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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: Mar 2, 2026

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

Specific RNP capture with antisense LNA/DNA mixmers.

Birgit Rogell¹, Bernd Fischer^1,2, Mandy Rettel¹

¹European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.

RNA (New York, N.Y.)

|May 7, 2017

Summary

This summary is machine-generated.

Researchers developed specific ribonucleoprotein (RNP) capture to identify RNA-binding proteins (RBPs) associated with specific RNA molecules. This method uses UV irradiation and magnetic beads to isolate and identify RBPs bound to target RNAs.

Keywords:

RNA interactome RNA-binding proteins RNA–protein interactions ribosomal RNA specific RNP capture

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Last Updated: Mar 2, 2026

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

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Published on: July 9, 2021

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Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

RNA-binding proteins (RBPs) are crucial for regulating gene expression in response to cellular stimuli.
While cellular RBP repertoires are largely known, identifying RBPs bound to specific transcripts remains challenging.
Understanding specific RBP-RNA interactions is key to deciphering gene regulation.

Purpose of the Study:

To develop a versatile method for identifying proteins bound to specific RNA transcripts.
To validate the new method in both in vitro and cellular systems.
To uncover novel RBP-RNA interactions.

Main Methods:

Developed "specific ribonucleoprotein (RNP) capture" utilizing UV irradiation to stabilize protein-RNA interactions.
Employed antisense locked nucleic acid (LNA)/DNA oligonucleotides coupled to magnetic resin for target RNA capture.
Utilized quantitative mass spectrometry for identification of captured proteins.

Main Results:

Successfully identified RBPs bound to a reporter mRNA with Sex-lethal (Sxl) binding motifs, revealing similar binding preferences for the Sxl homolog, sister of Sex lethal (Ssx).
Determined the repertoire of RBPs binding to 18S and 28S ribosomal RNAs (rRNAs) in HeLa cells.
Discovered previously unknown rRNA-binding proteins.

Conclusions:

Specific RNP capture is an effective and versatile method for identifying RBPs associated with specific RNA molecules.
The method provides insights into RBP binding preferences and expands the known repertoire of rRNA-binding proteins.
This technique facilitates a deeper understanding of RNA biology and gene regulation.