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Related Concept Videos

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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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3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
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Oligopaint FISH to Study Chromosomal Architecture and Structural Variations.

Hadrien Reboul1, Davide Normanno1, Quentin Szabo2

  • 1Institut de Génétique Humaine, Univ Montpellier, CNRS, Montpellier, France.

Methods in Molecular Biology (Clifton, N.J.)
|August 30, 2025
PubMed
Summary
This summary is machine-generated.

This study details a comprehensive Oligopaint FISH protocol for analyzing chromosome organization and structural variations. The method, applicable to various cell lines, enhances the study of DNA structures at multiple scales.

Keywords:
3D genome organizationChromosomal deletionsDNA FISHOligopaintTAD

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Area of Science:

  • Genetics and Molecular Biology
  • Cell Biology
  • Genomics

Background:

  • Three-dimensional DNA fluorescent in situ hybridization (3D-FISH) is crucial for understanding chromosome organization at various scales.
  • Oligo-based technology has significantly advanced 3D-FISH, enabling detailed analysis of structures like topologically associating domains (TADs) and chromatin loops.
  • 3D-FISH is vital for identifying chromosomal structural variations, including deletions, duplications, and translocations, which are implicated in diseases like cancer and chromothripsis.

Purpose of the Study:

  • To present a comprehensive Oligopaint FISH protocol.
  • To provide a detailed guide covering probe design, production, FISH procedure, microscopy, and data analysis.
  • To offer a versatile method applicable to diverse cell lines for studying chromosome organization and structural variations.

Main Methods:

  • Oligopaint probe design and synthesis.
  • Fluorescent in situ hybridization (FISH) on various cell lines.
  • High-resolution microscopy and image analysis for 3D DNA structures.

Main Results:

  • A detailed and optimized Oligopaint FISH protocol is presented.
  • The protocol demonstrates versatility across different cell types.
  • Successful application in visualizing large-scale chromosome territories, TADs, chromatin loops, and structural variations.

Conclusions:

  • The presented Oligopaint FISH protocol is a robust and versatile tool for high-resolution 3D genome structure analysis.
  • This method facilitates the study of chromosomal organization and structural variations in diverse biological contexts.
  • The protocol empowers researchers to investigate complex genomic rearrangements and their implications in various cell lines.