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Osmotic stress-responsive promoter upstream transcripts (PROMPTs) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii.

Identifieur interne : 000810 ( Main/Exploration ); précédent : 000809; suivant : 000811

Osmotic stress-responsive promoter upstream transcripts (PROMPTs) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii.

Auteurs : Yuepeng Song [République populaire de Chine] ; Anran Xuan [République populaire de Chine] ; Chenhao Bu [République populaire de Chine] ; Dong Ci [République populaire de Chine] ; Min Tian [République populaire de Chine] ; Deqiang Zhang [République populaire de Chine]

Source :

RBID : pubmed:29797449

Descripteurs français

English descriptors

Abstract

Complex RNA transcription and processing produces a diverse range catalog of long noncoding RNAs (lncRNAs), important biological regulators that have been implicated in osmotic stress responses in plants. Promoter upstream transcript (PROMPT) lncRNAs share some regulatory elements with the promoters of their neighbouring protein-coding genes. However, their function remains unknown. Here, using strand-specific RNA sequencing, we identified 209 differentially regulated osmotic-responsive PROMPTs in poplar (Populus simonii). PROMPTs are transcribed bidirectionally and are more stable than other lncRNAs. Co-expression analysis of PROMPTs and protein-coding genes divided the regulatory network into five independent subnetworks including 27 network modules. Significantly enriched PROMPTs in the network were selected to validate their regulatory roles. We used delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to transport synthetic nucleic acids into live tissues to mimic overexpression and interference of a specific PROMPT. The altered expression of PROMPT_1281 induced the expression of its cis and trans targets, and this interaction was governed by its secondary structure rather than just its primary sequence. Based on this example, we proposed a model that a concentration gradient of PROMPT_1281 is established, which increases the probability of its interaction with targets near its transcription site that shares common motifs. Our results firstly demonstrated that PROMPT_1281 act as carriers of MYB transcription factors to induce the expression of target genes under osmotic stress. In sum, our study identified and validated a set of poplar PROMPTs that likely have regulatory functions in osmotic responses.

DOI: 10.1111/pbi.12955
PubMed: 29797449
PubMed Central: PMC6330638


Affiliations:


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Le document en format XML

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<term>Gene Expression Regulation, Plant (genetics)</term>
<term>Gene Expression Regulation, Plant (physiology)</term>
<term>Genes, Plant (genetics)</term>
<term>Genes, Plant (physiology)</term>
<term>Osmotic Pressure (MeSH)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (physiology)</term>
<term>Populus (genetics)</term>
<term>Populus (metabolism)</term>
<term>Populus (physiology)</term>
<term>Promoter Regions, Genetic (genetics)</term>
<term>Promoter Regions, Genetic (physiology)</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (physiology)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (physiologie)</term>
<term>Gènes de plante (génétique)</term>
<term>Gènes de plante (physiologie)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Populus (physiologie)</term>
<term>Pression osmotique (MeSH)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (physiologie)</term>
<term>Régions promotrices (génétique) (génétique)</term>
<term>Régions promotrices (génétique) (physiologie)</term>
<term>Régulation de l'expression des gènes végétaux (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (physiologie)</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="genetics" xml:lang="en">
<term>Gene Expression Regulation, Plant</term>
<term>Genes, Plant</term>
<term>Populus</term>
<term>Promoter Regions, Genetic</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Facteurs de transcription</term>
<term>Gènes de plante</term>
<term>Populus</term>
<term>Protéines végétales</term>
<term>Régions promotrices (génétique)</term>
<term>Régulation de l'expression des gènes végétaux</term>
</keywords>
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<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
<term>Populus</term>
</keywords>
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<term>Facteurs de transcription</term>
<term>Gènes de plante</term>
<term>Populus</term>
<term>Protéines végétales</term>
<term>Régions promotrices (génétique)</term>
<term>Régulation de l'expression des gènes végétaux</term>
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<term>Gene Expression Regulation, Plant</term>
<term>Genes, Plant</term>
<term>Plant Proteins</term>
<term>Populus</term>
<term>Promoter Regions, Genetic</term>
<term>Transcription Factors</term>
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<keywords scheme="MESH" xml:lang="en">
<term>Osmotic Pressure</term>
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<term>Pression osmotique</term>
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<div type="abstract" xml:lang="en">Complex RNA transcription and processing produces a diverse range catalog of long noncoding RNAs (lncRNAs), important biological regulators that have been implicated in osmotic stress responses in plants. Promoter upstream transcript (PROMPT) lncRNAs share some regulatory elements with the promoters of their neighbouring protein-coding genes. However, their function remains unknown. Here, using strand-specific RNA sequencing, we identified 209 differentially regulated osmotic-responsive PROMPTs in poplar (Populus simonii). PROMPTs are transcribed bidirectionally and are more stable than other lncRNAs. Co-expression analysis of PROMPTs and protein-coding genes divided the regulatory network into five independent subnetworks including 27 network modules. Significantly enriched PROMPTs in the network were selected to validate their regulatory roles. We used delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to transport synthetic nucleic acids into live tissues to mimic overexpression and interference of a specific PROMPT. The altered expression of PROMPT_1281 induced the expression of its cis and trans targets, and this interaction was governed by its secondary structure rather than just its primary sequence. Based on this example, we proposed a model that a concentration gradient of PROMPT_1281 is established, which increases the probability of its interaction with targets near its transcription site that shares common motifs. Our results firstly demonstrated that PROMPT_1281 act as carriers of MYB transcription factors to induce the expression of target genes under osmotic stress. In sum, our study identified and validated a set of poplar PROMPTs that likely have regulatory functions in osmotic responses.</div>
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<Title>Plant biotechnology journal</Title>
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<AbstractText>Complex RNA transcription and processing produces a diverse range catalog of long noncoding RNAs (lncRNAs), important biological regulators that have been implicated in osmotic stress responses in plants. Promoter upstream transcript (PROMPT) lncRNAs share some regulatory elements with the promoters of their neighbouring protein-coding genes. However, their function remains unknown. Here, using strand-specific RNA sequencing, we identified 209 differentially regulated osmotic-responsive PROMPTs in poplar (Populus simonii). PROMPTs are transcribed bidirectionally and are more stable than other lncRNAs. Co-expression analysis of PROMPTs and protein-coding genes divided the regulatory network into five independent subnetworks including 27 network modules. Significantly enriched PROMPTs in the network were selected to validate their regulatory roles. We used delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to transport synthetic nucleic acids into live tissues to mimic overexpression and interference of a specific PROMPT. The altered expression of PROMPT_1281 induced the expression of its cis and trans targets, and this interaction was governed by its secondary structure rather than just its primary sequence. Based on this example, we proposed a model that a concentration gradient of PROMPT_1281 is established, which increases the probability of its interaction with targets near its transcription site that shares common motifs. Our results firstly demonstrated that PROMPT_1281 act as carriers of MYB transcription factors to induce the expression of target genes under osmotic stress. In sum, our study identified and validated a set of poplar PROMPTs that likely have regulatory functions in osmotic responses.</AbstractText>
<CopyrightInformation>© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</CopyrightInformation>
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<Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation>
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<Country>International</Country>
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<Grant>
<GrantID>31400553</GrantID>
<Agency>Project of the National Natural Science Foundation of China</Agency>
<Country>International</Country>
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<Grant>
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<ArticleId IdType="pubmed">23728302</ArticleId>
</ArticleIdList>
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<Reference>
<Citation>Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">19458158</ArticleId>
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</PubmedData>
</pubmed>
<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
</country>
<settlement>
<li>Pékin</li>
</settlement>
</list>
<tree>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name>
</noRegion>
<name sortKey="Bu, Chenhao" sort="Bu, Chenhao" uniqKey="Bu C" first="Chenhao" last="Bu">Chenhao Bu</name>
<name sortKey="Bu, Chenhao" sort="Bu, Chenhao" uniqKey="Bu C" first="Chenhao" last="Bu">Chenhao Bu</name>
<name sortKey="Bu, Chenhao" sort="Bu, Chenhao" uniqKey="Bu C" first="Chenhao" last="Bu">Chenhao Bu</name>
<name sortKey="Ci, Dong" sort="Ci, Dong" uniqKey="Ci D" first="Dong" last="Ci">Dong Ci</name>
<name sortKey="Ci, Dong" sort="Ci, Dong" uniqKey="Ci D" first="Dong" last="Ci">Dong Ci</name>
<name sortKey="Ci, Dong" sort="Ci, Dong" uniqKey="Ci D" first="Dong" last="Ci">Dong Ci</name>
<name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name>
<name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name>
<name sortKey="Tian, Min" sort="Tian, Min" uniqKey="Tian M" first="Min" last="Tian">Min Tian</name>
<name sortKey="Tian, Min" sort="Tian, Min" uniqKey="Tian M" first="Min" last="Tian">Min Tian</name>
<name sortKey="Tian, Min" sort="Tian, Min" uniqKey="Tian M" first="Min" last="Tian">Min Tian</name>
<name sortKey="Xuan, Anran" sort="Xuan, Anran" uniqKey="Xuan A" first="Anran" last="Xuan">Anran Xuan</name>
<name sortKey="Xuan, Anran" sort="Xuan, Anran" uniqKey="Xuan A" first="Anran" last="Xuan">Anran Xuan</name>
<name sortKey="Xuan, Anran" sort="Xuan, Anran" uniqKey="Xuan A" first="Anran" last="Xuan">Anran Xuan</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
<name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name>
</country>
</tree>
</affiliations>
</record>

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