Evidence map›Paper›PMID 35830792›Full record

ArticleCell reports2022

Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.

Jinsu Kim, Katherine M Sheu, Quen J Cheng, Alexander Hoffmann, German Enciso

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

Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.7field-weighted citation impact, top 33% 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

7 citing papers in PubMed, 8 citations in OpenAlex.

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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

5 authors at 4 institutions in 2 countries.

Jinsu KimDepartment of Mathematics, Pohang University of Science and Technology, Pohang, South Korea.
Katherine M SheuDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA.
Quen J ChengDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, CA, USA.
Alexander HoffmannDepartment of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: ahoffmann@ucla.edu.
German EncisoDepartment of Mathematics, University of California, Irvine, Irvine, CA, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. Electronic address: enciso@uci.edu.
University of California, Los Angeles · USPohang University of Science and Technology · KRQB3 · USUniversity of California, Irvine · US

Funding

Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Damoiseaux · 1985 to 2026
$134.5M
UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
Systems in Integrative BiologyT32GM008185 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHOU, TOM · 1987 to 2022
$4.6M
The NFkB System in Dendritic CellsR01AI127867 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HOFFMANN, ALEXANDER · 2018 to 2022
$2.2M
NFkB Signaling in MacrophagesR01AI127864 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HOFFMANN, ALEXANDER · 2017 to 2021
$1.9M
NCI NIH HHS P30 CA016042NIAID NIH HHS R01 AI127864NIAID NIH HHS R01 AI127867NIGMS NIH HHS T32 GM008042NIGMS NIH HHS T32 GM008185
6 · The paper itself

Abstract

The genomic positions of nucleosomes are a defining feature of the cell's epigenomic state, but signal-dependent transcription factors (SDTFs), upon activation, bind to specific genomic locations and modify nucleosome positioning. Here we leverage SDTFs as perturbation probes to learn about nucleosome dynamics in living cells. We develop Markov models of nucleosome dynamics and fit them to time course sequencing data of DNA accessibility. We find that (1) the dynamics of DNA unwrapping are significantly slower in cells than reported from cell-free experiments, (2) only models with cooperativity in wrapping and unwrapping fit the available data, (3) SDTF activity produces the highest eviction probability when its binding site is adjacent to but not on the nucleosome dyad, and (4) oscillatory SDTF activity results in high location variability. Our work uncovers the regulatory rules governing SDTF-induced nucleosome dynamics in live cells, which can predict chromatin accessibility alterations during inflammation at single-nucleosome resolution.

Indexed as

EpigenomeNucleosomesChromatin Assembly and DisassemblyDNATranscription FactorsDNANucleosomesTranscription FactorsATAC-seqcooperativityCP: Molecular biologyhistone evictionNF-κBnucleosome dynamicsrandom walksignal-dependent transcription factorstochastic modeltime-dependent Markov model

Identifiers

PMID35830792
PMCPMC10074953
OpenAlexW4285098954

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.