ArticlePLoS biology2021
Dynamic landscape of protein occupancy across the Escherichia coli chromosome.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 41 citations in OpenAlex.
- Profiling large-scale protein occupancy on bacterial genomes using IPOD-HR.Nature protocols · 2026Review
- Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.Nucleic acids research · 2026Article
- The role of the VirB ligand CTP in the molecular mechanism of transcriptional anti-silencing in Shigella flexneri.Nucleic acids research · 2026Article
- Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.bioRxiv : the preprint server for biology · 2026Article
- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
- LsrL modulates Lsr2-induced chromatin structure to tune biosynthetic gene cluster regulation inbioRxiv : the preprint server for biology · 2025Article
- Conserved Heterochromatin-like Structures with Local Regulators Mediate the Iron Stress Response in Mycobacteria.bioRxiv : the preprint server for biology · 2025Article
- DNA methylation affects gene expression but not global chromatin structure inJournal of bacteriology · 2025Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- The Environment-Dependent Regulatory Landscape of thebioRxiv : the preprint server for biology · 2025Article
- Article
- Clues to transcription/replication collision-induced DNA damage: it was RNAP, in the chromosome, with the fork.FEBS letters · 2025Review
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Membrane association of active genes organizes the chloroplast nucleoid structure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.Nature structural & molecular biology · 2024Article
- Article
- Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing.Nucleic acids research · 2023Article
- Article
- Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.FEMS microbiology reviews · 2023Review
- The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity.Frontiers in microbiology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Free-living bacteria adapt to environmental change by reprogramming gene expression through precise interactions of hundreds of DNA-binding proteins. A predictive understanding of bacterial physiology requires us to globally monitor all such protein-DNA interactions across a range of environmental and genetic perturbations. Here, we show that such global observations are possible using an optimized version of in vivo protein occupancy display technology (in vivo protein occupancy display-high resolution, IPOD-HR) and present a pilot application to Escherichia coli. We observe that the E. coli protein-DNA interactome organizes into 2 distinct prototypic features: (1) highly dynamic condition-dependent transcription factor (TF) occupancy; and (2) robust kilobase scale occupancy by nucleoid factors, forming silencing domains analogous to eukaryotic heterochromatin. We show that occupancy dynamics across a range of conditions can rapidly reveal the global transcriptional regulatory organization of a bacterium. Beyond discovery of previously hidden regulatory logic, we show that these observations can be utilized to computationally determine sequence specificity models for the majority of active TFs. Our study demonstrates that global observations of protein occupancy combined with statistical inference can rapidly and systematically reveal the transcriptional regulatory and structural features of a bacterial genome. This capacity is particularly crucial for non-model bacteria that are not amenable to routine genetic manipulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.