Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

摘要: Transcription factors (TFs) achieve DNA‐binding specificity through contacts with functional groups of bases (base readout) and readout structural properties the double helix (shape readout). Currently, it remains unclear whether DNA shape is utilized by only a few selected TF families, or this mechanism used extensively most families. We resequenced data from previously published HT‐SELEX experiments, extensive mammalian TF–DNA binding available to date. Using these data, we demonstrated contributions across diverse families its importance in core motif‐flanking regions. Statistical machine‐learning models combined feature‐selection techniques helped reveal nucleotide position‐dependent TF‐binding sites family‐specific position dependence. Based on results, proposed novel logos visualize preferences TFs. Overall, work suggests way obtaining mechanistic insights into without relying experimentally solved all‐atom structures. ![][1] The role transcription factor (TF)‐binding explored using dataset covering more than 400 important for many improves models. Mol Syst Biol. (2017) 13: 910 [1]: /embed/graphic-1.gif