ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
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- MOB rules: Antibiotic Exposure Reprograms Metabolism to MobilizebioRxiv : the preprint server for biology · 2024Article
- Two Distinct Regulatory Systems Control Pulcherrimin Biosynthesis inbioRxiv : the preprint server for biology · 2024Article
- GeF-seq: A Simple Procedure for Base-Pair Resolution ChIP-seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
- IHF and Fis asInternational journal of molecular sciences · 2023Review
- Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase.PLoS genetics · 2023Article
- Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Transition Phase Regulator AbrB Positively Regulates theMicrobiology spectrum · 2021Article
- Whole-Genome Analysis Reveals That the Nucleoid Protein IHF Predominantly Binds to the Replication OriginFrontiers in microbiology · 2021Article
- LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription.Nature communications · 2019Article
- Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis.Molecular microbiology · 2017Article
- Lrp, a global regulator, regulates the virulence of Vibrio vulnificus.Journal of biomedical science · 2017Article
- Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth byJournal of bacteriology · 2017Article
- AhpA is a peroxidase expressed during biofilm formation in Bacillus subtilis.MicrobiologyOpen · 2017Article
- Organization of DNA in a bacterial nucleoid.BMC microbiology · 2016Article
- Insights into the Function of a Second, Nonclassical Ahp Peroxidase, AhpA, in Oxidative Stress Resistance in Bacillus subtilis.Journal of bacteriology · 2016Article
- Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale.Nucleic acids research · 2015Article
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Authors and funding
8 authors.
Funding
Abstract
Accurate identification of the DNA-binding sites of transcription factors and other DNA-binding proteins on the genome is crucial to understanding their molecular interactions with DNA. Here, we describe a new method: Genome Footprinting by high-throughput sequencing (GeF-seq), which combines in vivo DNase I digestion of genomic DNA with ChIP coupled with high-throughput sequencing. We have determined the in vivo binding sites of a Bacillus subtilis global regulator, AbrB, using GeF-seq. This method shows that exact DNA-binding sequences, which were protected from in vivo DNase I digestion, were resolved at a comparable resolution to that achieved by in vitro DNase I footprinting, and this was simply attained without the necessity of prediction by peak-calling programs. Moreover, DNase I digestion of the bacterial nucleoid resolved the closely positioned AbrB-binding sites, which had previously appeared as one peak in ChAP-chip and ChAP-seq experiments. The high-resolution determination of AbrB-binding sites using GeF-seq enabled us to identify bipartite TGGNA motifs in 96% of the AbrB-binding sites. Interestingly, in a thousand binding sites with very low-binding intensities, single TGGNA motifs were also identified. Thus, GeF-seq is a powerful method to elucidate the molecular mechanism of target protein binding to its cognate DNA sequences.
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