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Related Experiment Video

Updated: Jun 6, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Jason G Underwood¹, Andrew V Uzilov, Sol Katzman

¹Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA.

|November 9, 2010

Summary

This summary is machine-generated.

We developed fragmentation sequencing (FragSeq), a new method to rapidly map RNA structures. This high-throughput technique simultaneously analyzes many noncoding RNAs, accelerating RNA structure inference.

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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Traditional RNA structure determination is slow, analyzing one noncoding RNA (ncRNA) at a time.
Existing methods rely on enzymes and chemicals, with gel electrophoresis for identifying reactive sites.

Purpose of the Study:

To accelerate RNA structure inference using a novel high-throughput method.
To simultaneously map RNA structures across the transcriptome.

Main Methods:

Developed fragmentation sequencing (FragSeq), a high-throughput RNA structure probing technique.
Utilized nuclease P1 digestion to generate RNA fragments, followed by high-throughput sequencing.
Applied FragSeq to probe the entire mouse nuclear transcriptome.

Main Results:

Accurately and simultaneously mapped single-stranded RNA regions in multiple ncRNAs with known structures.
Verified the reproducibility of FragSeq by probing in two distinct cell types.
Identified and validated novel structured regions in ncRNAs lacking prior probing data.

Conclusions:

FragSeq significantly accelerates RNA structure inference compared to classical methods.
The method enables simultaneous analysis of numerous ncRNAs, providing a comprehensive view of RNA structures.
FragSeq is a powerful tool for discovering and characterizing RNA structures across the transcriptome.