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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
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Structural atlas of human primary microRNAs generated by SHAPE-MaP
S Chan Baek1, Boseon Kim1, Harim Jang1
1Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea.
Molecular Cell
|March 6, 2024
Summary
This study reveals critical pri-miRNA structural features for microRNA maturation using SHAPE-MaP. It identifies a novel bulged GWG motif that enhances pri-miRNA processing.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- MicroRNA (miRNA) maturation is essential for gene regulation.
- Understanding primary miRNA (pri-miRNA) structures is key to miRNA maturation.
- Limited experimental data exists for pri-miRNA structures.
Purpose of the Study:
- To experimentally determine the secondary structures of human pri-miRNAs.
- To identify optimal structural features governing pri-miRNA processing.
- To uncover sequence-structure determinants influencing miRNA maturation.
Main Methods:
- Employed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP).
- Analyzed secondary structures of 476 high-confidence human pri-miRNAs.
- Compared experimental structures with computational predictions and high-throughput processing data.
Main Results:
- SHAPE-MaP revealed pri-miRNA structures differing from computational models, especially in apical loops and basal segments.
- Optimal pri-miRNA structural features for processing were determined.
- A novel bulged GWG motif (bGWG) in the lower stem was identified as promoting pri-miRNA processing.
- Sequence determinants of processing are significantly influenced by structural context.
Conclusions:
- Experimental RNA structure probing is crucial for accurate pri-miRNA structure prediction.
- Structure-function mapping enhances understanding of pri-miRNA processing.
- Findings have implications for designing small hairpin RNAs and predicting miRNA mutation impacts.
