Quantitative Biology

, Volume 6, Issue 3, pp 239–252 | Cite as

Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale

  • Jing Gong
  • Yanyan Ju
  • Di Shao
  • Qiangfeng Cliff ZhangEmail author



RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions (RRIs) are important in many basic cellular activities including transcription, RNA processing, localization, and translation. However, we just start to unveil the complexity of the knowledge and underlying mechanisms of RRIs.


In this review, we will summarize approaches for RRI identifications, including both conventional, focused biophysical and biochemical methods and recently developed large scale sequencing-based techniques. We will also discuss discoveries per RRI type revealed by using these technologies, as well as challenges towards a systematic and functional understanding of RRIs.


The development of sequencing-based techniques has revolutionized the study of RRIs. Applying these techniques in multiple organisms has identified thousands of RRIs, many of which could potentially regulate multiple aspects of gene expression. However, despite the great breakthrough, the RNA-RNA interactome of any species remains far from complete due to intrinsic complex nature of RRI and limitations in current techniques. More efficient experimental methods and computational framework are needed to obtain the full image of RRI networks, and their possible regulatory roles in biology and medicine.


RNA-RNA interactions PARIS SPLASH LIGR-seq next generation sequencing 



This work was supported by the National Natural Science Foundation of China (Nos. 31671355, 91740204 and 31761163007) and the National Thousand Young Talents Program of China to Qiangfeng Cliff Zhang. We thank Jinsong Zhang, Meiling Piao, Lei Tang and Yifan Wei for discussion.


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Copyright information

© Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Jing Gong
    • 1
  • Yanyan Ju
    • 1
  • Di Shao
    • 1
  • Qiangfeng Cliff Zhang
    • 1
    Email author
  1. 1.MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life SciencesTsinghua UniversityBeijingChina

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