Abstract
Background
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.
Results
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.
Conclusions
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.
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Acknowledgements
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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Author summary: RNA molecules play crucial roles in various biological processes by interacting with molecules including other RNAs. The recent breakthrough in resolving the transcriptome-wide RNA-RNA interaction (RRI) networks has identified a huge amount of data of RRIs and greatly advanced our understanding to the regulation of various RNAs.
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Gong, J., Ju, Y., Shao, D. et al. Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale. Quant Biol 6, 239–252 (2018). https://doi.org/10.1007/s40484-018-0146-5
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DOI: https://doi.org/10.1007/s40484-018-0146-5