Curation Information

Publication
Characterization of the RpoN regulon reveals differential regulation of T6SS and new flagellar operons in Vibrio cholerae O37 strain V52.;Dong TG, Mekalanos JJ;Nucleic acids research 2012 Sep; 40(16):7766-75 [22723378]
TF
RpoN [Q9KP49, view regulon]
Reported TF sp.
Vibrio cholerae O37 strain V52 [185332]
Reported site sp.
Vibrio cholerae O37 strain V52 [185332]
Created by
Erill Lab
Curation notes
ChIP-Seq on Ch-1 Vibrio cholerae O1 biovar El Tor str. N16961 chosen as reference by authors (gene names)

Experimental Process

ChIP-seq + RNA-seq

Transcription Factor Binding Sites


CGGCTCTTTTTTTGC
TGGCATCGATCTTGA
TGGCACGCCCCTTGG
TGGGCATTTGTTGGC
TGGCTAGATTTTTGC
TGGCACGATATGTGC
TGGCATATAATTTGC
TGGCACGTTTACTGC
TGGCACTCTAATTGC
TGGCGCGAATCTTGC
TAGCACGTTTTATGC
CGGTATAATAATTGC
TAGCACGTTTTATGC
AGGTACGAAATTTGC
TGGAACGCTATTTGC
TGGCGCAATTATTGC
TGGCATCCCATTTGC
TGGATTTATCTTTGC
TGGCATCGGTTTTGC
TGGCATTGGAATTGC
AGGCACAGCATTTGC
TGGAACAAATTTTGC
TGGACTGAAAATTGC
TGGCTTACTTCTTGC
TGGCATACAAATTGC
TGGCACTAAAATTGC
CGGTACGAAGTTTGC
TGGCATACATATTGC
TGGCACGATTTTTTA
TGGCATGCTGCTTGC
TGGTACGCTAATTGC
GGGTATAAATTTTGC
TGGAACGCTCCTTGC
CGGATCGCATAATTC
CGGCACAGCCTTTGC
CGGTTGAAAGAAACG
TGGCACGTGATATGC
TGGCACGCTGCTTGA
TGGCACGCTTTTCGC
CGGCAAGATTATTGC
CGGCTCTTTTTTTGC
TGGCATCGATCTTGA
TGGCACGCCCCTTGG
TGGGCATTTGTTGGC
TGGCTAGATTTTTGC
TGGCACGATATGTGC
TGGCATATAATTTGC
TGGCACGTTTACTGC
TGGCACTCTAATTGC
TGGCGCGAATCTTGC
TAGCACGTTTTATGC
CGGTATAATAATTGC
TAGCACGTTTTATGC
AGGTACGAAATTTGC
TGGAACGCTATTTGC
TGGCGCAATTATTGC
TGGCATCCCATTTGC
TGGATTTATCTTTGC
TGGCATCGGTTTTGC
TGGCATTGGAATTGC
AGGCACAGCATTTGC
TGGAACAAATTTTGC
TGGACTGAAAATTGC
TGGCTTACTTCTTGC
TGGCATACAAATTGC
TGGCACTAAAATTGC
CGGTACGAAGTTTGC
TGGCATACATATTGC
TGGCACGATTTTTTA
TGGCATGCTGCTTGC
TGGTACGCTAATTGC
GGGTATAAATTTTGC
TGGAACGCTCCTTGC
CGGATCGCATAATTC
CGGCACAGCCTTTGC
CGGTTGAAAGAAACG
TGGCACGTGATATGC
TGGCACGCTGCTTGA
TGGCACGCTTTTCGC
CGGCAAGATTATTGC

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
CGGCTCTTTTTTTGC
... ... VC0173 VC0172 VC0174
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATCGATCTTGA
... ... VC0486 VC0485 VC0487
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGCCCCTTGG VC0606,
... ... VC0606 VC0605 VC0607
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGGCATTTGTTGGC
... ... lysS prfB VC0665
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCTAGATTTTTGC VC1008,
... ... VC1008 VC1007 VC1006 VC1009
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGATATGTGC
... ... VC1020 uvrB VC1021 VC1022 VC1023
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATATAATTTGC
... ... VC1063 VC1062 VC1061 VC1064
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGTTTACTGC
... ... clpS VC1142 clpA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACTCTAATTGC VC1154,
... ... VC1154 VC1155 VC1156 VC1157
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCGCGAATCTTGC VC1171,
... ... VC1171 trpD VC1170 trpA VC1173 VC1174 VC1175 VC1176
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TAGCACGTTTTATGC
... ... VC1268 VC1269
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
CGGTATAATAATTGC
... ... VC1250 VC1249 VC1251
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TAGCACGTTTTATGC
... ... VC1268 VC1269
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
AGGTACGAAATTTGC VC1384,
... ... VC1384 VC1383 VC1382 VC1381 VC1380 VC1379 VC1385
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGAACGCTATTTGC VC1516, VC1515,
... ... VC1516 VC1515 VC1517 VC1518 VC1519
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCGCAATTATTGC VC1518, VC1517,
... ... VC1518 VC1517 VC1519 VC1520
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATCCCATTTGC VC1523, VC1524, VC1525, mobA, VC1527,
... ... VC1523 VC1524 VC1525 mobA VC1527 VC1522 VC1521
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGATTTATCTTTGC VC1678, pspB, VC1676,
... ... VC1678 pspB VC1676 VC1679
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATCGGTTTTGC VC1699,
... ... VC1699 VC1698 VC1697
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATTGGAATTGC
... ... VC1989 VC1988 VC1987 VC1986 VC1990 VC1991
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
AGGCACAGCATTTGC VC2005,
... ... VC2005 VC2004 rrmA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGAACAAATTTTGC flhF, VC2067, fliA,
... ... flhF VC2067 fliA flhA VC2065 VC2070 VC2071 VC2072 VC2073
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGACTGAAAATTGC flhA,
... ... flhA flhF VC2067 fliA VC2065 VC2070 VC2071 VC2072 VC2073
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCTTACTTCTTGC VC2128,
... ... VC2128 fliL fliM fliJ fliI fliH
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATACAAATTGC fliE, fliF, fliG,
... ... fliE fliF fliG VC2135 VC2136
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACTAAAATTGC fliD, VC2139, fliS,
... ... fliD VC2139 fliS VC2141 VC2142
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
CGGTACGAAGTTTGC
... ... VC2178 VC2177 VC2176 VC2175 prfA hemA
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATACATATTGC flgK, flgL,
... ... flgK flgL flgJ flgI
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGATTTTTTA flgI, flgJ,
... ... flgI flgJ flgH flgG flgF
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCATGCTGCTTGC flgF, flgG, flgH,
... ... flgF flgG flgH flgE flgD flgC flgB
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGTACGCTAATTGC flgB, flgC, flgD, flgE,
... ... flgB flgC flgD flgE VC2201 VC2202
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
GGGTATAAATTTTGC VC2207, VC2206,
... ... VC2207 VC2206 VC2208
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGAACGCTCCTTGC VC2208,
... ... VC2208 VC2207 VC2206
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
CGGATCGCATAATTC
... ... VC2288 VC2287 VC2289 VC2290 VC2291 VC2292 VC2293 VC2294 VC2295
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
CGGCACAGCCTTTGC
... ... VC2397 lpxC ftsA VC2399
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
CGGTTGAAAGAAACG
... ... rumA VC2451 VC2453 VC2454 VC2455 VC2456
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGTGATATGC
... ... VC2499 VC2498 VC2500
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGCTGCTTGA
... ... VC2624 VC2623 VC2625
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
TGGCACGCTTTTCGC glnA,
... ... glnA VC2745 VC2744
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer
CGGCAAGATTATTGC glnL,
... ... glnL VC2747 glnA VC2749 VC2750
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details RNA-Seq (ECO:0005664) - activator monomer