RT Journal
A1 Levo, Michal
A1 Zalckvar, Einat
A1 Sharon, Eilon
A1 Dantas Machado, Ana Carolina
A1 Kalma, Yael
A1 Lotam-Pompan, Maya
A1 Weinberger, Adina
A1 Yakhini, Zohar
A1 Rohs, Remo
A1 Segal, Eran
T1 Unraveling determinants of transcription factor binding outside the core binding site
JF Genome Research 
JO Genome Research 
YR 2015 
FD July 01 
VO 25 
IS 7 
SP 1018 
OP 1029 
DO 10.1101/gr.185033.114 
UL http://genome.cshlp.org/content/25/7/1018.abstract 
AB 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 differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences serving as promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences and allows the characterization of TF binding determinants within and outside of core binding sites.