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RNA-seq

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...

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Updated: Jan 3, 2026

mRNA Interactome Capture from Plant Protoplasts

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

Protein Interaction Profile Sequencing (PIP-seq) in Plants.

Stephen J Anderson¹, Matthew R Willmann¹, Brian D Gregory¹

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

Current Protocols in Plant Biology

|November 15, 2019

Summary

This summary is machine-generated.

This study introduces a method to map RNA secondary structure and protein binding sites across the entire transcriptome. This technique aids in understanding RNA

Keywords:

RNA secondary structure RNA-binding proteins RNA-protein interactions protein interaction profile sequencing (PIP-seq)

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Last Updated: Jan 3, 2026

mRNA Interactome Capture from Plant Protoplasts

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks

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Published on: May 17, 2020

AirID-Based Proximity Labeling for Protein-Protein Interaction in Plants

AirID-Based Proximity Labeling for Protein-Protein Interaction in Plants

Published on: September 16, 2022

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

RNA secondary structure and RNA-protein interactions are crucial for eukaryotic transcriptome regulation and function.
Identifying these structures and interactions globally is a key research objective.

Purpose of the Study:

To develop a global method for probing RNA secondary structure and RNA-protein interaction sites.
To enable comprehensive transcriptome-wide analysis in a single experiment for any plant species.

Main Methods:

Sequencing RNAs treated with single-strand- and double-strand-specific ribonucleases in the absence of proteins to infer RNA secondary structure.
Comparing these samples to RNAs treated with nucleases in the presence of proteins to identify protein-bound sequences.
Utilizing four distinct libraries for comprehensive analysis.

Main Results:

The developed method provides a comprehensive, transcriptome-wide view of RNA secondary structure.
It successfully identifies RNA-protein interaction sites across the transcriptome.
The approach is applicable to any plant species of interest.

Conclusions:

This method offers a powerful tool for studying RNA structure and interactions in plants.
It facilitates a deeper understanding of RNA's role in biological functionality and regulation.
Enables efficient, global mapping of RNA structural and interaction landscapes.