Characterizing the DNA binding site specificity of NF-κB with protein-binding microarrays (PBMs).
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.
Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA, tsiggers@bu.edu.
Trevor
T
Siggers
Thomas D
TD
Gilmore
Brian
B
Barron
Ashley
A
Penvose
D001665:Binding Sites; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D016328:NF-kappa B / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011485:Protein Binding
D016328:NF-kappa B; D004247:DNA