Direct microRNA Sequencing Using Nanopore-Induced Phase-Shift Sequencing

Jinyue Zhang; Shuanghong Yan; Le Chang; Weiming Guo; Yuqin Wang; Yu Wang; Panke Zhang; Hong-Yuan Chen; Shuo Huang

doi:10.1016/j.isci.2020.100916

Direct microRNA Sequencing Using Nanopore-Induced Phase-Shift Sequencing

iScience. 2020 Mar 27;23(3):100916. doi: 10.1016/j.isci.2020.100916. Epub 2020 Feb 14.

Authors

Jinyue Zhang¹, Shuanghong Yan¹, Le Chang¹, Weiming Guo², Yuqin Wang¹, Yu Wang¹, Panke Zhang¹, Hong-Yuan Chen³, Shuo Huang¹

Affiliations

¹ State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
² State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China; Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
³ State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.

Abstract

MicroRNAs (miRNAs) are a class of short non-coding RNAs that function in RNA silencing and post-transcriptional gene regulation. However, direct characterization of miRNA is challenging due to its unique properties such as its low abundance, sequence similarities, and short length. Although urgently needed, single molecule sequencing of miRNA has never been demonstrated, to the best of our knowledge. Nanopore-induced phase-shift sequencing (NIPSS), which is a variant form of nanopore sequencing, could directly sequence any short analytes including miRNA. In practice, NIPSS clearly discriminates between different identities, isoforms, and epigenetic variants of model miRNA sequences. This work thus demonstrates direct sequencing of miRNA, which serves as a complement to existing miRNA sensing routines by the introduction of the single molecule resolution. Future engineering of this technique may assist miRNA-based early stage diagnosis or inspire novel cancer therapeutics.

Keywords: Analytical Chemistry; Biotechnology; Molecular Biology; Nanotechnology.