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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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jun 22, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Unbiased RNA-protein interaction screen by quantitative proteomics.

Falk Butter1, Marion Scheibe, Mario Mörl

  • 1Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Proceedings of the National Academy of Sciences of the United States of America
|June 23, 2009
PubMed
Summary

This study introduces a new method for identifying RNA-binding proteins using mass spectrometry. The technique successfully mapped protein interactions with various RNA molecules, revealing new insights into RNA regulation.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Proteomics

Background:

  • Mass spectrometry (MS)-based quantitative interaction proteomics is established for protein-protein, DNA-protein, and small molecule-protein interactions.
  • Identifying RNA-protein interactions remains a critical area needing advanced technological solutions.

Purpose of the Study:

  • To develop a gel-free, sensitive, and scalable technology for identifying RNA-protein interactions.
  • To capture and analyze RNA-interacting proteins using a novel MS-based approach.

Main Methods:

  • Utilized aptamer-tagged RNA as bait to capture RNA-interacting proteins.
  • Employed stable isotope labeling by amino acids in cell culture (SILAC)-labeled mammalian cell extracts.
  • Analyzed captured proteins by high-resolution, quantitative MS, distinguishing specific binders via isotope ratios.

Main Results:

  • Successfully retrieved known and novel interaction partners for various RNA motifs, including HuR, H4 stem loop, zipcode sequence, tRNA, and DGCR-8/Pasha mRNA.
  • Unambiguously identified known interaction partners with a single affinity purification step.
  • Discovered that the 5' region of DGCR-8/Pasha mRNA interacts with translational machinery components, suggesting an internal ribosome entry site.

Conclusions:

  • The developed technology provides a sensitive and scalable method for studying RNA-protein interactions.
  • The findings highlight the role of the DGCR-8/Pasha mRNA 5' region in translational regulation.
  • This approach advances the field of quantitative interaction proteomics to include RNA-binding proteins.