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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
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,...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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Related Experiment Video

Updated: Jun 25, 2026

Robust 3D DNA FISH Using Directly Labeled Probes
12:16

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

FISH+ is a ready-to-use proximity labeling method for simultaneous RNA visualization and RNA-interacting protein

Mingxing Lu1, Fenglin Shen2, Yun Liu3

  • 1Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. mingxinglu@fudan.edu.cn.

Communications Biology
|June 23, 2026
PubMed
Summary

FISH+ is a novel RNA proximity labeling method for visualizing RNA and identifying interacting proteins in fixed cells without genetic manipulation. This technique enhances RNA visualization and captures spatial information on RNA-protein interactions.

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Related Experiment Videos

Last Updated: Jun 25, 2026

Robust 3D DNA FISH Using Directly Labeled Probes
12:16

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

  • Molecular Biology
  • Cell Biology
  • Biochemistry

Background:

  • Traditional proximity biotinylation methods for studying RNA-protein interactions are complex, requiring genetic engineering or difficult purification.
  • There is a need for efficient and accessible methods to visualize RNA and identify its interacting proteins in situ.

Purpose of the Study:

  • To develop and validate a ready-to-use RNA proximity labeling method for in situ visualization and protein interaction studies.
  • To demonstrate the capability of the new method for concurrent RNA visualization and proximal protein identification.

Main Methods:

  • Introduction of FISH+ (Fluorescence In Situ Hybridization plus proximity labeling), a method recruiting peroxidase to RNA targets for in situ biotinylation in fixed cells.
  • Application of FISH+ to visualize specific RNA molecules (45S, NEAT1, XIST) and identify proximal proteins using quantitative mass spectrometry.

Main Results:

  • FISH+ successfully visualized 45S and NEAT1 RNA, identifying proximal proteins and demonstrating concurrent RNA visualization and protein capture.
  • Targeting PNCTR RNA with FISH+ resulted in bright punctate signals, indicating enhanced RNA visualization potential.
  • FISH+ identified known XIST-interacting proteins (SPEN, CIZ1, RBM15) and validated RNA-protein interactions in human cells via mass spectrometry.

Conclusions:

  • FISH+ is an effective 'watch-and-catch' method integrating RNA fluorescence in situ hybridization (FISH) with proximity biotinylation.
  • This technique provides spatial information for characterizing RNA-centric interactions in fixed, genetically unperturbed samples.
  • FISH+ offers a simplified and powerful approach for studying RNA biology and interactions.