ArticlePLoS genetics2019
Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
34 citing papers in PubMed, 69 citations in OpenAlex.
- Article
- Teamwork of clustered low-affinity κB sites and accessory factors regulates transcriptional strength of NF-κB RelA dimers.Nucleic acids research · 2025Article
- Timing is everything: transcription bursting in development.Genes & development · 2025Review
- Activation of NF-κB Signaling by Optogenetic Clustering of IKKα and β.Advanced biology · 2025Article
- Short activation domains control chromatin association of transcription factors.bioRxiv : the preprint server for biology · 2025Article
- Quantification and potential functional relevance of binding cooperativity of adjacent transcription factors on DNA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding.Nature communications · 2025Article
- Single-molecule imaging for investigating the transcriptional control.Molecules and cells · 2025Review
- Transcription dynamics and genome organization in the mammalian nucleus: Recent advances.Molecular cell · 2025Review
- Chromatin organization drives the search mechanism of nuclear factors.Nature communications · 2023Article
- Review
- Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states.Science advances · 2023Article
- ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks.The Journal of cell biology · 2023Article
- Single-molecule tracking (SMT): a window into live-cell transcription biochemistry.Biochemical Society transactions · 2023Article
- Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient.Cell systems · 2023Article
- Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.Nature communications · 2022Article
- Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.Cell reports · 2022Article
- Following the tracks: How transcription factor binding dynamics control transcription.Biophysical journal · 2022Review
- Insights on the NF-κB System Using Live Cell Imaging: Recent Developments and Future Perspectives.Frontiers in immunology · 2022Review
- Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation.Nucleic acids research · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by recognizing and binding to specific DNA promoter sequences. In higher eukaryotes, it remains unclear how the duration of TF binding to DNA relates to downstream transcriptional output. Here, we address this question for the transcriptional activator NF-κB (p65), by live-cell single molecule imaging of TF-DNA binding kinetics and genome-wide quantification of p65-mediated transcription. We used mutants of p65, perturbing either the DNA binding domain (DBD) or the protein-protein transactivation domain (TAD). We found that p65-DNA binding time was predominantly determined by its DBD and directly correlated with its transcriptional output as long as the TAD is intact. Surprisingly, mutation or deletion of the TAD did not modify p65-DNA binding stability, suggesting that the p65 TAD generally contributes neither to the assembly of an "enhanceosome," nor to the active removal of p65 from putative specific binding sites. However, TAD removal did reduce p65-mediated transcriptional activation, indicating that protein-protein interactions act to translate the long-lived p65-DNA binding into productive transcription.
Indexed as
Identifiers
What OpenQuestion holds
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.