RNA-RNA Interaction Analysis


In addition to its mediating role in protein synthesis, RNA is a versatile molecule that directly participates in the regulation of most cellular processes, including epigenetic control, gene transcription, translation, RNA turnover, and also plays a key role in cell development and proliferation. In the past few decades, it has been shown that RNA works by interacting with different molecules (such as protein, nucleic acid). For example, hundreds of RNA-binding proteins (RBP) have been found in prokaryotes and eukaryotes, another important type of RNA interaction is between two RNA molecules, the RNA-RNA interaction (RRI). For example, during splicing, small nuclear RNAs (snRNAs) can recognize the intron region of precursor messenger RNAs (pre-mRNAs), which is a key step in determining RNA splicing products. A large number of such examples highlight the importance of RRI in regulating life activities.

There are many techniques used to identify and analyze RRI. However, due to the complexity and technical limitations of RRI, any type of method is not complete. Creative Proteomics has developed an RRI platform that includes multiple technologies, and fully combines experiments and calculations to explore their regulatory effects in biology and medicine.

Traditional biophysical and cellular methods for specific RNA-RNA interaction identificationFig 1. Traditional biophysical and cellular methods for specific RNA-RNA interaction identification (Gong, J. et al. 2018)


In order to study RRI, Creative Proteomics has developed a series of technologies with different strengths and different dimensions, including but not limited to the following aspects.

  • Traditional biophysical, biochemical and cellular methods, including EMSA, SPR, FRET, Co-sedimentation, yeast RNA-hybrid system, etc. Usually, these methods can only detect interactions at the molecular level, but cannot reveal the exact areas that mediate the interactions between molecules.
  • High-throughput and targeted methods, such as CLASH, hiCLIP, RAP, etc.
  • Large-scale identification methods at the transcriptome level, including SPLASH, LIGR-seq, MARIO, etc. Such methods can help us discover many unknown RRIs, and can greatly improve our understanding of RNA interactomes.

Customers can choose a certain technology according to the needs of the project, or contact us directly for consultation, and our expert team will provide you with a customized experimental program.


  • RNA function research
  • Gene regulation research
  • Discovery of unknown RNA-RNA interaction  
  • Mapping the RNA-RNA interaction in a transcriptome-wide scale
  • Medical application


  • Systematic technology platform
  • High accuracy and high-throughput
  • Able to provide information on interaction sites
  • Powerful data processing and calculation tools
  • Cost-effective

Creative Proteomics has a large number of sophisticated instruments and well-trained researchers, which can greatly help customers explore the regulatory functions of RRI and discover new RRIs. We are honored to be your competent research assistant.


  1. Guil, S.; Esteller, M. RNA-RNA interactions in gene regulation: the coding and noncoding players. Trends in Biochemical Sciences. 2015, 40(5): 248-256.
  2. Gong, J. et al. Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale. Quantitative Biology. 2018.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.