ArticleMolecular systems biology2021
TNF stimulation primarily modulates transcriptional burst size of NF-κB-regulated genes.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed, 33 citations in OpenAlex.
- Heritable single-cell gene expression states shape functional variability in innate immune responses.bioRxiv : the preprint server for biology · 2026Article
- Review
- BAF complexes maintain accessibility at stimulus-responsive chromatin and are required for transcriptional stimulus responses.bioRxiv : the preprint server for biology · 2026Article
- Heterogeneous NF-κB activation and enhancer features shape transcription in Drosophila immunity.Biophysical journal · 2026Article
- Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body.PLoS genetics · 2026Article
- Two distinct chromatin modules regulate proinflammatory gene expression.Nature cell biology · 2026Article
- Role of PBAF and Mediator kinase module in the RELA-dependent activation ofFrontiers in immunology · 2026Article
- Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data.Bioinformatics (Oxford, England) · 2025Article
- A conserved coupling of transcriptional ON and OFF periods underlies bursting dynamics.Nature structural & molecular biology · 2025Article
- Spatial microenvironments tune immune response dynamics in thebioRxiv : the preprint server for biology · 2025Article
- Gene regulatory logic of the interferon-β enhancer is characterized by two selectively deployed modes of transcription factor synergy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Heterogeneous NF-κB activation and enhancer features shape transcription inbioRxiv : the preprint server for biology · 2025Article
- An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs.Nature genetics · 2025Article
- Deciphering HIV-1 Transcription Initiation and Elongation from Single-Molecule Imaging Data.Research (Washington, D.C.) · 2025Article
- Single-Cell Analysis Reveals a Subset of High IL-12p40-Secreting Dendritic Cells within Mouse Bone Marrow-Derived Macrophages Differentiated with M-CSF.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Assessing the anti-inflammatory effects of whole-body vibration: a meta-analysis based on pre-clinical and clinical evidences.American journal of clinical and experimental immunology · 2024Review
- Review
- A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases.International journal of molecular sciences · 2023Article
- Variability of the innate immune response is globally constrained by transcriptional bursting.Frontiers in molecular biosciences · 2023Article
- Overexpression of IκB⍺ modulates NF-κB activation of inflammatory target gene expression.Frontiers in molecular biosciences · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Cell-to-cell heterogeneity is a feature of the tumor necrosis factor (TNF)-stimulated inflammatory response mediated by the transcription factor NF-κB, motivating an exploration of the underlying sources of this noise. Here, we combined single-transcript measurements with computational models to study transcriptional noise at six NF-κB-regulated inflammatory genes. In the basal state, NF-κB-target genes displayed an inverse correlation between mean and noise characteristic of transcriptional bursting. By analyzing transcript distributions with a bursting model, we found that TNF primarily activated transcription by increasing burst size while maintaining burst frequency for gene promoters with relatively high basal histone 3 acetylation (AcH3) that marks open chromatin environments. For promoters with lower basal AcH3 or when AcH3 was decreased with a small molecule drug, the contribution of burst frequency to TNF activation increased. Finally, we used a mathematical model to show that TNF positive feedback amplified gene expression noise resulting from burst size-mediated transcription, leading to a subset of cells with high TNF protein expression. Our results reveal potential sources of noise underlying intercellular heterogeneity in the TNF-mediated inflammatory response.
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.