|Title||The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.|
|Publication Type||Journal Article|
|Year of Publication||2015|
|Authors||Cho S, Cho Y-B, Kang TJin, Kim SChang, Palsson B, Cho B-K|
|Journal||Nucleic Acids Res|
DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the in vivo architecture of TF-DNA complexes on a genome-scale. Here, we determined the in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using high-throughput sequencing of exonuclease-treated chromatin-immunoprecipitated DNA (ChIP-exo). The ChIP-exo has a unique peak-pair pattern indicating 5' and 3' ends of ArgR-binding region. We identified 62 ArgR-binding loci, which were classified into three groups, comprising single, double and triple peak-pairs. Each peak-pair has a unique 93 base pair (bp)-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequences. Moreover, the three ArgR-binding modes defined by the position of the two ARG boxes indicate that DNA bends centered between the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks.
|Alternate Journal||Nucleic Acids Res.|
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.