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China xiaxl@bjfu.edu.cn yinwl@bjfu.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Weilun</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University, mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China xiaxl@bjfu.edu.cn yinwl@bjfu.edu.cn.</Affiliation></AffiliationInfo></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>2014</Year><Month>06</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Exp Bot</MedlineTA><NlmUniqueID>9882906</NlmUniqueID><ISSNLinking>0022-0957</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D062085">RNA, Long Noncoding</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055864" MajorTopicYN="N">Droughts</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D062085" MajorTopicYN="N">RNA, Long Noncoding</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" 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