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

Nucleic Acids Research
Suhyung ChoByung-Kwan Cho

Abstract

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.

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Jun 4, 2015·Methods : a Companion to Methods in Enzymology·Kevin S MyersPatricia J Kiley
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Aug 17, 2021·Frontiers in Microbiology·Ingrid M KeselerPeter D Karp

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Datasets Mentioned

BETA
GSE60546

Methods Mentioned

BETA
immunoprecipitation
ChIP-exo
electrophoresis
PCR
ChIP-chip
Illumina sequencing
electrophoretic mobility shift

Software Mentioned

CLC Genomics Workbench5
MEME
MEME Suite
iCycler iQ optical system

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