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FISH - Fluorescent In-situ Hybridization

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Robust 3D DNA FISH Using Directly Labeled Probes

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Published on: August 15, 2013

Measurement of Spatial Contact Map Using Sequential FISH.

Hiroaki Ohishi¹

¹Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

Methods in Molecular Biology (Clifton, N.J.)

|August 20, 2025

Summary

This study introduces a method to map genome spatial distances using DNA-seqFISH data. This technique enables precise analysis of gene transcription and protein localization within single cells.

Keywords:

Distance matrix Mouse embryonic stem cells Single allele Single cell seqFISH

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Area of Science:

Genomics
Cell Biology
Molecular Biology

Background:

Genome organization within the cell nucleus is crucial for gene expression and chromosome folding.
DNA sequential fluorescence in situ hybridization (DNA-seqFISH) allows for spatial mapping of genomic coordinates.

Purpose of the Study:

To present a methodology for generating DNA spatial distance maps using DNA-seqFISH bright spot coordinate data.
To enable precise calculation of distances between genomic regions within cells.

Main Methods:

Utilizing bright spot coordinate data obtained from DNA-seqFISH.
Applying computational analysis to derive spatial distance maps of the genome.

Main Results:

The methodology allows for the precise calculation of distances between specific genomic regions.
Spatial data facilitates analysis of gene transcription and protein localization at single-cell and single-allele resolutions.

Conclusions:

The developed method provides a powerful tool for studying higher-order genome structures.
This approach enhances our understanding of the relationship between genome organization and cellular functions.