MersV1, Main, Exploration, bibRecord, 002227

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

Identifieur interne : 002227 ( Main/Exploration ); précédent : 002226; suivant : 002228

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

Auteurs : Raghunath Chatterjee [États-Unis] ; Jianfei Zhao [États-Unis] ; Ximiao He [États-Unis] ; Andrey Shlyakhtenko [États-Unis] ; Ishminder Mann [États-Unis] ; Joshua J. Waterfall [États-Unis] ; Paul Meltzer [États-Unis] ; B. K. Sathyanarayana [États-Unis] ; Peter C. Fitzgerald [États-Unis] ; Charles Vinson [États-Unis]

Source :

G3: Genes|Genomes|Genetics [ 2160-1836 ] ; 2012.

RBID : PMC:3464117

Descripteurs français

English descriptors

KwdEn :
- Animals, Base Sequence, Binding Sites, Conserved Sequence, Cyclic AMP Response Element-Binding Protein (chemistry), Cyclic AMP Response Element-Binding Protein (metabolism), DNA Methylation, GA-Binding Protein Transcription Factor (chemistry), GA-Binding Protein Transcription Factor (metabolism), Humans, Mice, Molecular Docking Simulation, Nucleic Acid Conformation, Nucleotide Motifs, Promoter Regions, Genetic, Protein Binding, Protein Conformation, Proto-Oncogene Proteins c-ets (chemistry), Proto-Oncogene Proteins c-ets (genetics).
MESH :
- chemical , chemistry : Cyclic AMP Response Element-Binding Protein, GA-Binding Protein Transcription Factor, Proto-Oncogene Proteins c-ets.
- chemical , genetics : Proto-Oncogene Proteins c-ets.
- chemical , metabolism : Cyclic AMP Response Element-Binding Protein, GA-Binding Protein Transcription Factor.
- Animals, Base Sequence, Binding Sites, Conserved Sequence, DNA Methylation, Humans, Mice, Molecular Docking Simulation, Nucleic Acid Conformation, Nucleotide Motifs, Promoter Regions, Genetic, Protein Binding, Protein Conformation.

Abstract

Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X₄-N_1-30-X₄) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (^C/_GCCGGAAGCGGAA) and the ETS⇔CRE motif (^C/_GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464117

DOI: 10.1534/g3.112.004002
PubMed: 23050235
PubMed Central: 3464117

Affiliations:

Le document en format XML

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/<sub>C</sub>
CGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins</title>
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CGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins</title>
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<author><name sortKey="Sathyanarayana, B K" sort="Sathyanarayana, B K" uniqKey="Sathyanarayana B" first="B. K." last="Sathyanarayana">B. K. Sathyanarayana</name>
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<term>Base Sequence</term>
<term>Binding Sites</term>
<term>Conserved Sequence</term>
<term>Cyclic AMP Response Element-Binding Protein (chemistry)</term>
<term>Cyclic AMP Response Element-Binding Protein (metabolism)</term>
<term>DNA Methylation</term>
<term>GA-Binding Protein Transcription Factor (chemistry)</term>
<term>GA-Binding Protein Transcription Factor (metabolism)</term>
<term>Humans</term>
<term>Mice</term>
<term>Molecular Docking Simulation</term>
<term>Nucleic Acid Conformation</term>
<term>Nucleotide Motifs</term>
<term>Promoter Regions, Genetic</term>
<term>Protein Binding</term>
<term>Protein Conformation</term>
<term>Proto-Oncogene Proteins c-ets (chemistry)</term>
<term>Proto-Oncogene Proteins c-ets (genetics)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term>
<term>Conformation d'acide nucléique</term>
<term>Conformation des protéines</term>
<term>Facteur de transcription GABP ()</term>
<term>Facteur de transcription GABP (métabolisme)</term>
<term>Humains</term>
<term>Liaison aux protéines</term>
<term>Motifs nucléotidiques</term>
<term>Méthylation de l'ADN</term>
<term>Protéine de liaison à l'élément de réponse à l'AMP cyclique ()</term>
<term>Protéine de liaison à l'élément de réponse à l'AMP cyclique (métabolisme)</term>
<term>Protéines proto-oncogènes c-ets ()</term>
<term>Protéines proto-oncogènes c-ets (génétique)</term>
<term>Régions promotrices (génétique)</term>
<term>Simulation de docking moléculaire</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquence conservée</term>
<term>Séquence nucléotidique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cyclic AMP Response Element-Binding Protein</term>
<term>GA-Binding Protein Transcription Factor</term>
<term>Proto-Oncogene Proteins c-ets</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Proto-Oncogene Proteins c-ets</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cyclic AMP Response Element-Binding Protein</term>
<term>GA-Binding Protein Transcription Factor</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines proto-oncogènes c-ets</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteur de transcription GABP</term>
<term>Protéine de liaison à l'élément de réponse à l'AMP cyclique</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Base Sequence</term>
<term>Binding Sites</term>
<term>Conserved Sequence</term>
<term>DNA Methylation</term>
<term>Humans</term>
<term>Mice</term>
<term>Molecular Docking Simulation</term>
<term>Nucleic Acid Conformation</term>
<term>Nucleotide Motifs</term>
<term>Promoter Regions, Genetic</term>
<term>Protein Binding</term>
<term>Protein Conformation</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Conformation d'acide nucléique</term>
<term>Conformation des protéines</term>
<term>Facteur de transcription GABP</term>
<term>Humains</term>
<term>Liaison aux protéines</term>
<term>Motifs nucléotidiques</term>
<term>Méthylation de l'ADN</term>
<term>Protéine de liaison à l'élément de réponse à l'AMP cyclique</term>
<term>Protéines proto-oncogènes c-ets</term>
<term>Régions promotrices (génétique)</term>
<term>Simulation de docking moléculaire</term>
<term>Sites de fixation</term>
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<front><div type="abstract" xml:lang="en"><p>Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X<sub>4</sub>
-N<sub>1-30</sub>
-X<sub>4</sub>
) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (<sup>C</sup>
/<sub>G</sub>
CCGGAA<bold>G</bold>
CGGAA) and the ETS⇔CRE motif (<sup>C</sup>
/<sub>G</sub>
CGGAA<bold>GTG</bold>
ACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAA<bold>GTG</bold>
ACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. <italic>In vivo</italic>
 GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ahn, S" uniqKey="Ahn S">S. Ahn</name>
</author>
<author><name sortKey="Olive, M" uniqKey="Olive M">M. Olive</name>
</author>
<author><name sortKey="Aggarwal, S" uniqKey="Aggarwal S">S. Aggarwal</name>
</author>
<author><name sortKey="Krylov, D" uniqKey="Krylov D">D. Krylov</name>
</author>
<author><name sortKey="Ginty, D D" uniqKey="Ginty D">D. D. Ginty</name>
</author>
</analytic>
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</author>
<author><name sortKey="Berger, M F" uniqKey="Berger M">M. F. Berger</name>
</author>
<author><name sortKey="Philippakis, A A" uniqKey="Philippakis A">A. A. Philippakis</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S. Talukder</name>
</author>
<author><name sortKey="Gehrke, A R" uniqKey="Gehrke A">A. R. Gehrke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Batchelor, A H" uniqKey="Batchelor A">A. H. Batchelor</name>
</author>
<author><name sortKey="Piper, D E" uniqKey="Piper D">D. E. Piper</name>
</author>
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<author><name sortKey="Koo, S H" uniqKey="Koo S">S. H. Koo</name>
</author>
<author><name sortKey="Conkright, M D" uniqKey="Conkright M">M. D. Conkright</name>
</author>
<author><name sortKey="Canettieri, G" uniqKey="Canettieri G">G. Canettieri</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Maryland</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Maryland"><name sortKey="Chatterjee, Raghunath" sort="Chatterjee, Raghunath" uniqKey="Chatterjee R" first="Raghunath" last="Chatterjee">Raghunath Chatterjee</name>
</region>
<name sortKey="Fitzgerald, Peter C" sort="Fitzgerald, Peter C" uniqKey="Fitzgerald P" first="Peter C." last="Fitzgerald">Peter C. Fitzgerald</name>
<name sortKey="He, Ximiao" sort="He, Ximiao" uniqKey="He X" first="Ximiao" last="He">Ximiao He</name>
<name sortKey="Mann, Ishminder" sort="Mann, Ishminder" uniqKey="Mann I" first="Ishminder" last="Mann">Ishminder Mann</name>
<name sortKey="Meltzer, Paul" sort="Meltzer, Paul" uniqKey="Meltzer P" first="Paul" last="Meltzer">Paul Meltzer</name>
<name sortKey="Sathyanarayana, B K" sort="Sathyanarayana, B K" uniqKey="Sathyanarayana B" first="B. K." last="Sathyanarayana">B. K. Sathyanarayana</name>
<name sortKey="Shlyakhtenko, Andrey" sort="Shlyakhtenko, Andrey" uniqKey="Shlyakhtenko A" first="Andrey" last="Shlyakhtenko">Andrey Shlyakhtenko</name>
<name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name>
<name sortKey="Waterfall, Joshua J" sort="Waterfall, Joshua J" uniqKey="Waterfall J" first="Joshua J." last="Waterfall">Joshua J. Waterfall</name>
<name sortKey="Zhao, Jianfei" sort="Zhao, Jianfei" uniqKey="Zhao J" first="Jianfei" last="Zhao">Jianfei Zhao</name>
</country>
</tree>
</affiliations>
</record>

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   |wiki=    Sante
   |area=    MersV1
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   |étape=   Exploration
   |type=    RBID
   |clé=     PMC:3464117
   |texte=   Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins
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Serveur d'exploration MERS

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

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	Serveur d'exploration MERS
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