Unraveling the Complexities of RNA-Protein Interactions with ChIRP-MS

ChIRP-MS (Chromatin Isolation by RNA Purification followed by Mass Spectrometry) is a powerful tool used for the identification of proteins that bind to specific RNA molecules. This technique allows for the isolation of chromatin-associated RNA molecules and the identification of the proteins that interact with them. ChIRP-MS is a recent development in the field of RNA-directed proteomic discovery that has opened new avenues for the study of RNA-protein interactions.

The ChIRP-MS Protocol

The ChIRP-MS protocol consists of two main steps: chromatin isolation by RNA purification (ChIRP) and mass spectrometry (MS). The ChIRP step involves the isolation of RNA-protein complexes from chromatin using biotinylated oligonucleotides complementary to the RNA of interest. The biotinylated oligonucleotides are immobilized on streptavidin-coated magnetic beads, which are then used to pull down the RNA-protein complexes from the chromatin.

After the ChIRP step, the RNA-protein complexes are eluted from the beads and subjected to MS analysis. In the MS step, the proteins in the RNA-protein complexes are identified and quantified by mass spectrometry. The ChIRP-MS protocol can be used to identify proteins that interact with specific RNA molecules in vitro and in vivo.

ChIRP-MS: RNA-Directed Proteomic DiscoveryChIRP-MS: RNA-Directed Proteomic Discovery (Chu et al., 2018)

Advantages of ChIRP-MS

ChIRP-MS, boasts a plethora of advantages for researchers in the field of RNA biology. One of its most notable benefits lies in its capacity to pinpoint proteins that interact with particular RNA molecules, enabling researchers to uncover and study RNA-binding proteins (RBPs) and their associated RNA molecules. RBPs are crucial players in the regulation of post-transcriptional gene expression, rendering the identification of these proteins a fundamental piece of the RNA function puzzle.

Not only does ChIRP-MS aid in the identification of RBPs, but it also does so in vivo. The technique can be implemented to identify RBPs that interact with specific RNA molecules in various cells and tissues, allowing for the examination of RNA-protein interactions in a physiological context. This is particularly valuable in the quest to grasp RNA function in vivo, as it provides a more accurate representation of RNA-protein interactions under natural circumstances.

ChIRP-MS is a high-throughput technique that can detect multiple RBPs that interact with a specific RNA molecule. As a result, researchers can uncover all the RBPs that bind to a particular RNA molecule, contributing to a more comprehensive understanding of the intricate network of RNA-protein interactions.

Applications of ChIRP-MS

Chromatin Isolation by RNA Purification Mass Spectrometry (ChIRP-MS) is an innovative technique that has vast applications in the realm of RNA biology. One of the foremost applications of ChIRP-MS is the identification of RNA binding proteins (RBPs) that interact with long-stranded non-coding RNAs (lncRNAs). These ribonucleic acid molecules, surpassing a threshold length of 200 nucleotides and being non-coding in nature, are cardinal regulators of gene expression and have been linked with the onset and progression of diverse pathological states, including cancer.

Furthermore, ChIRP-MS has emerged as an invaluable tool for scrutinizing the RNA-protein interactions governing messenger RNA (mRNA) molecules. Being a crucial intermediary between DNA and proteins, mRNA plays a pivotal role in dictating the gene expression program. Deciphering the intricacies of mRNA regulation is essential to gain a comprehensive understanding of gene expression. Herein, the ChIRP-MS analysis allows for identifying specific RBPs that interact with distinct mRNA molecules, thus providing a profound insight into the molecular mechanisms steering mRNA regulation.

Expanding the horizon of its utilities, ChIRP-MS also stands out as a powerful technique for unraveling RNA-protein interactions that drive various ailments. For instance, scientists have harnessed the potential of ChIRP-MS to explore the repertoire of RBPs that interact with RNA molecules, which are implicated in the development of neurodegenerative maladies such as Alzheimer's and Huntington's chorea. Consequently, this investigative approach has empowered researchers to delve deeper into the underlying molecular pathways governing these debilitating diseases and identify prospective therapeutic targets.

ChIRP-MS identifies host and viral proteins associated with the SARS-CoV-2 RNA genome in infected cellsChIRP-MS identifies host and viral proteins associated with the SARS-CoV-2 RNA genome in infected cells (Flynn et al., 2021)

Challenges and Limitations of ChIRP-MS

Despite its numerous advantages, ChIRP-MS has several challenges and limitations. One challenge is the specificity of the biotinylated oligonucleotides used to isolate the RNA of interest. If the biotinylated oligonucleotides are not specific for the RNA of interest, non-specific RNA molecules may also be pulled down, leading to false-positive results. To overcome this challenge, it is important to validate the specificity of the biotinylated oligonucleotides before conducting ChIRP-MS experiments.

Another limitation of ChIRP-MS is its dependence on the quality of the antibodies used for MS analysis. If the antibodies are not specific for the RBPs of interest, false-negative results may occur. Additionally, the sensitivity of MS analysis may be limited, leading to the potential loss of low-abundance RBPs.

At Creative Proteomics, we offer a range of molecular interaction analysis services, including ChIRP-MS for the identification of proteins that interact with specific RNA molecules. Our team of experts is dedicated to providing high-quality, reliable results that meet the unique needs of each of our clients. Contact us today to learn more about our services and how we can help advance your research.


  1. Chu, Ci, and Howard Y. Chang. "ChIRP-MS: RNA-directed proteomic discovery." X-Chromosome Inactivation: Methods and Protocols (2018): 37-45.
  2. Flynn, Ryan A., et al. "Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions." Cell 184.9 (2021): 2394-2411.
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