Quantitative modeling of transcription factor binding specificities using DNA shape

• DOI: 10.1073/pnas.1422023112
• Publication Date: 2015-03-10T02:42:15Z
• Authors: Tianyin Zhou; Ning Shen; Lin Yang; Namiko Abe; John Horton; Richard S. Mann; Harmen J. Bussemaker; Raluca Gordân; Remo Rohs
• Keywords: DNA binding site; Sequence motif

Significance Genomes provide an abundance of putative binding sites for each transcription factor (TF). However, only small subsets these potential targets are functional. TFs the same protein family bind to target that very similar but not identical. This distinction allows closely related regulate different genes and thus execute distinct functions. Because nucleotide sequence core motif is often sufficient identifying a genomic target, we refined description TF by introducing combination DNA shape features, which consistently improved modeling in vitro TF−DNA specificities. Although additional factors affect vivo, shape-augmented models reveal specificity mechanisms apparent from alone.