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Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-?B family DNA binding.

ABSTRACT: The unique DNA-binding properties of distinct NF-?B dimers influence the selective regulation of NF-?B 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-?B 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-?B binding site (?B site) sequences and highlight the plasticity of NF-?B dimers in recognizing ?B sites with a single consensus half-site. This study provides a database that can be used in efforts to identify NF-?B target sites and uncover gene regulatory circuitry.

SUBMITTER: Siggers T

PROVIDER: S-EPMC3242931 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

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Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.

Siggers Trevor T Chang Abraham B AB Teixeira Ana A Wong Daniel D Williams Kevin J KJ Ahmed Bilal B Ragoussis Jiannis J Udalova Irina A IA Smale Stephen T ST Bulyk Martha L ML

Nature immunology 20111120 1

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 bin ...[more]

PMID: 22101729

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