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Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation.


ABSTRACT: ChIP coupled with next-generation sequencing (ChIP-seq) has revolutionized whole-genome mapping of DNA-binding protein sites. Although ChIP-seq rapidly gained support in eukaryotic systems, it remains underused in the mapping of bacterial transcriptional regulator-binding sites. Using the virulence-required iron-responsive ferric uptake regulator (Fur), we report a simple, broadly applicable ChIP-seq method in the pathogen Vibrio cholerae. Combining our ChIP-seq results with available microarray data, we clarify direct and indirect Fur regulation of known iron-responsive genes. We validate a subset of Fur-binding sites in vivo and show a common motif present in all Fur ChIP-seq peaks that has enhanced binding affinity for purified V. cholerae Fur. Further analysis shows that V. cholerae Fur directly regulates several additional genes associated with Fur-binding sites, expanding the role of this transcription factor into the regulation of ribosome formation, additional transport functions, and unique sRNAs.

SUBMITTER: Davies BW 

PROVIDER: S-EPMC3145737 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation.

Davies Bryan W BW   Bogard Ryan W RW   Mekalanos John J JJ  

Proceedings of the National Academy of Sciences of the United States of America 20110712 30


ChIP coupled with next-generation sequencing (ChIP-seq) has revolutionized whole-genome mapping of DNA-binding protein sites. Although ChIP-seq rapidly gained support in eukaryotic systems, it remains underused in the mapping of bacterial transcriptional regulator-binding sites. Using the virulence-required iron-responsive ferric uptake regulator (Fur), we report a simple, broadly applicable ChIP-seq method in the pathogen Vibrio cholerae. Combining our ChIP-seq results with available microarray  ...[more]

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