PMID:18340041
| Citation |
Cho, BK, Knight, EM, Barrett, CL and Palsson, BØ (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res. 18:900-10 |
|---|---|
| Abstract |
We determined the genome-wide distribution of the nucleoid-associated protein Fis in Escherichia coli using chromatin immunoprecipitation coupled with high-resolution whole genome-tiling microarrays. We identified 894 Fis-associated regions across the E. coli genome. A significant number of these binding sites were found within open reading frames (33%) and between divergently transcribed transcripts (5%). Analysis indicates that A-tracts and AT-tracts are an important signal for preferred Fis-binding sites, and that A(6)-tracts in particular constitute a high-affinity signal that dictates Fis phasing in stretches of DNA containing multiple and variably spaced A-tracts and AT-tracts. Furthermore, we find evidence for an average of two Fis-binding regions per supercoiling domain in the chromosome of exponentially growing cells. Transcriptome analysis shows that approximately 21% of genes are affected by the deletion of fis; however, the changes in magnitude are small. To address the differential Fis bindings under growth environment perturbation, ChIP-chip analysis was performed using cells grown under aerobic and anaerobic growth conditions. Interestingly, the Fis-binding regions are almost identical in aerobic and anaerobic growth conditions-indicating that the E. coli genome topology mediated by Fis is superficially identical in the two conditions. These novel results provide new insight into how Fis modulates DNA topology at a genome scale and thus advance our understanding of the architectural bases of the E. coli nucleoid. |
| Links |
PubMed PMC2413157 Online version:10.1101/gr.070276.107 |
| Keywords |
AT Rich Sequence; Adenine/analysis; Binding Sites; Chromosome Mapping; DNA, Bacterial/chemistry; DNA, Bacterial/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli/growth & development; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein/genetics; Factor For Inversion Stimulation Protein/metabolism; Gene Deletion; Genome, Bacterial; Immunoprecipitation; Sigma Factor/metabolism; Thymine/analysis; Transcription, Genetic |
| edit table |
Significance
You can help EcoliWiki by summarizing why this paper is useful
Useful Materials and Methods
You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.
Annotations
<annotationlinks/>
EcoliWiki Links
Add links to pages that link here (e.g. gene, product, method pages)
See also
References
See Help:References for how to manage references in EcoliWiki.