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Recent advances in RNA structurome

Abstract

RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers—including RNA processing, transport, localization, and mRNA translation—across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.

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Acknowledgements

This work was supported by the National Key Research and Development Program of China (2021YFE0114900), the National Natural Science Foundation of China (91940303, 91940306, 32025008, 32170262, 31922039, U1832215, 32170229), the Natural Science Foundation of Zhejiang Province (LD21C050002), the Starry Night Science Fund at Shanghai Institute for Advanced Study of Zhejiang University (SN-ZJU-SIAS-009), the Beijing Advanced Innovation Center for Structural Biology, Shenzhen Basic Research Project (JCYJ20180507181642811), Research Grants Council of the Hong Kong SAR, China Projects (CityU 11100421, CityU 11101519, CityU 11100218, N_CityU110/17), Croucher Foundation Project (9509003), State Key Laboratory of Marine Pollution Director Discretionary Fund, City University of Hong Kong Projects (7005503, 9667222, 9680261), and the United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC: BBS/E/J/000PR9788).

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Correspondence to Yiliang Ding, Xianyang Fang, Yongfeng Jin, Chun Kit Kwok, Aiming Ren, Yue Wan, Zhiye Wang, Yuanchao Xue, Huakun Zhang, Qiangfeng Cliff Zhang or Yu Zhou.

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Xu, B., Zhu, Y., Cao, C. et al. Recent advances in RNA structurome. Sci. China Life Sci. 65, 1285–1324 (2022). https://doi.org/10.1007/s11427-021-2116-2

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Keywords

  • RNA structurome
  • high-throughput techniques
  • genome-wide
  • 3D structure
  • RNA secondary structure
  • SARS-CoV-2
  • decoding
  • function