RNA-protein interactions can have a profound effect on controlling the spatial and temporal localization of mRNA within a cell and non-coding RNA function. With years of industry experience in mRNA research, Creative Biolabs has developed a variety of methods to comprehensively define RNA-protein interactions. We offer a comprehensive range of RNA-protein interactions analysis services characterized by quality, predictability, delivery, and customization.
RNA and proteins are interconnected biomolecules that can influence the fate of each other and function through physical interactions. Therefore, the importance of RNA-protein interactions in controlling many aspects of gene regulation is increasingly appreciated. Technologies to examine RNA-protein interaction have been developed from DNA-protein interaction technologies.
Fig.1 Tools for the characterization of RNA-protein interactions.1
RIP (RNA immunoprecipitation) can be coupled to microarray (RIP-chip) or sequencing (RIP-seq) to identify the association of RNA-binding proteins (RBPs) with specific RNA. RIP-seq is a revolutionary technology to map the sites at which proteins are bound to the RNA and provides a single-base resolution of protein-bound RNA at the genome-wide level.
Cross-linking immunoprecipitation (CLIP) involves UV cross-linking followed by purification of the protein of interest and identification of the bound RNAs. CLIP combines with high-throughput sequencing (HITS) forming the CLIP-seq which is an increasingly popular technique to study protein-RNA interactions.
Chromatin isolation by RNA purification (ChIRP) usually uses formaldehyde to cross-link RNA to proteins. It can be combined with deep sequencing and allow unbiased high-throughput discovery of RNA-bound DNA and proteins. The key turnaround was the use of short oligonucleotide probes tiling the length of an RNA of interest.
RNA antisense purification (RAP), often coupled with mass spectrometry (MS), is a method (RAP-MS) that enables the identification of direct and specific protein interaction partners of a specific RNA molecule. Notably, RAP-MS can provide a list of high-confidence protein interactors, because it uses direct RNA-protein cross-linking method coupled with highly denaturing purification conditions.
RNA interactome capture (RIC), based on the irradiation of living cells with UV light to generate covalent bonds between RNA and proteins, has emerged as a powerful tool to identify and study RBPs. It is a useful method for the proteome-wide identification of RBPs.
A: It involves studying how RNA molecules interact with proteins to understand their biological functions and regulatory mechanisms.
A: Methods include RIP-seq, CLIP-seq, ChIRP, RAP-MS, and mRNA Interactome Capture.
A: These interactions are crucial for gene regulation, RNA processing, and the overall understanding of cellular functions.
A: Yes, Creative Biolabs offers personalized analysis and bioinformatics support tailored to specific research needs.
A: RNA Immunoprecipitation followed by sequencing (RIP-seq) identifies RNA molecules bound to specific proteins using antibodies and sequencing.
A: High-throughput, high-accuracy techniques and expert bioinformatics support ensure detailed and reliable results.
This article discusses the application of crosslinking and immunoprecipitation (CLIP) methods to identify RNA-binding protein (RBP) interaction sites on RNA. It highlights the PAR-CLIP technique, which uses photoactivatable ribonucleoside analogs incorporated into nascent transcripts. These analogs create sequence changes upon crosslinking, allowing for the precise mapping of RBP binding sites. The study underscores the importance of understanding RBP interactions for insights into post-transcriptional gene regulation (PTGR), which influences mRNA splicing, stability, and translation, and has implications for treating genetic diseases.
Fig.2 RNA-binding proteins (RBPs) and their RNA-binding domains (RBDs).2
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