Abstract
NF-κB transcription factors control a wide array of important cellular and organismal processes in eukaryotes. All NF-κB transcription factors bind to DNA target sites as dimers. In vertebrates, there are five NF-κB subunits, p50, p52, RelA (p65), c-Rel, and RelB, that can form almost all combinations of homodimers and heterodimers, which recognize distinct, but overlapping, target sequences. In this chapter, we describe the use of protein-binding microarrays (PBMs), a high-throughput method to measure the binding of proteins to different DNA sequences. PBM datasets allow for sensitive comparisons of NF-κB dimer DNA-binding differences and can aid in the computational and experimental prediction of NF-κB target genes
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Acknowledgments
Research in the authors’ laboratories on DNA binding by NF-kB proteins was supported by NIH grant K22AI09379 (T.S.), NSF grant MCB-090461 (T.D.G), and NSF grant IOS-1354935 (T.S. and T.D.G).
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Siggers, T., Gilmore, T.D., Barron, B., Penvose, A. (2015). Characterizing the DNA Binding Site Specificity of NF-κB with Protein-Binding Microarrays (PBMs). In: May, M. (eds) NF-kappa B. Methods in Molecular Biology, vol 1280. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2422-6_36
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DOI: https://doi.org/10.1007/978-1-4939-2422-6_36
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