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Related Concept Videos

In-situ Hybridization02:31

In-situ Hybridization

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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
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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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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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Related Experiment Video

Updated: Feb 16, 2026

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
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A Novel Ultrasensitive In Situ Hybridization Approach to Detect Short Sequences and Splice Variants with Cellular

Larissa Erben1,2, Ming-Xiao He3, Annelies Laeremans3

  • 1Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Porter Neuroscience Research Center, Bldg. 35, Room 2C-1000, Bethesda, MD, 20892, USA.

Molecular Neurobiology
|December 22, 2017
PubMed
Summary
This summary is machine-generated.

A new BaseScope method allows researchers to visualize RNA variants within single cells. This technique reveals differences in ErbB4 receptor expression between cell types, offering potential diagnostic applications for diseases linked to RNA changes.

Keywords:
Alternative splicingBaseScopeErbB4NeuregulinOligodendrocytesRNA expressionSchizophreniaTranscriptome

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Area of Science:

  • Molecular Biology
  • Neuroscience
  • Genetics

Background:

  • Distinguishing RNA variants at the single-cell level in tissues is challenging with current in situ hybridization (ISH) methods.
  • Current RNA detection methods often require sample processing that loses spatial and cell-type-specific information.
  • Altered RNA splicing, editing, and single nucleotide polymorphisms are linked to various diseases.

Purpose of the Study:

  • To develop a highly sensitive ISH method for visualizing and quantifying short, isoform-specific RNA sequences within single cells.
  • To investigate the differential expression of neuregulin (NRG) receptor ErbB4 splice variants in different cell types.
  • To assess the evolutionary conservation of ErbB4 isoform expression.

Main Methods:

  • Development of a novel single-pair oligonucleotide probe (BaseScope) ISH approach targeting RNA splice junctions.
  • Application of BaseScope to visualize and quantify four ErbB4 splice variants in mouse tissues.
  • Comparison of ErbB4 expression in wild-type and ErbB4 knockout mice.
  • Utilizing cell-type-specific GFP reporter mice to analyze ErbB4 isoform expression in neurons and oligodendrocytes.

Main Results:

  • The BaseScope method demonstrated high sensitivity and specificity for visualizing and quantifying differential ErbB4 isoform expression.
  • ErbB4 isoforms showed distinct expression patterns between neurons and oligodendrocytes.
  • Differential expression of ErbB4 isoforms was found to be conserved in human tissues.
  • The approach confirmed the ability to detect specific ErbB4 isoforms using knockout models.

Conclusions:

  • The single-pair probe ISH (BaseScope) approach enables sensitive, single-cell resolution detection of RNA variants, including splice isoforms.
  • Differential expression of ErbB4 isoforms in neurons and oligodendrocytes is evolutionarily conserved.
  • BaseScope holds promise as a diagnostic tool for diseases associated with alternative splicing and single nucleotide polymorphisms.