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-PCR validated on Ch-2 Vibrio cholerae O1 biovar El Tor str. N16961 chosen as reference by authors (gene names)

Experimental Process

ChIP-seq, validated by qPCR in several genes RNA-seq, validated also by qPCR in a few genes

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

TGGCATTGAGTTTGC
TGGCATTCTTTATGC
TGGCATCAAATATGC
CGGCATGCTTTCTGC
TGGCACGTAATCTGC

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	Experimental techniques	TF function	TF type
TGGCATTGAGTTTGC	VCA0123,	Experimental technique details ChIP-PCR (ECO:0005620) ChIP-PCR - ECO:0005620 ChIP-chip (and to a lesser degree ChIP-Seq) results are often validated with ChIP-PCR, in which a PCR with specific primers is performed on the pulled-down DNA. As in the case of RNASeq, there are many variations of these main techniques. - Experimental technique details ChIP-Seq (ECO:0006009) ChIP-Seq - ECO:0006009 ChIP-Seq is equivalent to ChIP-chip down to the last step. In ChIP-Seq, immunoprecipiated DNA fragments are prepared for sequencing and funneled into a massively parallel sequencer that produces short reads. Even though the sonication step is the same as in ChIP-chip, ChIP-Seq will generate multiple short-reads within any given 500 bp region, thereby pinning down the location of TFBS to within 50-100 bp. A similar result can be obtained with ChIP-chip using high-density tiling-arrays. The downside of ChIP-Seq is that sensitivity is proportional to cost, as sensitivity increases with the number of (expensive) parallel sequencing runs. To control for biases, ChIP-seq experiments often use the "input" as a control. This is DNA sequence resulting from the same pipeline as the ChIP-seq experiment, but omitting the immunoprecipitation step. It therefore should have the same accessibility and sequencing biases as the experiment data. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	activator	monomer
TGGCATTCTTTATGC		Experimental technique details ChIP-PCR (ECO:0005620) ChIP-PCR - ECO:0005620 ChIP-chip (and to a lesser degree ChIP-Seq) results are often validated with ChIP-PCR, in which a PCR with specific primers is performed on the pulled-down DNA. As in the case of RNASeq, there are many variations of these main techniques. - Experimental technique details ChIP-Seq (ECO:0006009) ChIP-Seq - ECO:0006009 ChIP-Seq is equivalent to ChIP-chip down to the last step. In ChIP-Seq, immunoprecipiated DNA fragments are prepared for sequencing and funneled into a massively parallel sequencer that produces short reads. Even though the sonication step is the same as in ChIP-chip, ChIP-Seq will generate multiple short-reads within any given 500 bp region, thereby pinning down the location of TFBS to within 50-100 bp. A similar result can be obtained with ChIP-chip using high-density tiling-arrays. The downside of ChIP-Seq is that sensitivity is proportional to cost, as sensitivity increases with the number of (expensive) parallel sequencing runs. To control for biases, ChIP-seq experiments often use the "input" as a control. This is DNA sequence resulting from the same pipeline as the ChIP-seq experiment, but omitting the immunoprecipitation step. It therefore should have the same accessibility and sequencing biases as the experiment data. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	activator	monomer
TGGCATCAAATATGC		Experimental technique details ChIP-PCR (ECO:0005620) ChIP-PCR - ECO:0005620 ChIP-chip (and to a lesser degree ChIP-Seq) results are often validated with ChIP-PCR, in which a PCR with specific primers is performed on the pulled-down DNA. As in the case of RNASeq, there are many variations of these main techniques. - Experimental technique details ChIP-Seq (ECO:0006009) ChIP-Seq - ECO:0006009 ChIP-Seq is equivalent to ChIP-chip down to the last step. In ChIP-Seq, immunoprecipiated DNA fragments are prepared for sequencing and funneled into a massively parallel sequencer that produces short reads. Even though the sonication step is the same as in ChIP-chip, ChIP-Seq will generate multiple short-reads within any given 500 bp region, thereby pinning down the location of TFBS to within 50-100 bp. A similar result can be obtained with ChIP-chip using high-density tiling-arrays. The downside of ChIP-Seq is that sensitivity is proportional to cost, as sensitivity increases with the number of (expensive) parallel sequencing runs. To control for biases, ChIP-seq experiments often use the "input" as a control. This is DNA sequence resulting from the same pipeline as the ChIP-seq experiment, but omitting the immunoprecipitation step. It therefore should have the same accessibility and sequencing biases as the experiment data. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	activator	monomer
CGGCATGCTTTCTGC		Experimental technique details ChIP-PCR (ECO:0005620) ChIP-PCR - ECO:0005620 ChIP-chip (and to a lesser degree ChIP-Seq) results are often validated with ChIP-PCR, in which a PCR with specific primers is performed on the pulled-down DNA. As in the case of RNASeq, there are many variations of these main techniques. - Experimental technique details ChIP-Seq (ECO:0006009) ChIP-Seq - ECO:0006009 ChIP-Seq is equivalent to ChIP-chip down to the last step. In ChIP-Seq, immunoprecipiated DNA fragments are prepared for sequencing and funneled into a massively parallel sequencer that produces short reads. Even though the sonication step is the same as in ChIP-chip, ChIP-Seq will generate multiple short-reads within any given 500 bp region, thereby pinning down the location of TFBS to within 50-100 bp. A similar result can be obtained with ChIP-chip using high-density tiling-arrays. The downside of ChIP-Seq is that sensitivity is proportional to cost, as sensitivity increases with the number of (expensive) parallel sequencing runs. To control for biases, ChIP-seq experiments often use the "input" as a control. This is DNA sequence resulting from the same pipeline as the ChIP-seq experiment, but omitting the immunoprecipitation step. It therefore should have the same accessibility and sequencing biases as the experiment data. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	activator	monomer
TGGCACGTAATCTGC		Experimental technique details ChIP-PCR (ECO:0005620) ChIP-PCR - ECO:0005620 ChIP-chip (and to a lesser degree ChIP-Seq) results are often validated with ChIP-PCR, in which a PCR with specific primers is performed on the pulled-down DNA. As in the case of RNASeq, there are many variations of these main techniques. - Experimental technique details ChIP-Seq (ECO:0006009) ChIP-Seq - ECO:0006009 ChIP-Seq is equivalent to ChIP-chip down to the last step. In ChIP-Seq, immunoprecipiated DNA fragments are prepared for sequencing and funneled into a massively parallel sequencer that produces short reads. Even though the sonication step is the same as in ChIP-chip, ChIP-Seq will generate multiple short-reads within any given 500 bp region, thereby pinning down the location of TFBS to within 50-100 bp. A similar result can be obtained with ChIP-chip using high-density tiling-arrays. The downside of ChIP-Seq is that sensitivity is proportional to cost, as sensitivity increases with the number of (expensive) parallel sequencing runs. To control for biases, ChIP-seq experiments often use the "input" as a control. This is DNA sequence resulting from the same pipeline as the ChIP-seq experiment, but omitting the immunoprecipitation step. It therefore should have the same accessibility and sequencing biases as the experiment data. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time. -	activator	monomer