Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism.
Identifieur interne : 003189 ( Main/Exploration ); précédent : 003188; suivant : 003190Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism.
Auteurs : Rémy Merret [France] ; Bruno Moulia ; Irène Hummel ; David Cohen ; Erwin Dreyer ; Marie-Béatrice Bogeat-TriboulotSource :
- BMC biology [ 1741-7007 ] ; 2010.
Descripteurs français
- KwdFr :
- Facteur-1 d'élongation de la chaîne peptidique (génétique), Modèles théoriques (MeSH), Populus (génétique), Protéines végétales (génétique), Racines de plante (génétique), Réaction de polymérisation en chaîne (MeSH), Régulation de l'expression des gènes au cours du développement (génétique), Régulation de l'expression des gènes végétaux (génétique).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Peptide Elongation Factor 1, Plant Proteins.
- genetics : Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Plant Roots, Populus.
- Models, Theoretical, Polymerase Chain Reaction.
Abstract
BACKGROUND
Technological advances have enabled the accurate quantification of gene expression, even within single cell types. While transcriptome analyses are routinely performed, most experimental designs only provide snapshots of gene expression. Molecular mechanisms underlying cell fate or positional signalling have been revealed through these discontinuous datasets. However, in developing multicellular structures, temporal and spatial cues, known to directly influence transcriptional networks, get entangled as the cells are displaced and expand. Access to an unbiased view of the spatiotemporal regulation of gene expression occurring during development requires a specific framework that properly quantifies the rate of change of a property in a moving and expanding element, such as a cell or an organ segment.
RESULTS
We show how the rate of change in gene expression can be quantified by combining kinematics and real-time polymerase chain reaction data in a mechanistic model which considers any organ as a continuum. This framework was applied in order to assess the developmental regulation of the two reference genes Actin11 and Elongation Factor 1-beta in the apex of poplar root. The growth field was determined by time-lapse photography and transcript density was obtained at high spatial resolution. The net accumulation rates of the transcripts of the two genes were found to display highly contrasted developmental profiles. Actin11 showed pulses of up and down regulation in the accelerating and decelerating parts of the growth zone while the dynamic of EF1beta were much slower. This framework provides key information about gene regulation in a developing organ, such as the location, the duration and the intensity of gene induction/repression.
CONCLUSIONS
We demonstrated that gene expression patterns can be monitored using the continuity equation without using mutants or reporter constructions. Given the rise of imaging technologies, this framework in our view opens a new way to dissect the molecular basis of growth regulation, even in non-model species or complex structures.
DOI: 10.1186/1741-7007-8-18
PubMed: 20202192
PubMed Central: PMC2845557
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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type="eISSN">1741-7007</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Regulation, Developmental (genetics)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Models, Theoretical (MeSH)</term><term>Peptide Elongation Factor 1 (genetics)</term><term>Plant Proteins (genetics)</term><term>Plant Roots (genetics)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Facteur-1 d'élongation de la chaîne peptidique (génétique)</term><term>Modèles théoriques (MeSH)</term><term>Populus (génétique)</term><term>Protéines végétales (génétique)</term><term>Racines de plante (génétique)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Régulation de l'expression des gènes au cours du développement (génétique)</term><term>Régulation de l'expression des gènes végétaux (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Peptide Elongation Factor 1</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gene Expression Regulation, Developmental</term><term>Gene Expression Regulation, Plant</term><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Facteur-1 d'élongation de la chaîne peptidique</term><term>Populus</term><term>Protéines végétales</term><term>Racines de plante</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Régulation de l'expression des gènes végétaux</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Models, Theoretical</term><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Modèles théoriques</term><term>Réaction de polymérisation en chaîne</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Technological advances have enabled the accurate quantification of gene expression, even within single cell types. While transcriptome analyses are routinely performed, most experimental designs only provide snapshots of gene expression. Molecular mechanisms underlying cell fate or positional signalling have been revealed through these discontinuous datasets. However, in developing multicellular structures, temporal and spatial cues, known to directly influence transcriptional networks, get entangled as the cells are displaced and expand. Access to an unbiased view of the spatiotemporal regulation of gene expression occurring during development requires a specific framework that properly quantifies the rate of change of a property in a moving and expanding element, such as a cell or an organ segment.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We show how the rate of change in gene expression can be quantified by combining kinematics and real-time polymerase chain reaction data in a mechanistic model which considers any organ as a continuum. This framework was applied in order to assess the developmental regulation of the two reference genes Actin11 and Elongation Factor 1-beta in the apex of poplar root. The growth field was determined by time-lapse photography and transcript density was obtained at high spatial resolution. The net accumulation rates of the transcripts of the two genes were found to display highly contrasted developmental profiles. Actin11 showed pulses of up and down regulation in the accelerating and decelerating parts of the growth zone while the dynamic of EF1beta were much slower. This framework provides key information about gene regulation in a developing organ, such as the location, the duration and the intensity of gene induction/repression.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>We demonstrated that gene expression patterns can be monitored using the continuity equation without using mutants or reporter constructions. Given the rise of imaging technologies, this framework in our view opens a new way to dissect the molecular basis of growth regulation, even in non-model species or complex structures.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20202192</PMID><DateCompleted><Year>2010</Year><Month>05</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1741-7007</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><PubDate><Year>2010</Year><Month>Mar</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC biology</Title><ISOAbbreviation>BMC Biol</ISOAbbreviation></Journal><ArticleTitle>Monitoring the regulation of gene expression in a growing organ using a fluid mechanics formalism.</ArticleTitle><Pagination><MedlinePgn>18</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1741-7007-8-18</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Technological advances have enabled the accurate quantification of gene expression, even within single cell types. While transcriptome analyses are routinely performed, most experimental designs only provide snapshots of gene expression. Molecular mechanisms underlying cell fate or positional signalling have been revealed through these discontinuous datasets. However, in developing multicellular structures, temporal and spatial cues, known to directly influence transcriptional networks, get entangled as the cells are displaced and expand. Access to an unbiased view of the spatiotemporal regulation of gene expression occurring during development requires a specific framework that properly quantifies the rate of change of a property in a moving and expanding element, such as a cell or an organ segment.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We show how the rate of change in gene expression can be quantified by combining kinematics and real-time polymerase chain reaction data in a mechanistic model which considers any organ as a continuum. This framework was applied in order to assess the developmental regulation of the two reference genes Actin11 and Elongation Factor 1-beta in the apex of poplar root. The growth field was determined by time-lapse photography and transcript density was obtained at high spatial resolution. The net accumulation rates of the transcripts of the two genes were found to display highly contrasted developmental profiles. Actin11 showed pulses of up and down regulation in the accelerating and decelerating parts of the growth zone while the dynamic of EF1beta were much slower. This framework provides key information about gene regulation in a developing organ, such as the location, the duration and the intensity of gene induction/repression.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We demonstrated that gene expression patterns can be monitored using the continuity equation without using mutants or reporter constructions. Given the rise of imaging technologies, this framework in our view opens a new way to dissect the molecular basis of growth regulation, even in non-model species or complex structures.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Merret</LastName><ForeName>Rémy</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>INRA, Nancy Université, UMR1137 Ecologie et Ecophysiologie Forestières, IFR 110 EFABA, F-54280 Champenoux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Moulia</LastName><ForeName>Bruno</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Hummel</LastName><ForeName>Irène</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Cohen</LastName><ForeName>David</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Dreyer</LastName><ForeName>Erwin</ForeName><Initials>E</Initials></Author><Author 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IdType="pubmed">15657140</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Champenoux</li></settlement><orgName><li>Nancy-Université</li></orgName></list><tree><noCountry><name sortKey="Bogeat Triboulot, Marie Beatrice" sort="Bogeat Triboulot, Marie Beatrice" uniqKey="Bogeat Triboulot M" first="Marie-Béatrice" last="Bogeat-Triboulot">Marie-Béatrice Bogeat-Triboulot</name><name sortKey="Cohen, David" sort="Cohen, David" uniqKey="Cohen D" first="David" last="Cohen">David Cohen</name><name sortKey="Dreyer, Erwin" sort="Dreyer, Erwin" uniqKey="Dreyer E" first="Erwin" last="Dreyer">Erwin Dreyer</name><name sortKey="Hummel, Irene" sort="Hummel, Irene" uniqKey="Hummel I" first="Irène" last="Hummel">Irène Hummel</name><name sortKey="Moulia, Bruno" sort="Moulia, Bruno" uniqKey="Moulia B" first="Bruno" last="Moulia">Bruno Moulia</name></noCountry><country name="France"><region name="Grand Est"><name sortKey="Merret, Remy" sort="Merret, Remy" uniqKey="Merret R" first="Rémy" last="Merret">Rémy Merret</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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