Evidence map›Paper›PMID 37873344›Full record

ArticlebioRxiv : the preprint server for biology2023

Single-cell chromatin state transitions during epigenetic memory formation.

Taihei Fujimori, Carolina Rios-Martinez, Abby R Thurm, Michaela M Hinks, Benjamin R Doughty, Joydeb Sinha, Derek Le, Antonina Hafner, William J Greenleaf, Alistair N Boettiger and 1 more

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

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed, 7 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 3 institutions in 2 countries.

Taihei FujimoriDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Carolina Rios-MartinezDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Abby R ThurmBiophysics Program, Stanford University, Stanford, CA, USA.
Michaela M HinksDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Benjamin R DoughtyDepartment of Genetics, Stanford University, Stanford, CA, USA.
Joydeb SinhaDepartment of Chemical & Systems Biology, Stanford University, Stanford, CA, USA.
Derek LeDepartment of Dermatology, Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
Antonina HafnerDepartment of Developmental Biology, Stanford University, Stanford, CA, USA.
William J GreenleafDepartment of Genetics, Stanford University, Stanford, CA, USA.
Alistair N BoettigerDepartment of Developmental Biology, Stanford University, Stanford, CA, USA.
Lacramioara BintuDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Stanford University · USChan Zuckerberg Initiative (United States) · USGene Therapy Laboratory · FR

Funding

Live-cell multiplex super-resolution imaging of chromatin state transitionsU01DK127419 · NIDDK · STANFORD UNIVERSITY · PI BINTU, LACRAMIOARA, BOETTIGER, ALISTAIR N. · 2020 to 2024
$5.3M
NIDDK NIH HHS U01 DK127419
6 · The paper itself

Abstract

Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.

Identifiers

PMID37873344
PMCPMC10592931
OpenAlexW4387358485

What Socratic holds

Textmetadata
LicenceCC BY-NC
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 Socratic graph.