proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms

Abstract

The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.

RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS–StpA Nucleoprotein Filaments in Pathogenic Escherichiacoli

“…S1C and D ). We also analyzed published epitope-tagged H-NS and StpA ChIP-exo data for K-12 ( 57 ) and found that epitope-tagged H-NS and StpA are similarly distributed in K-12 ( Fig. S1E ), consistent with a ChIP-chip study of K-12 ( 29 ).…”

Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites

“…Similar patterns are also observed in ChIP binding intensities for multiple auto-activated E . coli TFs curated in the prokaryotic ChIP database, proChIPdb [ 27 ]. For individual TFs, binding peak intensities for positively autoregulated promoters are among the highest of all binding regions across the chromosome ( Fig 4B ), suggesting that strong affinities for the auto-activated promoters may be selected for.…”

“…Peak intensities from chromatin immunoprecipitation (ChIP) experiments can reflect binding strengths of a TF to various sites. ChIP peak intensities, defined as signal noise ratio (SNR), were obtained for autoregulated TFs from the prokaryotic ChIP database, proChIPdb [ 27 ]. After subtracting the median of logarithmic intensities of all identified peaks, the resulting values (Δlog 10 SNR) were used to assess the relative binding strength of individual TFBSs.…”

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

“…ChIP-seq raw samples and metadata were downloaded systematically from the SRA. The ChIP-exo subcollection was retrieved from the recently published proChIPdb [27]. This subcollection includes datasets tagged in proChIPdb as 'curated' , as well as TF binding information for OxyR, SoxR, SoxS, and UvrY, from [31,32].…”

“…Those have been uploaded into EcoCyc and RegulonDB with a clear HT evidence type along with those identified by classic LT methods. In addition to COLOMBOS with expression data [ 25 ], the Transcription Profile of Escherichia coli (TEC) database [ 26 ], released in 2016, offers gSELEX data in E. coli and the PROkaryotic Chromatin ImmunoPrecipitation database (proChIPdb, [ 27 ]), recently released, offers ChIP-seq and ChIP-exo datasets. However, to our knowledge, there is no comprehensive resource facilitating access in a single place to the diverse wealth of data of different types of objects relevant to the regulation of gene expression in E. coli K-12.…”