Unknown,Transcriptomics,Genomics,Proteomics

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In vivo probing of the DNA-binding Architecture by bacterial arginine repressor


ABSTRACT: Although DNA motifs recognized by the transcription factors (TFs) have been determined, challenges remain in probing in vivo architecture of TF-DNA complexes on a genome-wide scale. Here, we show in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using chromatin immunoprecipitation coupled with sequencing (ChIP-exo). The identified 62 ArgR-binding loci were classified into three groups, comprised of single, double, and triple peak-pairs, respectively. Each peak-pair has unique 93 bp-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequence. Moreover, the peak-pairs provided the three ArgR-binding modes defined by the position of the two ARG boxes, indicating that the formation of DNA bending apparently centered between the pair of ARG boxes facilitates the non-specific contacts between ArgR subunits and the residual sequences. Thus, our data postulate the in vivo architecture of ArgR-DNA complexes to understand its transcription regulatory mechanism. ChIP-exo profiles of ArgR (+Arginine) and ArgR (-Arginine) were generated by deep sequencing in duplicates using Illumina MiSeq.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Byung-Kwan Cho 

PROVIDER: E-GEOD-60546 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.

Cho Suhyung S   Cho Yoo-Bok YB   Kang Taek Jin TJ   Kim Sun Chang SC   Palsson Bernhard B   Cho Byung-Kwan BK  

Nucleic acids research 20150303 6


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.  ...[more]

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