Mapping circular RNA structures in living cells by SHAPE-MaP

Si-Kun Guo; Fang Nan; Chu-Xiao Liu; Li Yang; Ling-Ling Chen

doi:10.1016/j.ymeth.2021.01.011

Mapping circular RNA structures in living cells by SHAPE-MaP

Methods. 2021 Dec:196:47-55. doi: 10.1016/j.ymeth.2021.01.011. Epub 2021 Feb 9.

Authors

Si-Kun Guo¹, Fang Nan², Chu-Xiao Liu¹, Li Yang³, Ling-Ling Chen⁴

Affiliations

¹ State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
² CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
³ CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
⁴ State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China. Electronic address: linglingchen@sibcb.ac.cn.

PMID: 33571668
DOI: 10.1016/j.ymeth.2021.01.011

Abstract

Circular RNAs are produced from back-splicing of exons of precursor mRNAs (pre-mRNAs). The sequences of exons in circular RNAs are identical to their linear cognate mRNAs, but the circular format may confer constraints on their folding and conformation, leading to potentially different functions from their linear RNA cognates. Here, we describe experimental and computational steps that optimize the selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to probe circular RNA secondary structure at single-nucleotide resolution in living cells.

Keywords: Circular RNA; Living cell; SHAPE-MaP; Secondary structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Nucleic Acid Conformation
RNA Precursors
RNA Splicing / genetics
RNA* / chemistry
RNA, Circular* / genetics

Substances

RNA Precursors
RNA, Circular
RNA