TY  - JOUR
A1  - Chaudhari, Hemangi G.
A1  - Cohen, Barak A.
T1  - Local sequence features that influence AP-1 cis-regulatory activity
Y1  - 2018/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 171 
EP  - 181 
DO  - 10.1101/gr.226530.117 
VL  - 28 
IS  - 2 
UR  - http://genome.cshlp.org/content/28/2/171.abstract 
N2  - In the genome, most occurrences of transcription factor binding sites (TFBS) have no cis-regulatory activity, which suggests that flanking sequences contain information that distinguishes functional from nonfunctional TFBS. We interrogated the role of flanking sequences near Activator Protein 1 (AP-1) binding sites that reside in DNase I Hypersensitive Sites (DHS) and regions annotated as Enhancers. In these regions, we found that sequence features directly adjacent to the core motif distinguish high from low activity AP-1 sites. Some nearby features are motifs for other TFs that genetically interact with the AP-1 site. Other features are extensions of the AP-1 core motif, which cause the extended sites to match motifs of multiple AP-1 binding proteins. Computational models trained on these data distinguish between sequences with high and low activity AP-1 sites and also predict changes in cis-regulatory activity due to mutations in AP-1 core sites and their flanking sequences. Our results suggest that extended AP-1 binding sites, together with adjacent binding sites for additional TFs, encode part of the information that governs TFBS activity in the genome. 
ER  -