Abstract
In this study, we established a single nucleotide mutation matrix (SNMM) model based on the relative binding affinities of NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants detected with the double-stranded DNA microarray. We evaluated this model by scoring different groups of 10-bp DNA sequences with this model and analyzing the correlations between the scores and the relative binding affinities detected with three wet experiments, including the electrophoresis mobility shift assay (EMSA), the protein-binding microarray (PBM) and the systematic evolution of ligands by exponential enrichment-sequencing (SELEX-Seq). The results revealed that the SNMM scores were strongly correlated with the detected binding affinities. We also scored the DNA sequences with other three models, including the principal coordinate (PC) model, the position weight matrix scoring algorithm (PWMSA) model and the Match model, and analyzed the correlations between the scores and the detected binding affinities. In comparison with these models, the SNMM model achieved reliable results. We finally determined 0.747 as the optimal threshold for predicting the NF-κB DNA-binding sites with the SNMM model. The SNMM model thus provides a new alternative model for scoring the relative binding affinities of NF-κB to the 10-bp DNA sequences and predicting the NF-κB DNA-binding sites.
Highlights
NF-kB is a transcription factor (TF) identified in lymphocyte and found to regulate the transcriptions of a large number of genes in most of cell types [1]
The principal coordinate (PC) model was trained on the binding affinity data of the NF-kB p50 homodimer to 52 variant DNA sequences representing the consensus of GGRRNNYYCC [8]
When analyzing the correlations between the PC scores and the experimental data, we used the sequences with the PC scores, including 52, 41 and 114 sequences detected by electrophoresis mobility shift assay (EMSA), protein-binding microarray (PBM) and SELEX-Seq, respectively
Summary
NF-kB is a transcription factor (TF) identified in lymphocyte and found to regulate the transcriptions of a large number of genes in most of cell types [1]. The heterodimer formed by p50 and p65 is the most common functional NF-kB dimer in the mammalian cells, which regulates many important biological processes, such as immunity and inflammation [3,4]. In this dimer, both subunits contact DNA, but only p65 contains a transactivation domain [5]. Both subunits contact DNA, but only p65 contains a transactivation domain [5] Like this dimer, other dimers formed by different members of NF-kB family can bind the DNAbinding sites (DBSs) in the genome. NF-kB is a wellknown sequence-specific DNA-binding TF
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