ArticleThe EMBO journal2022
Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria.
Article in The EMBO journal, 2022. 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 14 papers.
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Who cites it
14 citing papers in PubMed, 27 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
- Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands.Nature communications · 2026Article
- Article
- 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
- The emerging role of DNA methylation in the pathogenicity of bacterial pathogens.Journal of bacteriology · 2025Review
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate ofmSphere · 2024Article
- CDBProm: the Comprehensive Directory of Bacterial Promoters.NAR genomics and bioinformatics · 2024Article
- Mechanisms of Regulation of Cryptic Prophage-Encoded Gene Products in Escherichia coli.Journal of bacteriology · 2023Article
- Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria.The EMBO journal · 2022Article
- Polyphosphate drives bacterial heterochromatin formation.Science advances · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
There is increasing evidence that prokaryotes maintain chromosome structure, which in turn impacts gene expression. We recently characterized densely occupied, multi-kilobase regions in the E. coli genome that are transcriptionally silent, similar to eukaryotic heterochromatin. These extended protein occupancy domains (EPODs) span genomic regions containing genes encoding metabolic pathways as well as parasitic elements such as prophages. Here, we investigate the contributions of nucleoid-associated proteins (NAPs) to the structuring of these domains, by examining the impacts of deleting NAPs on EPODs genome-wide in E. coli and B. subtilis. We identify key NAPs contributing to the silencing of specific EPODs, whose deletion opens a chromosomal region for RNA polymerase binding at genes contained within that region. We show that changes in E. coli EPODs facilitate an extra layer of transcriptional regulation, which prepares cells for exposure to exotic carbon sources. Furthermore, we distinguish novel xenogeneic silencing roles for the NAPs Fis and Hfq, with the presence of at least one being essential for cell viability in the presence of domesticated prophages. Our findings reveal previously unrecognized mechanisms through which genomic architecture primes bacteria for changing metabolic environments and silences harmful genomic elements.
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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 Socratic graph.