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Gene expression

Complex interactions

Nature Reviews Molecular Cell Biology volume 10, page 444 (2009)Cite this article

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Using protein-binding microarrays (PBMs) with all possible DNA sequence variants of a given length, Bulyk and colleagues determined the DNA-binding specificities of 104 known and predicted mouse TFs, which represent 22 structural classes of DNA-binding domains found in metazoa. For each TF, an algorithm was used to identify the single octamer that has the highest PBM enrichment score (the highest binding affinity). Next, they systematically tested the relative preference of each nucleotide variant at each position in the binding sequence and obtained a rank-ordered list of the binding preferences of each TF for every k-mer (in which k is “the number of informative nucleotide positions in the binding site”).

“Virtually every TF has a unique binding sequence preference...”

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ORIGINAL RESEARCH PAPER

  1. Badis, G. et al. Diversity and complexity in DNA recognition by transcription factors. Science 14 May 2009 (doi:10.1126/science.1162327)

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Authors
  1. Francesca Cesari
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Cesari, F. Complex interactions. Nat Rev Mol Cell Biol 10, 444 (2009). https://doi.org/10.1038/nrm2716

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