ArticlePLoS biology2013
Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.
Article in PLoS biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 64 citations in OpenAlex.
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- Differential effect of supercoiling on bacterial transcription in topological domains.PLoS computational biology · 2025Article
- Light-dependent modulation of protein localization and function in living bacteria cells.Nature communications · 2024Article
- Analysis of Fluorescent Proteins for Observing Single Gene Locus in a Live and FixedThe journal of physical chemistry. B · 2024Article
- A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation.PLoS computational biology · 2022Article
- Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging.Science (New York, N.Y.) · 2022Article
- Histone-like nucleoid structuring (H-NS) protein silences the beta-glucoside (Computational and structural biotechnology journal · 2022Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
- A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM.Nature methods · 2021Article
- The loopometer: a quantitative in vivo assay for DNA-looping proteins.Nucleic acids research · 2021Article
- Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales.Nature communications · 2021Article
- Single-molecule tracking reveals that the nucleoid-associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA.Molecular microbiology · 2021Article
- Regulation of Gene Activation by Competitive Cross Talking Pathways.Biophysical journal · 2020Article
- Transcription and translation contribute to gene locus relocation to the nucleoid periphery in E. coli.Nature communications · 2019Article
- FoxH1 represses miR-430 during early embryonic development of zebrafish via non-canonical regulation.BMC biology · 2019Article
- From single bacterial cell imaging towardsEssays in biochemistry · 2019Review
- Linking dynamical complexities from activation signals to transcription responses.Royal Society open science · 2019Article
- Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch.Nature communications · 2018Article
- Micro-patterned agarose gel devices for single-cell high-throughput microscopy of E. coli cells.Scientific reports · 2017Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R) and O(L) (separated by 2.3 kb), mediated by the λ repressor CI (accession number P03034), play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.
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