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

Yanyu Zhu¹, Ashwin Balaji², Mengting Han¹, Leonid Andronov³, Anish R Roy³, Zheng Wei⁴, Crystal Chen⁵, Leanne Miles¹, Sa Cai⁶, Zhengxi Gu¹, Ariana Tse⁶, Betty Chentzu Yu⁴, Takeshi Uenaka⁷, Xueqiu Lin⁴, Andrew J Spakowitz⁸, W E Moerner⁹, Lei S Qi¹⁰

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
² Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Biophysics PhD Program, Stanford University, Stanford, CA 94305, USA.
³ Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
⁴ Computational Biology Program, Public Health Sciences Division and Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
⁵ Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
⁶ Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
⁷ Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁸ Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
⁹ Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA. Electronic address: wmoerner@stanford.edu.
¹⁰ Department 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.

PMID: 40239646
PMCID: PMC12167157 (available on 2026-06-12)
DOI: 10.1016/j.cell.2025.03.032

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

Yanyu Zhu et al. Cell. 2025.

. 2025 Jun 12;188(12):3310-3328.e27.

doi: 10.1016/j.cell.2025.03.032. Epub 2025 Apr 15.

Authors

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
² Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Biophysics PhD Program, Stanford University, Stanford, CA 94305, USA.
³ Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
⁴ Computational Biology Program, Public Health Sciences Division and Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
⁵ Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
⁶ Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
⁷ Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁸ Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
⁹ Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA. Electronic address: wmoerner@stanford.edu.
¹⁰ Department 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.

PMID: 40239646
PMCID: PMC12167157 (available on 2026-06-12)
DOI: 10.1016/j.cell.2025.03.032

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.

Keywords: CRISPR imaging; DNA communication; Oligo-LiveFISH; dynamic tracking; enhancer-promoter interaction; high-resolution imaging; live DNA imaging; non-repetitive genome imaging; polymer modeling; primary cell.

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Conflict of interest statement

Declaration of interests Y.Z. and L.S.Q are inventors on a provisional patent filed via Stanford. W.E.M. is a member of the Scientific Advisory Board of Double-Helix Optics. L.S.Q. is a founder of Epicrispr Biotechnologies and a scientific advisor of the Laboratory of Genomic Research.

References

1. Zheng H; Xie W (2019). The role of 3D genome organization in development and cell differentiation. Nature Reviews Molecular Cell Biology 20, 535–550. - PubMed
1. Hnisz D; Weintraub AS; Day DS; Valton AL; Bak RO; Li CH; Goldmann J; Lajoie BR; Fan ZP; Sigova AA, et al. (2016). Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 351, 1454–8. - PMC - PubMed
1. Lupianez DG; Kraft K; Heinrich V; Krawitz P; Brancati F; Klopocki E; Horn D; Kayserili H; Opitz JM; Laxova R, et al. (2015). Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012–25. - PMC - PubMed
1. Beagan JA; Duong MT; Titus KR; Zhou L; Cao Z; Ma J; Lachanski CV; Gillis DR; Phillips-Cremins JE (2017). YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Genome Res. - PMC - PubMed
1. Waldman T (2020). Emerging themes in cohesin cancer biology. Nat Rev Cancer 20, 504–515. - PubMed

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

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

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