Quantitative prediction of NF-κB DNA– protein interactions

Abstract

We describe a general method based on principal coordinates analysis to predict the effects of single-nucleotide polymorphisms within regulatory sequences on DNA-protein interactions. We use binding data for the transcription factor NF-B as a test system. The method incorporates the effects of interactions between base pair positions in the binding site, and we demonstrate that such interactions are present for NF-B. Prediction accuracy is higher than with profile models, confirmed by crossvalidation and by the experimental verification of our predictions for additional sequences. The binding affinities of all potential NF-B sites on human chromosome 22, together with the effects of known single-nucleotide polymorphisms, are calculated to determine likely functional variants. We propose that this approach may be valuable, either on its own or in combination with other methods, when standard profile models are disadvantaged by complex internucleotide interactions.

Transcriptional regulation via the NF-κB signaling module

“…Early structural and biochemical experiments shed some light on the rules that discern the selection of kB target sites by the various NF-kB dimers. Ongoing systematic analysis of interactions combined with quantitative biochemical and biophysical studies may improve our predictive understanding of the specificity rules (Udalova et al, 2002). Although gene knockout studies have shown that biochemical affinity data are often not sufficient to explain the functional specificity in vivo of NF-kB dimers in gene expression, kB DNA-NF-kB interactions are probably a critical prerequisite for NF-kB in vivo function.…”

Prediction of transcription factor binding to DNA using rule induction methods

“…In the first data set (NF-κB [11]) only DNA target sequences vary. In the second (EGR [6]) both amino acids and nucleotides vary, but only in a limited number of positions.…”

“…We started by building regression models for NF-κB TF data (from [11]). This problem should be the easiest to solve, since only the DNA target sequences, and not the TFs varied (although two alternative TFs were examined).…”

“…Two of these have been used for model building earliernamely data for the NF-κB [11] and EGR [6] TF families. TFs in the NF-κB family coregulate many genes and have a critical role in immunity, inflammation and apoptosis [12].…”

“…TFs in the NF-κB family coregulate many genes and have a critical role in immunity, inflammation and apoptosis [12]. A recent study [11] first examined how well methods based on sequence profiles for NF-κB's DNA targets could predict the effects on binding specificity when the target nucleotides are varied, and then introduced an accurate method based on principal coordinates analysis. Here, only the nucleotides in the DNA target were varied, so the protein sequence was always constant within a model, although two different models corresponding to two separate NF-κB variants (p50p50 and p50p65) were constructed.…”