Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes

Sidika Tapsin, Miao Sun, Yang Shen, Huibin Zhang, Xin Ni Lim, Teodorus Theo Susanto, Siwy Ling Yang, Gui Sheng Zeng, Jasmine Lee, Alexander Lezhava, Ee Lui Ang, Lian Hui Zhang, Yue Wang, Huimin Zhao, Niranjan Nagarajan () and Yue Wan ()
Additional contact information
Sidika Tapsin: Genome Institute of Singapore
Miao Sun: Genome Institute of Singapore
Yang Shen: Genome Institute of Singapore
Huibin Zhang: Agency for Science, Technology, and Research (A*STAR)
Xin Ni Lim: Genome Institute of Singapore
Teodorus Theo Susanto: Genome Institute of Singapore
Siwy Ling Yang: Genome Institute of Singapore
Gui Sheng Zeng: Proteos
Jasmine Lee: Proteos
Alexander Lezhava: Genome Institute of Singapore
Ee Lui Ang: Agency for Science, Technology, and Research (A*STAR)
Lian Hui Zhang: Proteos
Yue Wang: Proteos
Huimin Zhao: Agency for Science, Technology, and Research (A*STAR)
Niranjan Nagarajan: Genome Institute of Singapore
Yue Wan: Genome Institute of Singapore

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract RNAs are well-suited to act as cellular sensors that detect and respond to metabolite changes in the environment, due to their ability to fold into complex structures. Here, we introduce a genome-wide strategy called PARCEL that experimentally identifies RNA aptamers in vitro, in a high-throughput manner. By applying PARCEL to a collection of prokaryotic and eukaryotic organisms, we have revealed 58 new RNA aptamers to three key metabolites, greatly expanding the list of natural RNA aptamers. The newly identified RNA aptamers exhibit significant sequence conservation, are highly structured and show an unexpected prevalence in coding regions. We identified a prokaryotic precursor tmRNA that binds vitamin B2 (FMN) to facilitate its maturation, as well as eukaryotic mRNAs that bind and respond to FMN, suggesting FMN as the second RNA-binding ligand to affect eukaryotic expression. PARCEL results show that RNA-based sensing and gene regulation is more widespread than previously appreciated in different organisms.

Date: 2018
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DOI: 10.1038/s41467-018-03675-1

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