SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.
Identifieur interne : 002395 ( Main/Corpus ); précédent : 002394; suivant : 002396SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.
Auteurs : Ying-Chung Lin ; Wei Li ; Ying-Hsuan Sun ; Sapna Kumari ; Hairong Wei ; Quanzi Li ; Sermsawat Tunlaya-Anukit ; Ronald R. Sederoff ; Vincent L. ChiangSource :
- The Plant cell [ 1532-298X ] ; 2013.
English descriptors
- KwdEn :
- Algorithms (MeSH), Cell Wall (genetics), Chromatin Immunoprecipitation (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Ontology (MeSH), Gene Regulatory Networks (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Models, Genetic (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Plants, Genetically Modified (MeSH), Polymerase Chain Reaction (methods), Populus (genetics), Populus (metabolism), Protoplasts (MeSH), Reproducibility of Results (MeSH), Transcription Factors (genetics), Transcription Factors (metabolism), Transfection (MeSH), Wood (genetics), Wood (metabolism), Xylem (cytology), Xylem (genetics).
- MESH :
- chemical , genetics : Plant Proteins, Transcription Factors.
- cytology : Xylem.
- genetics : Cell Wall, Populus, Wood, Xylem.
- chemical , metabolism : Plant Proteins, Populus, Transcription Factors, Wood.
- methods : Polymerase Chain Reaction.
- Algorithms, Chromatin Immunoprecipitation, Gene Expression Regulation, Plant, Gene Ontology, Gene Regulatory Networks, High-Throughput Nucleotide Sequencing, Models, Genetic, Plants, Genetically Modified, Protoplasts, Reproducibility of Results, Transfection.
Abstract
Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.
DOI: 10.1105/tpc.113.117697
PubMed: 24280390
PubMed Central: PMC3875721
Links to Exploration step
pubmed:24280390Le document en format XML
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Sederoff</name></author><author><name sortKey="Chiang, Vincent L" sort="Chiang, Vincent L" uniqKey="Chiang V" first="Vincent L" last="Chiang">Vincent L. Chiang</name></author></analytic><series><title level="j">The Plant cell</title><idno type="eISSN">1532-298X</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Cell Wall (genetics)</term><term>Chromatin Immunoprecipitation (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Gene Ontology (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Models, Genetic (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Plants, Genetically Modified (MeSH)</term><term>Polymerase Chain Reaction (methods)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>Protoplasts (MeSH)</term><term>Reproducibility of Results (MeSH)</term><term>Transcription Factors (genetics)</term><term>Transcription Factors (metabolism)</term><term>Transfection (MeSH)</term><term>Wood (genetics)</term><term>Wood (metabolism)</term><term>Xylem (cytology)</term><term>Xylem (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Xylem</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Wall</term><term>Populus</term><term>Wood</term><term>Xylem</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term><term>Populus</term><term>Transcription Factors</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Chromatin Immunoprecipitation</term><term>Gene Expression Regulation, Plant</term><term>Gene Ontology</term><term>Gene Regulatory Networks</term><term>High-Throughput Nucleotide Sequencing</term><term>Models, Genetic</term><term>Plants, Genetically Modified</term><term>Protoplasts</term><term>Reproducibility of Results</term><term>Transfection</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24280390</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-298X</ISSN><JournalIssue CitedMedium="Internet"><Volume>25</Volume><Issue>11</Issue><PubDate><Year>2013</Year><Month>Nov</Month></PubDate></JournalIssue><Title>The Plant cell</Title><ISOAbbreviation>Plant Cell</ISOAbbreviation></Journal><ArticleTitle>SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>4324-41</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1105/tpc.113.117697</ELocationID><Abstract><AbstractText>Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexpressed Secondary Wall-Associated NAC Domain 1s (Ptr-SND1-B1), a TF gene affecting wood formation, in these protoplasts and identified differentially expressed genes by RNA sequencing. Direct Ptr-SND1-B1-DNA interactions were then inferred by integration of time-course RNA sequencing data and top-down Graphical Gaussian Modeling-based algorithms. These Ptr-SND1-B1-DNA interactions were verified to function in differentiating xylem by anti-PtrSND1-B1 antibody-based chromatin immunoprecipitation (97% accuracy) and in stable transgenic P. trichocarpa (90% accuracy). In this way, we established a Ptr-SND1-B1-directed quantitative hGRN involving 76 direct targets, including eight TF and 61 enzyme-coding genes previously unidentified as targets. The network can be extended to the third layer from the second-layer TFs by computation or by overexpression of a second-layer TF to identify a new group of direct targets (third layer). This approach would allow the sequential establishment, one two-layered hGRN at a time, of all layers involved in a more comprehensive hGRN. Our approach may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Ying-Chung</ForeName><Initials>YC</Initials><AffiliationInfo><Affiliation>Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Wei</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Ying-Hsuan</ForeName><Initials>YH</Initials></Author><Author ValidYN="Y"><LastName>Kumari</LastName><ForeName>Sapna</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Hairong</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Quanzi</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Tunlaya-Anukit</LastName><ForeName>Sermsawat</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Sederoff</LastName><ForeName>Ronald R</ForeName><Initials>RR</Initials></Author><Author ValidYN="Y"><LastName>Chiang</LastName><ForeName>Vincent L</ForeName><Initials>VL</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GEO</DataBankName><AccessionNumberList><AccessionNumber>GSE49911</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>11</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Cell</MedlineTA><NlmUniqueID>9208688</NlmUniqueID><ISSNLinking>1040-4651</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Plant Cell. 2013 Nov;25(11):4282</RefSource><PMID Version="1">24285792</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName 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MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030821" MajorTopicYN="N">Plants, Genetically Modified</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</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="D011523" MajorTopicYN="N">Protoplasts</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName 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