Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
- 13 March 2008
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 18 (6), 900-910
- https://doi.org/10.1101/gr.070276.107
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 A6-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 ∼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.Keywords
This publication has 78 references indexed in Scilit:
- Correlation between binding rate constants and individual information of E. coli Fis binding sitesNucleic Acids Research, 2007
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genomeNature Genetics, 2007
- Mechanism of Chromosome Compaction and Looping by the Escherichia coli Nucleoid Protein FisJournal of Molecular Biology, 2006
- Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genomeNucleic Acids Research, 2006
- RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complexThe EMBO Journal, 2006
- Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genomeEMBO Reports, 2006
- Integrating high-throughput and computational data elucidates bacterial networksNature, 2004
- Genome-Wide Location and Function of DNA Binding ProteinsScience, 2000
- Sequence logos: a new way to display consensus sequencesNucleic Acids Research, 1990
- Fis binding to the recombinational enhancer of the Hin DNA inversion system.Genes & Development, 1987