title: GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays.
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 GT: ) and CRE ( GT: GACGTCAC) motifs overlap precisely, producing the ETS↔CRE motif ((C)/GCGGAA GT: 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 (C)/GCGGA--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 in vivo, and demonstrate their ability to identify human genetic variants that might inhibit cooperative binding.
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Ximiao
authors.identifier: http://orcid.org/0000-0003-1253-5275
authors.initials: X
authors.lastname: He
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Khund Sayeed
authors.initials: KS
authors.lastname: Syed
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Desiree
authors.initials: D
authors.lastname: Tillo
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Ishminder
authors.initials: I
authors.lastname: Mann
authors.affiliation: 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 matthew.weirauch@cchmc.org vinsonc@mail.nih.gov.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Weirauch
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 matthew.weirauch@cchmc.org vinsonc@mail.nih.gov.
authors.forename: Charles
authors.initials: C
authors.lastname: Vinson
mesh_terms: D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D017362:Cyclic AMP Response Element-Binding Protein / Q000378:metabolism*; D051268:GA-Binding Protein Transcription Factor / Q000378:metabolism*; D056426:Genetic Loci; D006801:Humans; D051379:Mice; D059372:Nucleotide Motifs; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D050783:Proto-Oncogene Proteins c-ets / Q000378:metabolism*; D011993:Recombinant Fusion Proteins / Q000378:metabolism
chemical_list: D017362:Cyclic AMP Response Element-Binding Protein; D051268:GA-Binding Protein Transcription Factor; D050783:Proto-Oncogene Proteins c-ets; D011993:Recombinant Fusion Proteins
keywords: CRE; CREB1; ETS; GABPα; cooperative DNA binding