Defining bacterial regulons using ChIP-seq

Myers, Kevin S.; Park, Dan M.; Beauchene, Nicole A.; Kiley, Patricia J.

doi:10.1016/j.ymeth.2015.05.022

Cited by 40 publications

(31 citation statements)

References 82 publications

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“…While great strides have been made toward systematic mapping of physical protein-protein and protein-DNA interaction networks (Cai & Huang, 2012;Syafrizayanti et al, 2014;Myers et al, 2015;Smits & Vermeulen, 2016), systematic mapping of protein-metabolite interactions is lagging behind. One challenge is the generally low affinity (mM range) of protein-metabolite interactions (Reznik et al, 2017) and their fleeting nature.…”

Section: Introductionmentioning

confidence: 99%

Systematic mapping of protein‐metabolite interactions in central metabolism of Escherichia coli

Diether

Nikolaev

Allain

et al. 2019

Molecular Systems Biology

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Metabolite binding to proteins regulates nearly all cellular processes, but our knowledge of these interactions originates primarily from empirical in vitro studies. Here, we report the first systematic study of interactions between water‐soluble proteins and polar metabolites in an entire biological subnetwork. To test the depth of our current knowledge, we chose to investigate the well‐characterized Escherichia coli central metabolism. Using ligand‐detected NMR , we assayed 29 enzymes towards binding events with 55 intracellular metabolites. Focusing on high‐confidence interactions at a false‐positive rate of 5%, we detected 98 interactions, among which purine nucleotides accounted for one‐third, while 50% of all metabolites did not interact with any enzyme. In contrast, only five enzymes did not exhibit any metabolite binding and some interacted with up to 11 metabolites. About 40% of the interacting metabolites were predicted to be allosteric effectors based on low chemical similarity to their target's reactants. For five of the eight tested interactions, in vitro assays confirmed novel regulatory functions, including ATP and GTP inhibition of the first pentose phosphate pathway enzyme. With 76 new candidate regulatory interactions that have not been reported previously, we essentially doubled the number of known interactions, indicating that the presently available information about protein–metabolite interactions may only be the tip of the iceberg.

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Section: Introductionmentioning

confidence: 99%

Systematic mapping of protein‐metabolite interactions in central metabolism of Escherichia coli

Diether

Nikolaev

Allain

et al. 2019

Molecular Systems Biology

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“…A few points to be considered while designing a ChIP‐seq experiment are as follows and have also been described in earlier reviews (Myers et al ., ). First, the quality of the ChIP‐seq data depends on the quality of the antibody.…”

Section: Binding Site Mapping Techniquesmentioning

confidence: 97%

Tools to map target genes of bacterial two‐component system response regulators

Rajeev

Garber

Mukhopadhyay

2020

Environ Microbiol Rep

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Studies on bacterial physiology are incomplete without knowledge of the signalling and regulatory systems that a bacterium uses to sense and respond to its environment. Two-component systems (TCSs) are among the most prevalent bacterial signalling systems, and they control essential and secondary physiological processes; however, even in model organisms, we lack a complete understanding of the signals sensed, the phosphotransfer partners and the functions regulated by these systems. In this review, we discuss several tools to map the genes targeted by transcriptionally acting TCSs. Many of these tools have been used for studying individual TCSs across diverse species, but systematic approaches to delineate entire signalling networks have been very few. Since genome sequences and high-throughput technologies are now readily available, the methods presented here can be applied to characterize the entire DNA-binding TCS signalling network in any bacterial species and are especially useful for non-model environmental bacteria.

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“…Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is a technique for the genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes [36]. ChIP-Seq has become an essential tool for studying gene regulation and epigenetic mechanisms.…”

Section: Chromatin Immunoprecipitation Followed By Sequencing (Chip-seq)mentioning

confidence: 99%

“…After peaks are associated with genes downstream, a number of bioinformatics analyses can be carried out, including identification and analysis of motifs, differential analysis and association with expression data for deep understanding of bacterial regulon. This is shown in Figure 3 [36]. As whole-genome transcription profiling cannot reveal whether the influence of the transcription factors (TF) on RNA levels is direct or indirect, this requires identification of transcription factors binding within the appropriate promoter region.…”

Section: Chromatin Immunoprecipitation Followed By Sequencing (Chip-seq)mentioning

confidence: 99%

“…For example, work carried out by Stringer et al (2014) on the araC gene of Escherichia coli and Salmonella enterica has identified direct regulatory targets of AraC, including five novel target genes: ytfQ, ydeN, ydeM, ygeA and polB [42]. Although ChIP-seq has been used only in moderation to study bacterial systems in a few bacterial species, such as Vibrio harveyi, V. cholerae, Rhodobacter sphaeroides, Mycobacterium tuberculosis, S. enterica and Caulobacter crescentus [36,37,[43][44][45], it is used to identify novel regulatory interactions, even for well-studied proteins [46,47].…”

Section: Chromatin Immunoprecipitation Followed By Sequencing (Chip-seq)mentioning

confidence: 99%

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RNA-seq – Revealing Biological Insights in Bacteria

Santana¹,

Aburjaile²,

Parise³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

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New technologies are constantly being released and the improvements therein bring advances not only to transcriptome, the focus of this chapter, but also to diverse areas of biological research. Since the announcement and application of the RN"-seq approach, discoveries are being made in this field, but when we consider bacterial species, this progress proceeded a few years behind. However, with the application of RN"-seq derivative approaches, we can gain biological insights into the bacterial world and aspire to uncover the mysteries involving gene expression, organization and other functional genomic features.

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Defining bacterial regulons using ChIP-seq

Cited by 40 publications

References 82 publications

Systematic mapping of protein‐metabolite interactions in central metabolism of Escherichia coli

Systematic mapping of protein‐metabolite interactions in central metabolism of Escherichia coli

Tools to map target genes of bacterial two‐component system response regulators

RNA-seq – Revealing Biological Insights in Bacteria

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