PoplarV1, Main, Exploration, bibRecord, 001F10

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.

Identifieur interne : 001F10 ( Main/Exploration ); précédent : 001F09; suivant : 001F11

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.

Auteurs : Lijun Liu [États-Unis] ; Trevor Ramsay [États-Unis] ; Matthew Zinkgraf [États-Unis] ; David Sundell [Suède] ; Nathaniel Robert Street [Suède] ; Vladimir Filkov [États-Unis] ; Andrew Groover [États-Unis]

Source :

The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2015.

RBID : pubmed:25903933

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Binding Sites (MeSH), Chromatin Immunoprecipitation (MeSH), Gene Expression Profiling (methods), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genome, Plant (MeSH), Image Processing, Computer-Assisted (MeSH), Molecular Sequence Data (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (genetics), Populus (growth & development), Transcription Factors (genetics), Transcription Factors (metabolism), Wood (genetics), Wood (growth & development), Workflow (MeSH).
MESH :
- chemical , genetics : Plant Proteins, Transcription Factors.
- chemical , metabolism : Plant Proteins, Transcription Factors.
- genetics : Populus, Wood.
- growth & development : Populus, Wood.
- methods : Gene Expression Profiling.
- Amino Acid Sequence, Binding Sites, Chromatin Immunoprecipitation, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome, Plant, Image Processing, Computer-Assisted, Molecular Sequence Data, Workflow.

Abstract

Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.

DOI: 10.1111/tpj.12850
PubMed: 25903933

Affiliations:

Suède, États-Unis

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

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Le document en format XML

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<term>Chromatin Immunoprecipitation (MeSH)</term>
<term>Gene Expression Profiling (methods)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Gene Regulatory Networks (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Image Processing, Computer-Assisted (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Populus (genetics)</term>
<term>Populus (growth & development)</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (metabolism)</term>
<term>Wood (genetics)</term>
<term>Wood (growth & development)</term>
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<term>Bois (génétique)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Flux de travaux (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Immunoprécipitation de la chromatine (MeSH)</term>
<term>Populus (croissance et développement)</term>
<term>Populus (génétique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Réseaux de régulation génique (MeSH)</term>
<term>Sites de fixation (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Traitement d'image par ordinateur (MeSH)</term>
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<term>Transcription Factors</term>
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<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term>
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<term>Wood</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bois</term>
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<term>Protéines végétales</term>
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<term>Binding Sites</term>
<term>Chromatin Immunoprecipitation</term>
<term>Gene Expression Regulation, Plant</term>
<term>Gene Regulatory Networks</term>
<term>Genome, Plant</term>
<term>Image Processing, Computer-Assisted</term>
<term>Molecular Sequence Data</term>
<term>Workflow</term>
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<term>Flux de travaux</term>
<term>Génome végétal</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Réseaux de régulation génique</term>
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<front><div type="abstract" xml:lang="en">Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.</div>
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<Abstract><AbstractText>Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.</AbstractText>
<CopyrightInformation>© 2015 Society for Experimental Biology and John Wiley & Sons Ltd This article has been contributed to by US Government employees and their work is in the public domain in the USA.</CopyrightInformation>
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<MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName>
</MeshHeading>
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<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
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<QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName>
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<MeshHeading><DescriptorName UI="D057188" MajorTopicYN="N">Workflow</DescriptorName>
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<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus trichocarpa</Keyword>
<Keyword MajorTopicYN="N">cambium</Keyword>
<Keyword MajorTopicYN="N">chromatin immunoprecipitation sequencing</Keyword>
<Keyword MajorTopicYN="N">secondary growth</Keyword>
<Keyword MajorTopicYN="N">transcription factor</Keyword>
<Keyword MajorTopicYN="N">wood formation</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year>
<Month>12</Month>
<Day>20</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2015</Year>
<Month>04</Month>
<Day>01</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2015</Year>
<Month>04</Month>
<Day>02</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2015</Year>
<Month>4</Month>
<Day>24</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2015</Year>
<Month>4</Month>
<Day>24</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2016</Year>
<Month>5</Month>
<Day>11</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">25903933</ArticleId>
<ArticleId IdType="doi">10.1111/tpj.12850</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>Suède</li>
<li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Liu, Lijun" sort="Liu, Lijun" uniqKey="Liu L" first="Lijun" last="Liu">Lijun Liu</name>
</noRegion>
<name sortKey="Filkov, Vladimir" sort="Filkov, Vladimir" uniqKey="Filkov V" first="Vladimir" last="Filkov">Vladimir Filkov</name>
<name sortKey="Groover, Andrew" sort="Groover, Andrew" uniqKey="Groover A" first="Andrew" last="Groover">Andrew Groover</name>
<name sortKey="Groover, Andrew" sort="Groover, Andrew" uniqKey="Groover A" first="Andrew" last="Groover">Andrew Groover</name>
<name sortKey="Ramsay, Trevor" sort="Ramsay, Trevor" uniqKey="Ramsay T" first="Trevor" last="Ramsay">Trevor Ramsay</name>
<name sortKey="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name>
</country>
<country name="Suède"><noRegion><name sortKey="Sundell, David" sort="Sundell, David" uniqKey="Sundell D" first="David" last="Sundell">David Sundell</name>
</noRegion>
<name sortKey="Street, Nathaniel Robert" sort="Street, Nathaniel Robert" uniqKey="Street N" first="Nathaniel Robert" last="Street">Nathaniel Robert Street</name>
</country>
</tree>
</affiliations>
</record>

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A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.

A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.

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