title: Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.
abstract: The unique DNA-binding properties of distinct NF-κB dimers influence the selective regulation of NF-κB target genes. To more thoroughly investigate these dimer-specific differences, we combined protein-binding microarrays and surface plasmon resonance to evaluate DNA sites recognized by eight different NF-κB dimers. We observed three distinct binding-specificity classes and clarified mechanisms by which dimers might regulate distinct sets of genes. We identified many new nontraditional NF-κB binding site (κB site) sequences and highlight the plasticity of NF-κB dimers in recognizing κB sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-κB target sites and uncover gene regulatory circuitry.
authors.affiliation: Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Siggers
authors.forename: Abraham B
authors.initials: AB
authors.lastname: Chang
authors.forename: Ana
authors.initials: A
authors.lastname: Teixeira
authors.forename: Daniel
authors.initials: D
authors.lastname: Wong
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Williams
authors.forename: Bilal
authors.initials: B
authors.lastname: Ahmed
authors.forename: Jiannis
authors.initials: J
authors.lastname: Ragoussis
authors.forename: Irina A
authors.initials: IA
authors.lastname: Udalova
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Smale
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D016000:Cluster Analysis; D004247:DNA / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D006801:Humans; D008264:Macrophages / Q000378:metabolism; D051379:Mice; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism*; D040081:Protein Array Analysis; D011485:Protein Binding; D055503:Protein Multimerization
chemical_list: D016328:NF-kappa B; D004247:DNA
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