Evidence map›Paper›PMID 42757094›Full record

ArticleBiochemistry and biophysics reports2026

AI-assisted Cryo-ET workflow for 3D visualization of chromatin during cellular differentiation.

John Watt, Cullen Roth, Isaac Huber, Alexander S Hall, Manish Kumar Singh, Sofiya Micheva-Viteva, Karissa Y Sanbonmatsu, Shawn R Starkenburg, Christina R Steadman

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In one paragraph

Article in Biochemistry and biophysics reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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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

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

9 authors.

John WattMaterials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Cullen RothBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Isaac HuberMaterials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Alexander S HallThermo Fisher Scientific, Houston, TX, 77080, USA.
Manish Kumar SinghMaterials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Sofiya Micheva-VitevaBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Karissa Y SanbonmatsuTheoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Shawn R StarkenburgBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
Christina R SteadmanBioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Understanding how chromatin architecture changes during cellular differentiation requires structural methods that can resolve native genomic organization at high resolution. Here, we present an AI-assisted cryo-electron tomography (cryo-ET) and segmentation workflow to quantify chromatin compaction across various stages of motor neuron differentiation from induced pluripotent stem cells (iPSC). By directly imaging extracted and vitrified chromatin, we preserve native structure and avoid artifacts from heavy metal staining and resin embedding. Using three-dimensional (3D) density analysis, we measure chromatin density and capture the progressive increase in chromatin compaction with lineage commitment. This is then correlated with population-averaged Hi-C experiments, observing consistency between the microscale higher order structure of chromatin and global contact patterns. Our approach enables direct visualization of chromatin organization under near-physiological conditions, bridging the gap between structural imaging and genome-wide contact mapping. This platform therefore establishes an AI-assisted experimental framework for linking chromatin architecture to regulatory mechanisms during differentiation.

Indexed as

Cellular differentiationChromatinCryo-EMHi-CTomography

Identifiers

PMID42757094
PMCPMC13584007

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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.