Unraveling determinants of transcription factor binding outside the core binding site

ABSTRACT: Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured diffe

ORGANISM(S): synthetic construct

SUBMITTER: Michal Levo 

PROVIDER: E-GEOD-66143 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress