ArticleGenome biology2014
TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 49 citations in OpenAlex.
- Two distinct chromatin modules regulate proinflammatory gene expression.Nature cell biology · 2026Article
- nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.Science advances · 2024Article
- Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation.Nucleic acids research · 2024Article
- Remodeling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO.iScience · 2024Article
- Changes in adenoviral chromatin organization precede early gene activation upon infection.The EMBO journal · 2023Article
- Nucleosome repositioning in chronic lymphocytic leukemia.Genome research · 2023Article
- Article
- An Expanded Interplay Network between NF-κB p65 (RelA) and E2F1 Transcription Factors: Roles in Physiology and Pathology.Cancers · 2022Article
- NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.Chromosoma · 2022Article
- Differences in nanoscale organization of regulatory active and inactive human chromatin.Biophysical journal · 2022Article
- Review
- Peculiarities ofInternational journal of molecular sciences · 2021Review
- Review
- The histone demethylase KDM6B fine-tunes the host response to Streptococcus pneumoniae.Nature microbiology · 2021Article
- Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals.Nature communications · 2021Article
- Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses.Frontiers in immunology · 2021Review
- Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation.Epigenetics · 2021Article
- A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer.Cancer cell · 2020Article
- Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner.The EMBO journal · 2020Article
- Monitoring the prolonged Tnf stimulation in space and time with topological-functional networks.Computational and structural biotechnology journal · 2020Article
Corrections and comments
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Authors and funding
13 authors at 7 institutions in 4 countries.
Funding
Abstract
backgroundThe rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to allow establishment of new transcriptional programs.
resultsUsing micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFα) - a proinflammatory cytokine that signals through nuclear factor kappa-B (NF-κB). Within 10 min, nucleosomes reposition at regions both proximal and distal to NF-κB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFα-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 min, widespread repositioning throughout megabase pair-long chromosomal segments, with consequential effects on three-dimensional structure (detected using chromosome conformation capture), is seen.
conclusionsWhilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFα-induced priming mechanism, mostly independent of NF-κB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains.
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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.