ArticleGenome research2016
Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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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
33 citing papers in PubMed, 52 citations in OpenAlex.
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- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- Two distinct chromatin modules regulate proinflammatory gene expression.Nature cell biology · 2026Article
- Fuzzy protein-DNA interactions and beyond: A common theme in transcription?Current opinion in structural biology · 2024Review
- DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part I - the impact of inflammation.Epigenetics · 2023Article
- Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes.Cell reports · 2023Article
- Article
- Three-dimensional genome organization in immune cell fate and function.Nature reviews. Immunology · 2023Review
- A novel intergenic enhancer that regulatesiScience · 2023Article
- An Expanded Interplay Network between NF-κB p65 (RelA) and E2F1 Transcription Factors: Roles in Physiology and Pathology.Cancers · 2022Article
- Chromatin basis of the senescence-associated secretory phenotype.Trends in cell biology · 2022Review
- Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues.G3 (Bethesda, Md.) · 2022Article
- Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer.Frontiers in cell and developmental biology · 2022Review
- Review
- Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis.iScience · 2021Article
- Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals.Nature communications · 2021Article
- Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation.Epigenetics · 2021Article
- Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses.Frontiers in immunology · 2021Review
- Low Input Targeted Chromatin Capture (Low-T2C).Methods in molecular biology (Clifton, N.J.) · 2021Article
- Chromatin Conformation in Development and Disease.Frontiers in cell and developmental biology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 4 institutions in 3 countries.
Funding
Abstract
Mammalian cells have developed intricate mechanisms to interpret, integrate, and respond to extracellular stimuli. For example, tumor necrosis factor (TNF) rapidly activates proinflammatory genes, but our understanding of how this occurs against the ongoing transcriptional program of the cell is far from complete. Here, we monitor the early phase of this cascade at high spatiotemporal resolution in TNF-stimulated human endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters. Notably, >50% of these enhancers do not encode canonical NF-κB binding motifs. Using a combination of genomics tools, we find that binding site selection plays a key role in NF-κΒ-mediated transcriptional activation and repression. We demonstrate the latter by describing the synergy between NF-κΒ and the corepressor JDP2. Finally, detailed analysis of a 2.8-Mbp locus using sub-kbp-resolution targeted chromatin conformation capture and genome editing uncovers how NF-κΒ that has just entered the nucleus exploits pre-existing chromatin looping to exert its multimodal role. This work highlights the involvement of topology in cis-regulatory element function during acute transcriptional responses, where primary DNA sequence and its higher-order structure constitute a regulatory context leading to either gene activation or repression.
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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.