Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.
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.
Cho
Byung-Kwan
BK
Department of Bioengineering, University of California-San Diego, La Jolla, California 92093-0412, USA.
Knight
Eric M
EM
Barrett
Christian L
CL
Palsson
Bernhard Ø
BØ
D020856:AT Rich Sequence; D000225:Adenine / Q000032:analysis; D001665:Binding Sites; D002874:Chromosome Mapping; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D035021:Factor For Inversion Stimulation Protein / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D016680:Genome, Bacterial; D047468:Immunoprecipitation; D012808:Sigma Factor / Q000378:metabolism; D013941:Thymine / Q000032:analysis; D014158:Transcription, Genetic
D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D000225:Adenine; D013941:Thymine