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

ABSTRACT: Transcription factors (TFs) achieve DNA-binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT-SELEX experiments, the most extensive mammalian TF-DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif-flanking regions. Statistical machine-learning models combined with feature-selection techniques helped to reveal the nucleotide position-dependent DNA shape read

SUBMITTER: Yang L 

PROVIDER: S-EPMC5327724 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature