Evidence map›Paper›PMID 38430908›Full record

ArticleImmunity2024

The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling.

An-Chieh Feng, Brandon J Thomas, Prabhat K Purbey, Filipe Menegatti de Melo, Xin Liu, Allison E Daly, Fei Sun, Jerry Hung-Hao Lo, Lijing Cheng, Michael F Carey and 2 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Immunity, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.

0numbers the graph read from it
0cells of the map it votes in
38citing papers in PubMed
11.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

38 citing papers in PubMed, 48 citations in OpenAlex.

  1. Review
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  12. ThemBio · 2025
    Article
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  15. Review
  16. Review
  17. The Role of Lactylation in Virus-Host Interactions.International journal of molecular sciences · 2025
    Review
  18. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 2 institutions in 1 country.

An-Chieh FengDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Brandon J ThomasDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA 98195, USA.
Prabhat K PurbeyMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Filipe Menegatti de MeloDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Xin LiuDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Allison E DalyDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Fei SunMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Jerry Hung-Hao LoDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Lijing ChengDepartment of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Michael F CareyMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Philip O ScumpiaMolecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Stephen T SmaleDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: smale@mednet.ucla.edu.
University of California, Los Angeles · USHoward Hughes Medical Institute · US

Funding

UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
MULTIDISCIPLINARY TRAINING IN MICROBIAL PATHOGENESIST32AI007323 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Peter John Bradley · 1988 to 2026
$8.6M
Vitamin D Metabolism in LeprosyP50AR063020 · NIAMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI PELLEGRINI, MATTEO · 2012 to 2016
$7.8M
Interplay Between Chromatin and Co-Activator ComplexesR01GM074701 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CAREY, MICHAEL F · 2005 to 2025
$6.7M
Selective Regulation of Pro-Inflammatory Genes in MacrophagesR01GM086372 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SMALE, STEPHEN T · 2008 to 2015
$2.5M
Selective gene activation by the NF-kappaB family of transcription factorsR01AI073868 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SMALE, STEPHEN T · 2007 to 2011
$1.8M
Pro-inflammatory gene regulation in a native chromatin environmentR01CA127279 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SMALE, STEPHEN T · 2008 to 2011
$1.2M
Mechanistically defining the role for each NFkB family member in pro-inflammatory macrophage activationF31AI157267 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DALY, ALLISON E · 2021 to 2022
$78k
NCI NIH HHS R01 CA127279NIAID NIH HHS F31 AI157267NIAID NIH HHS R01 AI073868NIAID NIH HHS T32 AI007323NIAMS NIH HHS P50 AR063020NIGMS NIH HHS R01 GM074701NIGMS NIH HHS R01 GM086372NIGMS NIH HHS T32 GM008042
6 · The paper itself

Abstract

Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regions was conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.

Indexed as

NF-kappa BToll-Like Receptor 4Gene Expression RegulationNucleosomesSignal TransductionTranscription Factor RelANF-kappa BNucleosomesToll-Like Receptor 4Transcription Factor RelAchromatinIRF3macrophagesNF-κBnucleosome remodelingtranscription

Identifiers

PMID38430908
PMCPMC10984581
OpenAlexW4392359599

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.