ArticleNucleic acids research2022
Genomic landscape of single-stranded DNA gapped intermediates in Escherichia coli.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Direct visualisation of post-replication gap formation at the bacterial RRS.bioRxiv : the preprint server for biology · 2026Article
- Visualizing the interplay of Cas1-Cas2 with DNA replication-repair that creates CRISPR-Cas immunity.Nucleic acids research · 2026Article
- Spatiotemporal characterization of single-stranded DNA Intermediates after UV Irradiation: I: Post-replication gaps formed during slow growth.PLoS genetics · 2026Article
- Spatiotemporal characterization of single-stranded DNA intermediates after UV irradiation: II. Rapid growth and effects of recA and recJ.PLoS genetics · 2026Article
- The RecBC complex protects single-stranded DNA gaps during lesion bypass.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Hallmarks of DNA replication stress responses in Escherichia coli and Bacillus subtilis.FEMS microbiology reviews · 2025Review
- Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli.Nucleic acids research · 2025Article
- Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance.Nucleic acids research · 2024Article
- A bacterial expression cloning screen reveals single-stranded DNA-binding proteins as potent desicco-protectants.Cell reports · 2024Article
- Escherichia coli DNA replication: the old model organism still holds many surprises.FEMS microbiology reviews · 2024Review
- Ribonucleotide and R-Loop Damage in Plastid DNA and Mitochondrial DNA during Maize Development.Plants (Basel, Switzerland) · 2023Article
- Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method.International journal of molecular sciences · 2023Article
- Generation and Repair of Postreplication Gaps in Escherichia coli.Microbiology and molecular biology reviews : MMBR · 2023Review
- RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli.Nucleic acids research · 2023Article
- RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes.Nucleic acids research · 2023Article
- Enzymatic Supercoiling of Bacterial Chromosomes Facilitates Genome Manipulation.ACS synthetic biology · 2022Article
- Single strand gap repair: The presynaptic phase plays a pivotal role in modulating lesion tolerance pathways.PLoS genetics · 2022Article
- Molecular insights into the prototypical single-stranded DNA-binding protein fromCritical reviews in biochemistry and molecular biologyReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Single-stranded (ss) gapped regions in bacterial genomes (gDNA) are formed on W- and C-strands during replication, repair, and recombination. Using non-denaturing bisulfite treatment to convert C to U on ssDNA, combined with deep sequencing, we have mapped gDNA gap locations, sizes, and distributions in Escherichia coli for cells grown in mid-log phase in the presence and absence of UV irradiation, and in stationary phase cells. The fraction of ssDNA on gDNA is similar for W- and C-strands, ∼1.3% for log phase cells, ∼4.8% for irradiated log phase cells, and ∼8.5% for stationary phase cells. After UV irradiation, gaps increased in numbers and average lengths. A monotonic reduction in ssDNA occurred symmetrically between the DNA replication origin of (OriC) and terminus (Ter) for log phase cells with and without UV, a hallmark feature of DNA replication. Stationary phase cells showed no OriC → Ter ssDNA gradient. We have identified a spatially diverse gapped DNA landscape containing thousands of highly enriched 'hot' ssDNA regions along with smaller numbers of 'cold' regions. This analysis can be used for a wide variety of conditions to map ssDNA gaps generated when DNA metabolic pathways have been altered, and to identify proteins bound in the gaps.
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