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Related Experiment Video

Updated: Mar 13, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Protein Interaction Profile Sequencing (PIP-seq).

Shawn W Foley^1,2, Brian D Gregory^1,2

¹Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania.

Current Protocols in Molecular Biology

|October 11, 2016

Summary

This summary is machine-generated.

Protein interaction profile sequencing (PIP-seq) reveals RNA secondary structure and protein binding sites across the transcriptome. This method globally maps RNA-protein interactions and structural dynamics, enhancing our understanding of post-transcriptional regulation.

Keywords:

RNA secondary structure RNA-protein interactions protein interaction profile sequencing (PIP-seq)structure-specific ribonucleases

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Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Eukaryotic RNA transcripts undergo complex post-transcriptional modifications.
RNA-binding proteins regulate these processes by recognizing RNA sequence and structure.
Understanding these interactions is crucial for gene expression control.

Purpose of the Study:

To introduce a novel technique, protein interaction profile sequencing (PIP-seq).
To globally assess RNA secondary structure and RNA-binding protein interactions.
To provide a comprehensive view of RNA regulation.

Main Methods:

PIP-seq employs ribonuclease-based footprinting and high-throughput sequencing.
It uses single- and double-stranded RNA-specific nucleases to infer RNA secondary structure.
Comparison of nuclease digestion with and without proteins identifies protein-bound regions.

Main Results:

PIP-seq provides a transcriptome-wide assessment of RNA secondary structure.
The technique globally maps RNA-binding protein interaction sites.
Four distinct libraries offer a comprehensive view of RNA regulation.

Conclusions:

PIP-seq is a powerful, single-technique solution for studying RNA structure and protein interactions.
This method enhances the understanding of post-transcriptional RNA regulation.
PIP-seq offers a global perspective on RNA dynamics.