Project description:We mapped the genome-wide binding of the flagellar regulators FlhD, FlhC, and FliA in FLAG-tagged derivatives of E. coli K-12 MG1655 using ChIP coupled with deep sequencing (ChIP-seq). We identify new binding sites for each factor.
Project description:We mapped the genome-wide binding of C-terminally FLAG-tagged AraC in S. enterica subsp. enterica serovar Typhimurium strain 14028s using ChIP coupled with deep sequencing (ChIP-seq). We identified five putative target loci for AraC: upstream of araB/araC, araE, araJ, STM14_0178, and within sseD.
Project description:We mapped the genome-wide binding of sigma 70 in E. coli K-12 MG1655 and an hns mutant that is otherwise isogenic using ChIP coupled with deep sequencing (ChIP-seq). We show that intragenic binding of sigma 70 is increased in the hns mutant.
Project description:We used ChIP-seq to map the binding of of C-terminally FLAG3-tagged PhoB to the Escherichia coli K-12 genome during growth in MOPS minimal media with low phosphate or high phosphate (0.2 mM or 1.32 mM, respectively). As a control, we performed ChIP-seq in an untagged strain. We also used ChIP-seq to map Sigma 70 (associates with initiating RNA polymerase) binding across the E. coli K-12 genome in wild-type, ΔphoB, Δhns, and Δhns ΔphoB strains grown in low phosphate medium to determine whether PhoB modulates recruitment of RNA polymerase to promoters and whether this is modulated by H-NS.
Project description:We used ChIP-chip to map the binding of C-terminally TAP (tandem affinity purification)-tagged GalR (tagged at its native locus in an unmarked strain) across the E. coli genome.
Project description:ChIP-seq was performed to map the association of SPA-tagged DnaA across the Escherichia coli MG1655 chromosome during exponential phase growth in LB. As a control to remove background, ChIP-Seq was also performed on SPA-tagged AcpS, a protein that is not known to bind DNA.
Project description:To determine sites where RpoS binds (and hence likely plays a direct role in transcription), we used ChIP-seq to map the association of RpoS across the Escherichia coli chromosome during stationary phase growth in minimal medium. To facilitate ChIP, RpoS was C-terminally SPA-tagged at its native locus.