High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.
Identifieur interne : 000575 ( Ncbi/Curation ); précédent : 000574; suivant : 000576High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.
Auteurs : Dean Tantin [États-Unis] ; Matthew Gemberling ; Catherine Callister ; William G. Fairbrother ; William FairbrotherSource :
- Genome research [ 1088-9051 ] ; 2008.
Descripteurs français
- KwdFr :
- ADN (), ADN (métabolisme), Animaux, Cellules souches embryonnaires (métabolisme), Facteur de transcription Oct-3 (métabolisme), Génomique, Humains, Immunoprécipitation de la chromatine, Lignée cellulaire, Régions promotrices (génétique), Sites de fixation, Sondes oligonucléotidiques, Souris, Séquençage par oligonucléotides en batterie (), Test de retard de migration électrophorétique (), Éléments de régulation transcriptionnelle.
- MESH :
- métabolisme : ADN, Cellules souches embryonnaires, Facteur de transcription Oct-3.
- ADN, Animaux, Génomique, Humains, Immunoprécipitation de la chromatine, Lignée cellulaire, Régions promotrices (génétique), Sites de fixation, Sondes oligonucléotidiques, Souris, Séquençage par oligonucléotides en batterie, Test de retard de migration électrophorétique, Éléments de régulation transcriptionnelle.
English descriptors
- KwdEn :
- Animals, Binding Sites, Cell Line, Chromatin Immunoprecipitation, DNA (chemistry), DNA (metabolism), Electrophoretic Mobility Shift Assay (methods), Embryonic Stem Cells (metabolism), Genomics, Humans, Mice, Octamer Transcription Factor-3 (metabolism), Oligonucleotide Array Sequence Analysis (methods), Oligonucleotide Probes, Promoter Regions, Genetic, Regulatory Elements, Transcriptional.
- MESH :
- chemical , chemistry : DNA.
- chemical , metabolism : DNA, Octamer Transcription Factor-3.
- metabolism : Embryonic Stem Cells.
- methods : Electrophoretic Mobility Shift Assay, Oligonucleotide Array Sequence Analysis.
- Animals, Binding Sites, Cell Line, Chromatin Immunoprecipitation, Genomics, Humans, Mice, Oligonucleotide Probes, Promoter Regions, Genetic, Regulatory Elements, Transcriptional.
Abstract
The transcription factor POU5F1 is a key regulator of embryonic stem (ES) cell pluripotency and a known oncoprotein. We have developed a novel high-throughput binding assay called MEGAshift (microarray evaluation of genomic aptamers by shift) that we use to pinpoint the exact location, affinity, and stoichiometry of the DNA-protein complexes identified by chromatin immunoprecipitation studies. We consider all genomic regions identified as POU5F1-ChIP-enriched in both human and mouse. Compared with regions that are ChIP-enriched in a single species, we find these regions more likely to be near actively transcribed genes in ES cells. We resynthesize these genomic regions as a pool of tiled 35-mers. This oligonucleotide pool is then assayed for binding to recombinant POU5F1 by gel shift. The degree of binding for each oligonucleotide is accurately measured on a custom oligonucleotide microarray. We explore the relationship between experimentally determined and computationally predicted binding strengths, find many novel functional combinations of POU5F1 half sites, and demonstrate efficient motif discovery by incorporating binding information into a motif finding algorithm. In addition to further refining location studies for transcription factors, this method holds promise for the high-throughput screening of promoters, SNP regions, and epigenetic modifications for factor binding.
DOI: 10.1101/gr.072942.107
PubMed: 18212089
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :002130
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :002130
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001F87
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000575
Links to Exploration step
pubmed:18212089Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.</title><author><name sortKey="Tantin, Dean" sort="Tantin, Dean" uniqKey="Tantin D" first="Dean" last="Tantin">Dean Tantin</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112</wicri:regionArea><wicri:noRegion>Utah 84112</wicri:noRegion></affiliation></author><author><name sortKey="Gemberling, Matthew" sort="Gemberling, Matthew" uniqKey="Gemberling M" first="Matthew" last="Gemberling">Matthew Gemberling</name></author><author><name sortKey="Callister, Catherine" sort="Callister, Catherine" uniqKey="Callister C" first="Catherine" last="Callister">Catherine Callister</name></author><author><name sortKey="Fairbrother, William G" sort="Fairbrother, William G" uniqKey="Fairbrother W" first="William G" last="Fairbrother">William G. Fairbrother</name></author><author><name sortKey="Fairbrother, William" sort="Fairbrother, William" uniqKey="Fairbrother W" first="William" last="Fairbrother">William Fairbrother</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18212089</idno><idno type="pmid">18212089</idno><idno type="doi">10.1101/gr.072942.107</idno><idno type="wicri:Area/PubMed/Corpus">002130</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002130</idno><idno type="wicri:Area/PubMed/Curation">002130</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002130</idno><idno type="wicri:Area/PubMed/Checkpoint">001F87</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F87</idno><idno type="wicri:Area/Ncbi/Merge">000575</idno><idno type="wicri:Area/Ncbi/Curation">000575</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.</title><author><name sortKey="Tantin, Dean" sort="Tantin, Dean" uniqKey="Tantin D" first="Dean" last="Tantin">Dean Tantin</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112</wicri:regionArea><wicri:noRegion>Utah 84112</wicri:noRegion></affiliation></author><author><name sortKey="Gemberling, Matthew" sort="Gemberling, Matthew" uniqKey="Gemberling M" first="Matthew" last="Gemberling">Matthew Gemberling</name></author><author><name sortKey="Callister, Catherine" sort="Callister, Catherine" uniqKey="Callister C" first="Catherine" last="Callister">Catherine Callister</name></author><author><name sortKey="Fairbrother, William G" sort="Fairbrother, William G" uniqKey="Fairbrother W" first="William G" last="Fairbrother">William G. Fairbrother</name></author><author><name sortKey="Fairbrother, William" sort="Fairbrother, William" uniqKey="Fairbrother W" first="William" last="Fairbrother">William Fairbrother</name></author></analytic><series><title level="j">Genome research</title><idno type="ISSN">1088-9051</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>Cell Line</term><term>Chromatin Immunoprecipitation</term><term>DNA (chemistry)</term><term>DNA (metabolism)</term><term>Electrophoretic Mobility Shift Assay (methods)</term><term>Embryonic Stem Cells (metabolism)</term><term>Genomics</term><term>Humans</term><term>Mice</term><term>Octamer Transcription Factor-3 (metabolism)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotide Probes</term><term>Promoter Regions, Genetic</term><term>Regulatory Elements, Transcriptional</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (métabolisme)</term><term>Animaux</term><term>Cellules souches embryonnaires (métabolisme)</term><term>Facteur de transcription Oct-3 (métabolisme)</term><term>Génomique</term><term>Humains</term><term>Immunoprécipitation de la chromatine</term><term>Lignée cellulaire</term><term>Régions promotrices (génétique)</term><term>Sites de fixation</term><term>Sondes oligonucléotidiques</term><term>Souris</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Test de retard de migration électrophorétique ()</term><term>Éléments de régulation transcriptionnelle</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Octamer Transcription Factor-3</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Embryonic Stem Cells</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Electrophoretic Mobility Shift Assay</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Cellules souches embryonnaires</term><term>Facteur de transcription Oct-3</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>Cell Line</term><term>Chromatin Immunoprecipitation</term><term>Genomics</term><term>Humans</term><term>Mice</term><term>Oligonucleotide Probes</term><term>Promoter Regions, Genetic</term><term>Regulatory Elements, Transcriptional</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Animaux</term><term>Génomique</term><term>Humains</term><term>Immunoprécipitation de la chromatine</term><term>Lignée cellulaire</term><term>Régions promotrices (génétique)</term><term>Sites de fixation</term><term>Sondes oligonucléotidiques</term><term>Souris</term><term>Séquençage par oligonucléotides en batterie</term><term>Test de retard de migration électrophorétique</term><term>Éléments de régulation transcriptionnelle</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The transcription factor POU5F1 is a key regulator of embryonic stem (ES) cell pluripotency and a known oncoprotein. We have developed a novel high-throughput binding assay called MEGAshift (microarray evaluation of genomic aptamers by shift) that we use to pinpoint the exact location, affinity, and stoichiometry of the DNA-protein complexes identified by chromatin immunoprecipitation studies. We consider all genomic regions identified as POU5F1-ChIP-enriched in both human and mouse. Compared with regions that are ChIP-enriched in a single species, we find these regions more likely to be near actively transcribed genes in ES cells. We resynthesize these genomic regions as a pool of tiled 35-mers. This oligonucleotide pool is then assayed for binding to recombinant POU5F1 by gel shift. The degree of binding for each oligonucleotide is accurately measured on a custom oligonucleotide microarray. We explore the relationship between experimentally determined and computationally predicted binding strengths, find many novel functional combinations of POU5F1 half sites, and demonstrate efficient motif discovery by incorporating binding information into a motif finding algorithm. In addition to further refining location studies for transcription factors, this method holds promise for the high-throughput screening of promoters, SNP regions, and epigenetic modifications for factor binding.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000575 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 000575 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Curation
|type= RBID
|clé= pubmed:18212089
|texte= High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:18212089" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |