GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays
Identifieur interne : 001785 ( Main/Exploration ); précédent : 001784; suivant : 001786GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays
Auteurs : Ximiao He [États-Unis] ; Khund Sayeed Syed [États-Unis] ; Desiree Tillo [États-Unis] ; Ishminder Mann [États-Unis] ; Matthew T. Weirauch [États-Unis] ; Charles Vinson [États-Unis]Source :
- G3: Genes|Genomes|Genetics [ 2160-1836 ] ; 2015.
Descripteurs français
- KwdFr :
- Animaux, Facteur de transcription GABP (métabolisme), Humains, Liaison aux protéines, Lignée cellulaire, Locus génétiques, Motifs nucléotidiques, Polymorphisme de nucléotide simple, Protéine de liaison à l'élément de réponse à l'AMP cyclique (métabolisme), Protéines de fusion recombinantes (métabolisme), Protéines proto-oncogènes c-ets (métabolisme), Sites de fixation, Souris, Séquençage par oligonucléotides en batterie.
- MESH :
- métabolisme : Facteur de transcription GABP, Protéine de liaison à l'élément de réponse à l'AMP cyclique, Protéines de fusion recombinantes, Protéines proto-oncogènes c-ets.
- Animaux, Humains, Liaison aux protéines, Lignée cellulaire, Locus génétiques, Motifs nucléotidiques, Polymorphisme de nucléotide simple, Sites de fixation, Souris, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Animals, Binding Sites, Cell Line, Cyclic AMP Response Element-Binding Protein (metabolism), GA-Binding Protein Transcription Factor (metabolism), Genetic Loci, Humans, Mice, Nucleotide Motifs, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Protein Binding, Proto-Oncogene Proteins c-ets (metabolism), Recombinant Fusion Proteins (metabolism).
- MESH :
- chemical , metabolism : Cyclic AMP Response Element-Binding Protein, GA-Binding Protein Transcription Factor, Proto-Oncogene Proteins c-ets, Recombinant Fusion Proteins.
- Animals, Binding Sites, Cell Line, Genetic Loci, Humans, Mice, Nucleotide Motifs, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Protein Binding.
Abstract
To achieve proper spatiotemporal control of gene expression, transcription factors cooperatively assemble onto specific DNA sequences. The ETS domain protein monomer of GABPα and the B-ZIP domain protein dimer of CREB1 cooperatively bind DNA only when the ETS (C/GCGGAA
Url:
DOI: 10.1534/g3.115.020248
PubMed: 26185160
PubMed Central: 4555227
Affiliations:
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Le document en format XML
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Motifs Is Enhanced by CREB1: Custom DNA Microarrays</title><author><name sortKey="He, Ximiao" sort="He, Ximiao" uniqKey="He X" first="Ximiao" last="He">Ximiao He</name><affiliation wicri:level="2"><nlm:aff id="aff1">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda</wicri:cityArea></affiliation></author><author><name sortKey="Syed, Khund Sayeed" sort="Syed, Khund Sayeed" uniqKey="Syed K" first="Khund Sayeed" last="Syed">Khund Sayeed Syed</name><affiliation wicri:level="2"><nlm:aff id="aff1">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda</wicri:cityArea></affiliation></author><author><name sortKey="Tillo, Desiree" sort="Tillo, Desiree" uniqKey="Tillo D" first="Desiree" last="Tillo">Desiree Tillo</name><affiliation wicri:level="2"><nlm:aff id="aff1">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda</wicri:cityArea></affiliation></author><author><name sortKey="Mann, Ishminder" sort="Mann, Ishminder" uniqKey="Mann I" first="Ishminder" last="Mann">Ishminder Mann</name><affiliation wicri:level="2"><nlm:aff id="aff1">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda</wicri:cityArea></affiliation></author><author><name sortKey="Weirauch, Matthew T" sort="Weirauch, Matthew T" uniqKey="Weirauch M" first="Matthew T." last="Weirauch">Matthew T. Weirauch</name><affiliation wicri:level="2"><nlm:aff id="aff2">Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Ohio</region></placeName><wicri:cityArea>Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati</wicri:cityArea></affiliation></author><author><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name><affiliation wicri:level="2"><nlm:aff id="aff1">Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda</wicri:cityArea></affiliation></author></analytic><series><title level="j">G3: Genes|Genomes|Genetics</title><idno type="eISSN">2160-1836</idno><imprint><date when="2015">2015</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>Cyclic AMP Response Element-Binding Protein (metabolism)</term><term>GA-Binding Protein Transcription Factor (metabolism)</term><term>Genetic Loci</term><term>Humans</term><term>Mice</term><term>Nucleotide Motifs</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymorphism, Single Nucleotide</term><term>Protein Binding</term><term>Proto-Oncogene Proteins c-ets (metabolism)</term><term>Recombinant Fusion Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Facteur de transcription GABP (métabolisme)</term><term>Humains</term><term>Liaison aux protéines</term><term>Lignée cellulaire</term><term>Locus génétiques</term><term>Motifs nucléotidiques</term><term>Polymorphisme de nucléotide simple</term><term>Protéine de liaison à l'élément de réponse à l'AMP cyclique (métabolisme)</term><term>Protéines de fusion recombinantes (métabolisme)</term><term>Protéines proto-oncogènes c-ets (métabolisme)</term><term>Sites de fixation</term><term>Souris</term><term>Séquençage par oligonucléotides en batterie</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><term>Proto-Oncogene Proteins c-ets</term><term>Recombinant Fusion Proteins</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><term>Protéines de fusion recombinantes</term><term>Protéines proto-oncogènes c-ets</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Binding Sites</term><term>Cell Line</term><term>Genetic Loci</term><term>Humans</term><term>Mice</term><term>Nucleotide Motifs</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymorphism, Single Nucleotide</term><term>Protein Binding</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Liaison aux protéines</term><term>Lignée cellulaire</term><term>Locus génétiques</term><term>Motifs nucléotidiques</term><term>Polymorphisme de nucléotide simple</term><term>Sites de fixation</term><term>Souris</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>To achieve proper spatiotemporal control of gene expression, transcription factors cooperatively assemble onto specific DNA sequences. The ETS domain protein monomer of GABPα and the B-ZIP domain protein dimer of CREB1 cooperatively bind DNA only when the ETS (<sup>C</sup>/<sub>G</sub>CGGAA<bold>GT</bold>) and CRE (<bold>GT</bold>GACGTCAC) motifs overlap precisely, producing the ETS↔CRE motif (<sup>C</sup>/<sub>G</sub>CGGAA<bold>GT</bold>GACGTCAC). We designed a Protein Binding Microarray (PBM) with 60-bp DNAs containing four identical sectors, each with 177,440 features that explore the cooperative interactions between GABPα and CREB1 upon binding the ETS↔CRE motif. The DNA sequences include all 15-mers of the form <sup>C</sup>/<sub>G</sub>CGGA—–CG—, the ETS↔CRE motif, and all single nucleotide polymorphisms (SNPs), and occurrences in the human and mouse genomes. CREB1 enhanced GABPα binding to the canonical ETS↔CRE motif CCGGAAGT two-fold, and up to 23-fold for several SNPs at the beginning and end of the ETS motif, which is suggestive of two separate and distinct allosteric mechanisms of cooperative binding. We show that the ETS-CRE array data can be used to identify regions likely cooperatively bound by GABPα and CREB1 <italic>in vivo</italic>, and demonstrate their ability to identify human genetic variants that might inhibit cooperative binding.</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></biblStruct><biblStruct><analytic><author><name sortKey="Arnosti, D N" uniqKey="Arnosti D">D. N. Arnosti</name></author><author><name sortKey="Kulkarni, M M" uniqKey="Kulkarni M">M. M. 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Moll</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wei, G H" uniqKey="Wei G">G. H. Wei</name></author><author><name sortKey="Badis, G" uniqKey="Badis G">G. Badis</name></author><author><name sortKey="Berger, M F" uniqKey="Berger M">M. F. Berger</name></author><author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T. Kivioja</name></author><author><name sortKey="Palin, K" uniqKey="Palin K">K. Palin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Weirauch, M T" uniqKey="Weirauch M">M. T. Weirauch</name></author><author><name sortKey="Yang, A" uniqKey="Yang A">A. Yang</name></author><author><name sortKey="Albu, M" uniqKey="Albu M">M. Albu</name></author><author><name sortKey="Cote, A G" uniqKey="Cote A">A. G. Cote</name></author><author><name sortKey="Montenegro Montero, A" uniqKey="Montenegro Montero A">A. Montenegro-Montero</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wunderlich, Z" uniqKey="Wunderlich Z">Z. Wunderlich</name></author><author><name sortKey="Mirny, L A" uniqKey="Mirny L">L. A. Mirny</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y. Zhao</name></author><author><name sortKey="Granas, D" uniqKey="Granas D">D. Granas</name></author><author><name sortKey="Stormo, G D" uniqKey="Stormo G">G. D. Stormo</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li><li>Ohio</li></region></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="He, Ximiao" sort="He, Ximiao" uniqKey="He X" first="Ximiao" last="He">Ximiao He</name></region><name sortKey="Mann, Ishminder" sort="Mann, Ishminder" uniqKey="Mann I" first="Ishminder" last="Mann">Ishminder Mann</name><name sortKey="Syed, Khund Sayeed" sort="Syed, Khund Sayeed" uniqKey="Syed K" first="Khund Sayeed" last="Syed">Khund Sayeed Syed</name><name sortKey="Tillo, Desiree" sort="Tillo, Desiree" uniqKey="Tillo D" first="Desiree" last="Tillo">Desiree Tillo</name><name sortKey="Vinson, Charles" sort="Vinson, Charles" uniqKey="Vinson C" first="Charles" last="Vinson">Charles Vinson</name><name sortKey="Weirauch, Matthew T" sort="Weirauch, Matthew T" uniqKey="Weirauch M" first="Matthew T." last="Weirauch">Matthew T. 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