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High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH
Yanyu Zhu1, Ashwin Balaji2, Mengting Han1
1Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Cell
|April 16, 2025
Summary
Oligo-LiveFISH enables real-time tracking of specific DNA regions in live cells with unprecedented resolution. This new method visualizes dynamic genome organization, crucial for understanding cellular functions and diseases.
Area of Science:
- Genomics
- Cell Biology
- Molecular Biology
Background:
- Three-dimensional (3D) genome dynamics are vital for cellular functions and disease progression.
- Current live-cell DNA visualization methods face limitations in resolution, targeting specific regions, and require complex genome engineering.
Purpose of the Study:
- To develop a high-resolution, reagent-based platform for dynamic tracking of non-repetitive genomic loci in live cells.
- To characterize the impact of guide RNA design and chromatin features on imaging efficiency using machine learning.
Main Methods:
- Oligo-LiveFISH platform utilizing fluorescent guide RNA (gRNA) oligo pools.
- Computational design, in vitro transcription, chemical labeling, and ribonucleoprotein delivery.
- Machine learning for analyzing gRNA design and chromatin feature impacts on imaging.
Main Results:
- Achieved 20-nm spatial and 50-ms temporal resolution in 3D live-cell imaging.
- Captured real-time dynamics of enhancer and promoter regions.
- Revealed two distinct modes of chromatin communication and identified that active transcription slows enhancer-promoter dynamics.
Conclusions:
- Oligo-LiveFISH provides a versatile platform for studying 3D genome dynamics in diverse cell types, including primary cells.
- The platform facilitates research into the links between genome organization, cellular processes, and disease.
