Curation Information

Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation.;Davies BW, Bogard RW, Mekalanos JJ;Proceedings of the National Academy of Sciences of the United States of America 2011 Jul 26; 108(30):12467-72 [21750152]
Fur [P0C6C8, view regulon]
Reported TF sp.
Vibrio cholerae El Tor biotype strain C6706 (948564)
Reported site sp.
Vibrio cholerae El Tor biotype strain C6706 (948564)
Created by
Erill Lab
Curation notes

Experimental Process

ChIP-Seq + MEME validation with ChIP-PCR Expression data curated from previous source. Details of ChIP-seq: "We compared the peak lists generated from all three samples and required that a peak be called in at least two of the three experiments to be considered a vcFur-binding site (Table S1). The average ChIP peak length was ∼500 bp."

ChIP assay conditions
VchFur: Vibrio cholerae El Tor biotype strain C6706 and a spontaneous lacZ− derivative of C6706 were used as parental (WT) strains. Fiftymilliliters ofexponentiallygrowing cultureinLB+ 40μM FeSO4 were induced with 0.1% arabinose for 30 min at 37° C.
ChIP notes
Formaldehyde was added to a final concentration of 1% and incubated at RT for 20 min with occasional swirling. Crosslinking was quenched by adding glycine to 0.5M. Cell pellets were washed in 1× TBS and resuspended in lysis buffer [10 mM Tris (pH 8.0), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% deoxycholate (DOC), 0.5% N-lauroylsarcosine] plus protease inhibitor mixture (Sigma) and 1 mg/mL lysozyme and were incubated at 37° C for 30 min. The cells were sonicated 1×for 30 s with a needle sonicator, and unlysed debris was pelleted by centrifugation. The lysate was sonicated for 20 min with a 10-s on/10-s off cycle (Mixsonix). A sample was taken as a sequencing input control. Following clarification by centrifugation, 1/10 volume of 10% Triton X-100 in lysis buffer was added to each sample followed by 100 μL of Dynal-Protein G beads coated with anti-V5 monoclonal antibody (Sigma), and samples were incubated overnight with rotation. The beads were washed 5× with RIPA buffer [50 mM Hepes (pH7.5), 500 mM LiCl, 1 mM EDTA, 1% Nonidet P-40, 0.7% DOC] and then 1× in Tris-EDTA pH 8.0 plus 50 mM NaCl and were resuspended in 100μL elution buffer [50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1% SDS]. Samples were incubated at 65° C for 30 min, and the beads were pelleted by centrifugation. Supernatants were incubated at 65° C overnight to reverse crosslinks. Samples were incubated with 8 μL of 10-mg/mL RNase A for 2 h at 37° C and then with 4μL of 20 mg/mL proteinase K at 55° C for 2 h and were purified with Qiagen MinElute Reaction Cleanup Kit and quantitated with Pico green kit (Invitrogen). Experiments were performed in triplicate. One to three nanograms of ChIP or input DNA was processed for sequencing by the addition of a polyA tail as described by Helicos protocols ( Samples were sequenced using the HeliScope Single Molecule Sequencer at the Molecular Biology Core Facility in the Dana-Farber Cancer Institute, Boston, MA. The sequence reads were aligned to th

Transcription Factor Binding Sites


Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
... ... VCA0910 VCA0909 VCA0908 VCA0907 VCA0911 VCA0912 VCA0913 VCA0914 hmuV
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
... ... VCA1098 VCA1097 VCA1096 VCA1095 VCA1094 VCA1093 VCA1092 VCA1091 VCA1090 VCA1089 VCA1088 VCA1087 VCA1086 VCA1099 VCA1100 VCA1101
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer