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Updated: Jun 19, 2026

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay

Published on: January 16, 2017

In situ proximity ligation assay for analysing spatial interactions between ciliary proteins.

Thorsten Pfirrmann¹, Ulrich Rüther², Christoph Gerhardt^3,4

¹Institute of Molecular Medicine, Department of Medicine, Health and Medical University Potsdam, 14471, Potsdam, Germany.

BMC Molecular and Cell Biology

|October 16, 2025

Summary

The in situ proximity ligation assay (in situ PLA) detects protein proximity in cilia, aiding ciliopathy research. This method maps protein interactions within subciliary compartments, crucial for understanding ciliary function and disease.

Keywords:

Cilia Ciliopathy Fluorescence microscopy In situ proximity ligation assay Protein interaction Rolling circle amplification Rpgrip1l Subcellular localization Transition zone

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Area of Science:

Cell Biology
Molecular Biology
Genetics

Background:

Cilia are vital eukaryotic cell structures with critical roles in human health.
Defects in cilia, particularly the transition zone, cause ciliopathies.
Understanding transition zone protein interactions is key to deciphering ciliary function and disease.

Purpose of the Study:

To investigate protein proximities within subciliary compartments.
To explore the utility of in situ proximity ligation assay (in situ PLA) for studying ciliary protein interactions.

Main Methods:

Utilized in situ proximity ligation assay (in situ PLA) to detect protein proximity (<40 nm).
Employed primary antibodies for target protein recognition.
Secondary antibodies conjugated with oligonucleotides (PLA probes) facilitated detection via rolling circle amplification and fluorescence microscopy.

Main Results:

Demonstrated in situ PLA's capability to visualize protein proximities in subciliary compartments.
Enabled precise spatial mapping of protein interactions within the cellular environment.
Provided evidence for potential protein interactions based on proximity.

Conclusions:

In situ PLA is a powerful technique for high-resolution detection of protein proximities in cilia.
This method aids in identifying novel protein interactions within subciliary compartments.
Contributes to understanding ciliary architecture and its role in ciliopathies.