ReviewMethods (San Diego, Calif.)2015
Defining bacterial regulons using ChIP-seq.
Review in Methods (San Diego, Calif.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed.
- OxyR regulates the oxidative stress response inApplied and environmental microbiology · 2026Article
- DAP-seq Reveals Cluster-Situated Regulator Control of NumerousbioRxiv : the preprint server for biology · 2026Article
- Laboratory Evolution Reveals Transcriptional Mechanisms Underlying Thermal Adaptation of Escherichia coli.Genome biology and evolution · 2025Article
- Genome-Wide Analysis of DtxR and HrrA Regulons Reveals Novel Targets and a High Level of Interconnectivity Between Iron and Heme Regulatory Networks in Corynebacterium glutamicum.Molecular microbiology · 2025Article
- The CarSR two-component system directly controlsJournal of bacteriology · 2025Article
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.Nucleic acids research · 2025Article
- Repeated glucose oscillations in high cell-density cultures influence stress-related functions ofPNAS nexus · 2024Article
- Inferred regulons are consistent with regulator binding sequences in E. coli.PLoS computational biology · 2024Article
- Exposing the small protein load of bacterial life.FEMS microbiology reviews · 2023Review
- Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell reports · 2023Article
- Elucidating the CodY regulon inmSystems · 2023Article
- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum.Scientific data · 2022Article
- Tunable transcription factor library for robust quantification of regulatory properties in Escherichia coli.Molecular systems biology · 2022Article
- Genome-wide promoter assembly inGenome research · 2022Article
- proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.Nucleic acids research · 2022Article
- Identification of Group II Intron RmInt1 Binding Sites in a Bacterial Genome.Frontiers in molecular biosciences · 2022Article
- Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome.mSystems · 2021Article
- ChIP-seq Analysis of the Global Regulator Vfr Reveals Novel Insights Into the Biocontrol AgentFrontiers in microbiology · 2021Article
- Tools to map target genes of bacterial two-component system response regulators.Environmental microbiology reports · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful method that identifies protein-DNA binding sites in vivo. Recent studies have illustrated the value of ChIP-seq in studying transcription factor binding in various bacterial species under a variety of growth conditions. These results show that in addition to identifying binding sites, correlation of ChIP-seq data with expression data can reveal important information about bacterial regulons and regulatory networks. In this chapter, we provide an overview of the current state of knowledge about ChIP-seq methodology in bacteria, from sample preparation to raw data analysis. We also describe visualization and various bioinformatic analyses of processed ChIP-seq data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.