Evidence map›Paper›PMID 40442089›Full record

ArticleNature communications2025

Cell-context response to germ layer differentiation signals is predetermined by the epigenome in regionalized epiblast populations.

Niels Alvaro Menezes, Kathryn Johanna Peterson, Xiaogang Guo, Veronica Castiglioni, Adrija Kalvisa, Katarzyna Filimonow, Karen Schachter, Christina Maria Schuh, Athanasios Pasias, Luca Mariani and 3 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Article
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

13 authors.

Niels Alvaro MenezesNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.ORCID http://orcid.org/0009-0005-5352-3491
Kathryn Johanna PetersonNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.ORCID http://orcid.org/0000-0002-1059-8208
Xiaogang GuoNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.
Veronica CastiglioniNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.
Adrija KalvisaNovo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark.ORCID http://orcid.org/0000-0002-7811-6316
Katarzyna FilimonowNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.
Karen SchachterNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.
Christina Maria SchuhNovo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark.
Athanasios PasiasNovo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark.
Luca MarianiNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.ORCID http://orcid.org/0000-0002-5693-8415
Joshua Mark BrickmanNovo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark.ORCID http://orcid.org/0000-0003-1580-7491
Jakub SedzinskiNovo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark.ORCID http://orcid.org/0000-0002-1788-0329
Elisabetta FerrettiNovo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark. elisabetta.ferretti@sund.ku.dk.ORCID http://orcid.org/0000-0002-3339-9818

Funding

Danmarks Grundforskningsfond (Danish National Research Foundation) 4183-00516AEC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020) H2020-MSCA-IF-2014_RILundbeckfonden (Lundbeck Foundation) R180-2014-2980Novo Nordisk Fonden (Novo Nordisk Foundation) NNF17CC0027852Novo Nordisk Fonden (Novo Nordisk Foundation) NNF21CC0073729
6 · The paper itself

Abstract

Stem cells hold promise in regenerative medicine as they have the potential to differentiate into a variety of specialized cell types. However, mechanisms underlying stem cell potency and lineage acquisition remain elusive. Epigenetic modifications and genome accessibility prime cellular feedback to signalling cues, influencing lineage differentiation outcomes. Deciphering how this epigenetic code influences the context-dependent response of pluripotent cells to differentiation cues will elucidate how mammalian tissue diversity is established. Using in vitro and in vivo models, we show that lineage-specific epigenetic signatures precede transcriptional activation of germ layer differentiation programs. We provide evidence that while distinct chromatin accessibility and methylome states prime extraembryonic mesodermal fate decisions, it is DNA methylation, and not chromatin accessibility that predetermines the fates of neuroectoderm, definitive endoderm and neuromesodermal lineages. This study establishes that epigenetic machinery fine-tunes epiblast potency, allowing context-specific spatiotemporal responses to promiscuously used signalling cues controlling organogenesis.

Indexed as

Cell DifferentiationEpigenesis, GeneticEpigenomeGerm LayersAnimalsCell LineageChromatinDNA MethylationEndodermGene Expression Regulation, DevelopmentalMiceSignal TransductionChromatin

Identifiers

PMID40442089
PMCPMC12122723

What OpenQuestion holds

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LicenceCC BY-NC-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.