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FISH - Fluorescent In-situ Hybridization

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...

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Updated: Sep 4, 2025

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

High-throughput DNA Extraction and Genotyping of 3dpf Zebrafish Larvae by Fin Clipping

Published on: June 29, 2018

High-Throughput DNA FISH (hiFISH).

Elizabeth Finn¹, Tom Misteli², Gianluca Pegoraro³

¹Cell Biology of Genomes (CBGE), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD, USA. elizabeth.finn@nih.gov.

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

|July 22, 2022

Summary

This summary is machine-generated.

High-throughput DNA fluorescence in situ hybridization (hiFISH) enables precise measurement of genomic locus distances in millions of cells. This advanced technique reveals insights into genome architecture and cellular heterogeneity.

Keywords:

3D genome DNA FISH High-throughput imaging Nuclear architecture

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Last Updated: Sep 4, 2025

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Area of Science:

Genomics
Cell Biology
Biotechnology

Background:

Understanding 3D genome architecture is crucial for studying cellular function and disease.
Existing methods for analyzing genome organization are often limited in scale and throughput.
High-throughput DNA fluorescence in situ hybridization (hiFISH) offers a novel approach to overcome these limitations.

Purpose of the Study:

To provide detailed protocols for implementing hiFISH.
To enable the measurement of spatial distances between genomic loci and nuclear structures.
To facilitate the study of genome architecture and cellular heterogeneity at an unprecedented scale.

Main Methods:

Development and application of multicolor combinatorial DNA FISH staining.
Automated image acquisition and analysis of millions of cells.
Detailed protocols for probe design, cell culture, staining, and statistical analysis.

Main Results:

hiFISH allows visualization and localization of tens to hundreds of genomic loci.
Accurate measurement of physical distances between genomic loci, to nuclear boundaries, and to specific nuclear structures.
Generation of large datasets of 3D spatial distances for comprehensive analysis.

Conclusions:

hiFISH is a powerful, scalable technique for dissecting 3D genome organization.
The generated data provides insights into cellular heterogeneity in genome architecture.
This method facilitates the study of molecular mechanisms underlying genome organization in diverse cellular systems.