Evidence map›Paper›PMID 40239646›Full record

ArticleCell2025

High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH.

Yanyu Zhu, Ashwin Balaji, Mengting Han, Leonid Andronov, Anish R Roy, Zheng Wei, Crystal Chen, Leanne Miles, Sa Cai, Zhengxi Gu and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

  1. Review
  2. Article
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  7. Review
  8. Organization of Myosin H in the Apical Complex ofbioRxiv : the preprint server for biology · 2026
    Article
  9. Review
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. The Biological Function of Genome Organization.International journal of molecular sciences · 2025
    Review
  16. Article
  17. Review
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

17 authors.

Yanyu ZhuDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Ashwin BalajiDepartment of Chemistry, Stanford University, Stanford, CA 94305, USA; Biophysics PhD Program, Stanford University, Stanford, CA 94305, USA.
Mengting HanDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Leonid AndronovDepartment of Chemistry, Stanford University, Stanford, CA 94305, USA.
Anish R RoyDepartment of Chemistry, Stanford University, Stanford, CA 94305, USA.
Zheng WeiComputational Biology Program, Public Health Sciences Division and Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Crystal ChenDepartment of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
Leanne MilesDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Sa CaiDepartment of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
Zhengxi GuDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Ariana TseDepartment of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
Betty Chentzu YuComputational Biology Program, Public Health Sciences Division and Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Takeshi UenakaInstitute for Stem Cell Biology & Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Xueqiu LinComputational Biology Program, Public Health Sciences Division and Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Andrew J SpakowitzDepartment of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
W E MoernerDepartment of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA. Electronic address: wmoerner@stanford.edu.
Lei S QiDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94080, USA. Electronic address: slqi@stanford.edu.

Funding

Single-Molecule Imaging for Cell Biology and Super-Resolution MicroscopyR35GM118067 · NIGMS · STANFORD UNIVERSITY · PI MOERNER, WILLIAM E · 2016 to 2025
$6.2M
Engineering and Imaging 3D genome structure-function dynamics across time scalesU01DK127405 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BLOBEL, GERD A, PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2020 to 2024
$5.7M
Manipulating and Interrogating Spatial TranscriptomicsDP1NS137219 · NINDS · STANFORD UNIVERSITY · PI Lei Stanley Qi · 2023 to 2026
$4.3M
High resolution dissection of oncogene enhancer networks via CRISPR screening and live-cell imaging.R01CA266470 · NCI · STANFORD UNIVERSITY · PI Lei Stanley Qi · 2022 to 2026
$1.9M
Development of multi-color 3D super-localization LiveFISH and LiveFISH PAINT to investigate the chromatin dynamics at any genomic scaleR21HG013133 · NHGRI · STANFORD UNIVERSITY · PI QI, LEI STANLEY · 2023 to 2023
$420k
NCI NIH HHS R01 CA266470NHGRI NIH HHS R21 HG013133NIDDK NIH HHS U01 DK127405NIGMS NIH HHS R35 GM118067NINDS NIH HHS DP1 NS137219
6 · The paper itself

Abstract

Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease.

Indexed as

ChromatinDNAIn Situ Hybridization, FluorescenceAnimalsEnhancer Elements, GeneticHumansImaging, Three-DimensionalMicePromoter Regions, GeneticChromatinDNACRISPR imagingDNA communicationdynamic trackingenhancer-promoter interactionhigh-resolution imaginglive DNA imagingnon-repetitive genome imagingOligo-LiveFISHpolymer modelingprimary cell

Identifiers

PMID40239646
PMCPMC12167157

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.