ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2007
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed, 70 citations in OpenAlex.
- DnaA binding to oriCII regulates transcription from Pseudomonas aeruginosa gidAB-parAB locus linked to the chromosome segregation and streptomycin resistance.Scientific reports · 2026Article
- Mechanisms of chromosomal DNA replication in Escherichia coli and Bacillus subtilis.FEMS microbiology reviews · 2026Review
- An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis.PLoS genetics · 2025Article
- Rok from B. subtilis: Bridging genome structure and transcription regulation.Molecular microbiology · 2025Review
- Hallmarks of DNA replication stress responses in Escherichia coli and Bacillus subtilis.FEMS microbiology reviews · 2025Review
- SirA inhibits the essential DnaA:DnaD interaction to block helicase recruitment during Bacillus subtilis sporulation.Nucleic acids research · 2023Article
- Transcriptional Activity of the Bacterial Replication Initiator DnaA.Frontiers in microbiology · 2021Review
- Evolutionary Changes in DnaA-Dependent Chromosomal Replication in Cyanobacteria.Frontiers in microbiology · 2020Article
- Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.Cell systems · 2019Article
- Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions.Bioinformation · 2018Article
- Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis.Molecular microbiology · 2017Article
- Genetic and biochemical interactions between the bacterial replication initiator DnaA and the nucleoid-associated protein Rok in Bacillus subtilis.Molecular microbiology · 2017Article
- Diversification of DnaA dependency for DNA replication in cyanobacterial evolution.The ISME journal · 2016Article
- H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.PLoS genetics · 2016Article
- In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA.PLoS genetics · 2015Article
- Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis.BMC microbiology · 2015Article
- The orisome: structure and function.Frontiers in microbiology · 2015Review
- Chromosome I controls chromosome II replication in Vibrio cholerae.PLoS genetics · 2014Article
- The ResD response regulator, through functional interaction with NsrR and fur, plays three distinct roles in Bacillus subtilis transcriptional control.Journal of bacteriology · 2014Article
- High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed a modified ChIP-chip method, designated ChAP-chip (Chromatin Affinity Precipitation coupled with tiling chip). The binding sites of Bacillus subtilis Spo0J determined using this technique were consistent with previous findings. A DNA replication initiator protein, DnaA, formed stable complexes at eight intergenic regions on the B. subtilis genome. Characterization of the binding sequences suggested that two factors -- the local density of DnaA boxes and their affinities for DnaA -- are critical for stable binding. We further showed that in addition to autoregulation, DnaA directly modulate the expression of sda in a positive, and ywlC and yydA in a negative manner. Examination of possible stable DnaA-binding sequences in other Bacillus species suggested that DnaA-dependent regulation of those genes is maintained in most bacteria examined, supporting their biological significance. In addition, a possible stable DnaA-binding site downstream of gcp is also suggested to be conserved. Furthermore, potential DnaA-binding sequences specific for each bacterium have been identified, generally in close proximity to oriC. These findings suggest that DnaA plays several additional roles, such as control of the level of effective initiator, ATP-DnaA, and/or stabilization of the domain structure of the genome around oriC for the proper initiation of chromosome replication.
Indexed as
Identifiers
What OpenQuestion holds
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.