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RNA Structure01:23

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Mapping circular RNA structures in living cells by SHAPE-MaP.

Si-Kun Guo1, Fang Nan2, Chu-Xiao Liu1

  • 1State 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.

Methods (San Diego, Calif.)
|February 11, 2021
PubMed
Summary
This summary is machine-generated.

Circular RNAs (circRNAs) have unique structures and functions. This study optimizes SHAPE-MaP methods to reveal circRNA secondary structures in living cells.

Keywords:
Circular RNALiving cellSHAPE-MaPSecondary structure

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Genomics

Background:

  • Circular RNAs (circRNAs) are formed by the back-splicing of precursor mRNAs (pre-mRNAs).
  • The unique circular structure of circRNAs may influence their folding, conformation, and function compared to linear mRNAs.
  • Understanding circRNA secondary structure is crucial for elucidating their biological roles.

Purpose of the Study:

  • To optimize experimental and computational protocols for probing circRNA secondary structure.
  • To enable single-nucleotide resolution analysis of circRNA conformation in living cells.
  • To provide a robust method for studying circRNA structure-function relationships.

Main Methods:

  • Adaptation and optimization of selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP).
  • Integration of computational approaches to analyze SHAPE-MaP data specifically for circular RNA molecules.
  • Application of the optimized SHAPE-MaP technique in living cellular environments.

Main Results:

  • Demonstration of optimized SHAPE-MaP protocols for accurate circRNA secondary structure determination.
  • Successful application of the method to reveal single-nucleotide resolution structural information of circRNAs in cells.
  • Validation of the experimental and computational workflow for circRNA structure probing.

Conclusions:

  • The optimized SHAPE-MaP method provides unprecedented insights into circRNA secondary structures within their native cellular context.
  • This technique facilitates the study of how circRNA structure impacts their function and interactions.
  • The developed methodology is a valuable tool for advancing the field of circular RNA biology.