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Updated: Dec 25, 2025
Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells
Published on: June 1, 2018
mRNA interactome capture in mammalian cells
Nicolai Kastelic1, Markus Landthaler2
1RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine Berlin, Berlin Institute for Molecular Systems Biology, 13125 Berlin, Germany.
Abstract:
Throughout their entire life cycle, mRNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions. Their interplay is one key to control gene regulatory mechanisms from mRNA synthesis to decay. To assay the global scope of RNA-protein interactions, we and others have published a method combining crosslinking with highly stringent oligo(dT) affinity purification to enrich proteins associated with polyadenylated RNA (poly(A)+ RNA). Identification of the poly(A)+ RNA-bound proteome (also: mRNA interactome capture) has by now been applied to a diversity of cell lines and model organisms, uncovering comprehensive repertoires of RBPs and hundreds of novel RBP candidates. In addition to determining the RBP catalog in a given biological system, mRNA interactome capture allows the examination of changes in protein-mRNA interactions in response to internal and external stimuli, altered cellular programs and disease.
Insights
This study explores RNA-protein interactions using mRNA interactome capture. This method identifies proteins bound to messenger RNA (mRNA), revealing dynamic changes in gene regulation.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Messenger RNAs (mRNAs) associate with RNA-binding proteins (RBPs) throughout their lifecycle, forming dynamic ribonucleoprotein (RNP) complexes.
- The interplay between mRNAs and RBPs is crucial for regulating gene expression, from synthesis to decay.
Purpose of the Study:
- To globally assay RNA-protein interactions and identify the mRNA-bound proteome.
- To understand the dynamic composition of RNP complexes and their role in gene regulation.
Main Methods:
- Utilizing a method combining crosslinking with highly stringent oligo(dT) affinity purification.
- Applying mRNA interactome capture to diverse cell lines and model organisms.
Main Results:
- Uncovered comprehensive repertoires of known RBPs.
- Identified hundreds of novel RBP candidates.
- Demonstrated the ability to examine changes in protein-mRNA interactions under various conditions.
Conclusions:
- mRNA interactome capture is a powerful tool for cataloging RBPs.
- This technique facilitates the study of dynamic changes in RNA-protein interactions in response to biological stimuli and disease.
