ArticlePloS one2018
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
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- A multi-scale expression and regulation knowledge base for Escherichia coli.Nucleic acids research · 2023Article
- Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.Briefings in bioinformatics · 2023Article
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- Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins.microLife · 2023Review
- ChEAP: ChIP-exo analysis pipeline and the investigation ofComputational and structural biotechnology journal · 2023Article
- Global pleiotropic effects in adaptively evolvedOpen biology · 2022Article
- Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids.Nucleic acids research · 2021Article
- Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.Communications biology · 2021Article
- XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing.Molecular cell · 2020Article
- Reframing gene essentiality in terms of adaptive flexibility.BMC systems biology · 2018Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70 are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.
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