Evidence map›Paper›PMID 38496446›Full record

ArticlebioRxiv : the preprint server for biology2024

Regulation of immune signal integration and memory by inflammation-induced chromosome conformation.

Bence Daniel, Andy Y Chen, Katalin Sandor, Wenxi Zhang, Zhuang Miao, Caleb A Lareau, Kathryn E Yost, Howard Y Chang, Ansuman T Satpathy

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors at 3 institutions in 1 country.

Bence DanielDepartment of Pathology, Stanford University, Stanford, CA, USA.
Andy Y ChenDepartment of Pathology, Stanford University, Stanford, CA, USA.
Katalin SandorDepartment of Pathology, Stanford University, Stanford, CA, USA.
Wenxi ZhangDepartment of Pathology, Stanford University, Stanford, CA, USA.
Zhuang MiaoDepartment of Pathology, Stanford University, Stanford, CA, USA.
Caleb A LareauDepartment of Pathology, Stanford University, Stanford, CA, USA.
Kathryn E YostCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
Ansuman T SatpathyDepartment of Pathology, Stanford University, Stanford, CA, USA.
Gladstone Institutes · USHoward Hughes Medical Institute · USWhitehead Institute for Biomedical Research · US

Funding

4DN Interrogation of T Cell Exhaustion in CancerU01CA260852 · NCI · STANFORD UNIVERSITY · PI SATPATHY, ANSUMAN · 2020 to 2024
$2.6M
High Throughput DNA Sequencer UpgradeS10OD018220 · OD · STANFORD UNIVERSITY · PI COLLER, JOHN · 2014 to 2014
$596k
Computer ClusterS10OD021763 · OD · STANFORD UNIVERSITY · PI JI, HANLEE P · 2016 to 2016
$481k
NCI NIH HHS U01 CA260852NIH HHS S10 OD018220NIH HHS S10 OD021763
6 · The paper itself

Abstract

3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.

Identifiers

PMID38496446
PMCPMC10942375
OpenAlexW4392367718

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
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.