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Related Concept Videos

FISH - Fluorescent In-situ Hybridization02:07

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,...
In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...

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upsFISH: An Occupancy-Reporting Fluorescence In Situ Hybridization Method for Single-Cell Detection of Chromatin

Yifen Shen1, Liang Chen2, Xiaosong Li2

  • 1Central Laboratory, Suzhou Ninth People's Hospital, Suzhou, Jiangsu 215200, China.

Analytical Chemistry
|June 20, 2026
PubMed
Summary

We developed ultraproximal specificity FISH (upsFISH), a novel method to detect gene regulatory interactions at single-cell resolution. upsFISH measures probe occupancy, offering a more accurate view of chromatin interactions than previous techniques.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Chromatin interactions are crucial for gene regulation.
  • Existing methods lack single-cell resolution and direct measurement of regulatory engagement.
  • Current techniques rely on spatial proximity or population averages, limiting insights into dynamic interactions.

Purpose of the Study:

  • To introduce ultraproximal specificity FISH (upsFISH), a new method for detecting chromatin interactions.
  • To enable single-cell resolution of regulatory engagement.
  • To overcome limitations of existing spatial and population-averaged approaches.

Main Methods:

  • Developed upsFISH, a fluorescence in situ hybridization technique.
  • Utilized a dual-arm primary probe targeting two genomic elements.
  • Employed secondary probes binding unoccupied probe arms for combinatorial signal generation.
  • Established an occupancy-reporting mechanism instead of relying on spatial proximity.

Main Results:

  • upsFISH accurately detects enhancer-promoter interactions with high sequence specificity.
  • The method is sensitive to transcription factor binding motifs.
  • upsFISH captures biologically relevant changes in chromatin interactions upon perturbations.
  • It resolves allele-specific and cell-to-cell heterogeneity in interactions.
  • upsFISH outperforms conventional DNA FISH and micro-4C for short-range interactions.

Conclusions:

  • upsFISH provides a novel occupancy-based framework for studying chromatin interactions.
  • This method offers high resolution and specificity for detecting regulatory elements.
  • upsFISH advances the understanding of gene regulation at the single-cell level.