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Related Experiment Video

Updated: Apr 10, 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

Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure.

Yizhu Lin¹, Gemma E May¹, C Joel McManus¹

¹Department of Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

Methods in Enzymology

|June 13, 2015

Summary

This summary is machine-generated.

Mod-seq is a high-throughput method that maps chemical modification sites on large RNAs. This technique, along with the Mod-seeker software, aids in predicting RNA secondary structures.

Keywords:

Chemical probing RNA SHAPE Sequencing Structure

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Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Large RNA molecules, particularly long noncoding RNAs, are crucial for gene regulation.
The structural organization of most large cellular RNAs remains largely uncharacterized.
Traditional methods for identifying RNA chemical modification sites are often laborious.

Purpose of the Study:

To present Mod-seq, a high-throughput sequencing method for mapping chemical modification sites on RNAs of all sizes.
To introduce Mod-seeker, a Python-based software package for analyzing Mod-seq data.
To facilitate RNA secondary structure prediction using modification site data.

Main Methods:

Preparation of Mod-seq high-throughput sequencing libraries from chemically modified RNA.
Utilizing the Mod-seeker software package for data analysis.
Identifying statistically significant RNA modification sites.

Main Results:

Mod-seq enables high-throughput mapping of chemical modification sites on diverse RNA molecules.
The Mod-seeker software efficiently analyzes Mod-seq data to pinpoint modification sites.
Statistically significant modification sites are identified for downstream structural analysis.

Conclusions:

Mod-seq is an effective high-throughput method for characterizing RNA structure.
Mod-seeker streamlines the analysis of Mod-seq data, aiding RNA structure prediction.
This approach advances the understanding of large RNA molecule structures and functions.