Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq.
Identifieur interne : 001F97 ( Main/Corpus ); précédent : 001F96; suivant : 001F98Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq.
Auteurs : Jinhui Chen ; Mingyang Quan ; Deqiang ZhangSource :
- Planta [ 1432-2048 ] ; 2015.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Ontology (MeSH), Gene Regulatory Networks (MeSH), Genome, Plant (MeSH), High-Throughput Nucleotide Sequencing (methods), Molecular Sequence Data (MeSH), Nucleic Acid Conformation (MeSH), Populus (genetics), RNA, Long Noncoding (chemistry), RNA, Long Noncoding (genetics), Reverse Transcriptase Polymerase Chain Reaction (MeSH), Sequence Homology, Nucleic Acid (MeSH), Wood (genetics), Xylem (genetics).
- MESH :
- chemical , chemistry : RNA, Long Noncoding.
- genetics : Populus, RNA, Long Noncoding, Wood, Xylem.
- methods : High-Throughput Nucleotide Sequencing.
- Base Sequence, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Ontology, Gene Regulatory Networks, Genome, Plant, Molecular Sequence Data, Nucleic Acid Conformation, Reverse Transcriptase Polymerase Chain Reaction, Sequence Homology, Nucleic Acid.
Abstract
Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus.
DOI: 10.1007/s00425-014-2168-1
PubMed: 25230698
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq.</title><author><name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Quan, Mingyang" sort="Quan, Mingyang" uniqKey="Quan M" first="Mingyang" last="Quan">Mingyang Quan</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25230698</idno><idno type="pmid">25230698</idno><idno type="doi">10.1007/s00425-014-2168-1</idno><idno type="wicri:Area/Main/Corpus">001F97</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001F97</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq.</title><author><name sortKey="Chen, Jinhui" sort="Chen, Jinhui" uniqKey="Chen J" first="Jinhui" last="Chen">Jinhui Chen</name><affiliation><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.</nlm:affiliation></affiliation></author><author><name sortKey="Quan, Mingyang" sort="Quan, Mingyang" uniqKey="Quan M" first="Mingyang" last="Quan">Mingyang Quan</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></analytic><series><title level="j">Planta</title><idno type="eISSN">1432-2048</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Genome, Plant (MeSH)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Molecular Sequence Data (MeSH)</term><term>Nucleic Acid Conformation (MeSH)</term><term>Populus (genetics)</term><term>RNA, Long Noncoding (chemistry)</term><term>RNA, Long Noncoding (genetics)</term><term>Reverse Transcriptase Polymerase Chain Reaction (MeSH)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term><term>Wood (genetics)</term><term>Xylem (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term><term>RNA, Long Noncoding</term><term>Wood</term><term>Xylem</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Ontology</term><term>Gene Regulatory Networks</term><term>Genome, Plant</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Homology, Nucleic Acid</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25230698</PMID><DateCompleted><Year>2016</Year><Month>01</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-2048</ISSN><JournalIssue CitedMedium="Internet"><Volume>241</Volume><Issue>1</Issue><PubDate><Year>2015</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Planta</Title><ISOAbbreviation>Planta</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq.</ArticleTitle><Pagination><MedlinePgn>125-43</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00425-014-2168-1</ELocationID><Abstract><AbstractText>Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jinhui</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Quan</LastName><ForeName>Mingyang</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Deqiang</ForeName><Initials>D</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>2014</Year><Month>09</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Planta</MedlineTA><NlmUniqueID>1250576</NlmUniqueID><ISSNLinking>0032-0935</ISSNLinking></MedlineJournalInfo><ChemicalList><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="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063990" MajorTopicYN="N">Gene Ontology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D062085" MajorTopicYN="N">RNA, Long Noncoding</DescriptorName><QualifierName UI="Q000737" 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