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Series GSE60546 Query DataSets for GSE60546
Status Public on Apr 01, 2015
Title In vivo probing of the DNA-binding Architecture by bacterial arginine repressor
Organism Escherichia coli str. K-12 substr. MG1655
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design ChIP-exo profiles of ArgR (+Arginine) and ArgR (-Arginine) were generated by deep sequencing in duplicates using Illumina MiSeq.
 
Contributor(s) Cho S, Cho Y, Yum H, Kang T, Kim SC, Cho B
Citation(s) 25735747
Submission date Aug 20, 2014
Last update date May 15, 2019
Contact name Byung-Kwan Cho
Organization name KAIST
Lab Systems and Synthetic Biology Lab
Street address 291 Daehak-ro
City Daejeon
ZIP/Postal code 305-701
Country South Korea
 
Platforms (1)
GPL17439 Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)
Samples (2)
GSM1482120 ArgR (+arg) rep1 and rep2
GSM1482121 ArgR (-arg) rep1 and rep2
Relations
BioProject PRJNA258521
SRA SRP045631

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Supplementary file Size Download File type/resource
GSE60546_RAW.tar 24.0 Mb (http)(custom) TAR (of GFF)
Raw data are available in SRA
Processed data provided as supplementary file

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