Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.
Identifieur interne : 001C53 ( PubMed/Checkpoint ); précédent : 001C52; suivant : 001C54Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.
Auteurs : Raghunath Chatterjee [États-Unis] ; Jianfei Zhao ; Ximiao He ; Andrey Shlyakhtenko ; Ishminder Mann ; Joshua J. Waterfall ; Paul Meltzer ; B K Sathyanarayana ; Peter C. Fitzgerald ; Charles VinsonSource :
- G3 (Bethesda, Md.) [ 2160-1836 ] ; 2012.
Descripteurs français
- KwdFr :
- Animaux, Conformation d'acide nucléique, Conformation des protéines, Facteur de transcription GABP (), Facteur de transcription GABP (métabolisme), Humains, Liaison aux protéines, Motifs nucléotidiques, Méthylation de l'ADN, Protéine de liaison à l'élément de réponse à l'AMP cyclique (), Protéine de liaison à l'élément de réponse à l'AMP cyclique (métabolisme), Protéines proto-oncogènes c-ets (), Protéines proto-oncogènes c-ets (génétique), Régions promotrices (génétique), Simulation de docking moléculaire, Sites de fixation, Souris, Séquence conservée, Séquence nucléotidique.
- MESH :
- génétique : Protéines proto-oncogènes c-ets.
- métabolisme : Facteur de transcription GABP, Protéine de liaison à l'élément de réponse à l'AMP cyclique.
- Animaux, Conformation d'acide nucléique, Conformation des protéines, Facteur de transcription GABP, Humains, Liaison aux protéines, Motifs nucléotidiques, Méthylation de l'ADN, Protéine de liaison à l'élément de réponse à l'AMP cyclique, Protéines proto-oncogènes c-ets, Régions promotrices (génétique), Simulation de docking moléculaire, Sites de fixation, Souris, Séquence conservée, Séquence nucléotidique.
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 (X(4)-N(1-30)-X(4)) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif ((C/G)CCGGAAGCGGAA) and the ETS⇔CRE motif ((C/G)CGGAAGTGACGTCAC). 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.
DOI: 10.1534/g3.112.004002
PubMed: 23050235
Affiliations:
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pubmed:23050235Le document en format XML
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<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>
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<term>Proto-Oncogene Proteins c-ets (genetics)</term>
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<term>Conformation d'acide nucléique</term>
<term>Conformation des protéines</term>
<term>Facteur de transcription GABP ()</term>
<term>Facteur de transcription GABP (métabolisme)</term>
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<term>Motifs nucléotidiques</term>
<term>Méthylation de l'ADN</term>
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<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>
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<term>GA-Binding Protein Transcription Factor</term>
<term>Proto-Oncogene Proteins c-ets</term>
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<term>Protéine de liaison à l'élément de réponse à l'AMP cyclique</term>
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<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>
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<term>Conformation des protéines</term>
<term>Facteur de transcription GABP</term>
<term>Humains</term>
<term>Liaison aux protéines</term>
<term>Motifs nucléotidiques</term>
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<term>Simulation de docking moléculaire</term>
<term>Sites de fixation</term>
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<front><div type="abstract" xml:lang="en">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(4)-N(1-30)-X(4)) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif ((C/G)CCGGAAGCGGAA) and the ETS⇔CRE motif ((C/G)CGGAAGTGACGTCAC). 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.</div>
</front>
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<Abstract><AbstractText>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(4)-N(1-30)-X(4)) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif ((C/G)CCGGAAGCGGAA) and the ETS⇔CRE motif ((C/G)CGGAAGTGACGTCAC). 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.</AbstractText>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chatterjee</LastName>
<ForeName>Raghunath</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhao</LastName>
<ForeName>Jianfei</ForeName>
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<ForeName>Ximiao</ForeName>
<Initials>X</Initials>
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<ForeName>Andrey</ForeName>
<Initials>A</Initials>
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<ForeName>Joshua J</ForeName>
<Initials>JJ</Initials>
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<Author ValidYN="Y"><LastName>Meltzer</LastName>
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<Initials>P</Initials>
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<ForeName>B K</ForeName>
<Initials>BK</Initials>
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<Author ValidYN="Y"><LastName>FitzGerald</LastName>
<ForeName>Peter C</ForeName>
<Initials>PC</Initials>
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