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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Jul 14, 2025

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

MRT-ModSeq - Rapid Detection of RNA Modifications with MarathonRT.

Rafael de Cesaris Araujo Tavares¹, Gandhar Mahadeshwar², Han Wan³

¹Department of Chemistry, Yale University, New Haven, CT 06511, USA.

Journal of Molecular Biology

|October 6, 2023

Summary

This study introduces MRT-ModSeq, a rapid method for detecting multiple RNA modifications. It accurately maps diverse chemical modifications on RNA transcripts, improving RNA research speed and accuracy.

Keywords:

Epitranscriptomics RNA processing group II reverse transcriptase machine learning mutational profiling

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Last Updated: Jul 14, 2025

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

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Published on: December 9, 2022

A Nonsequencing Approach for the Rapid Detection of RNA Editing

A Nonsequencing Approach for the Rapid Detection of RNA Editing

Published on: April 21, 2022

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Cellular RNA chemical modifications are crucial for regulating RNA function and behavior.
Existing sequencing-based RNA modification mapping methods often lack a balance between speed and accuracy.
Accurate and rapid detection of RNA modifications is essential for understanding gene regulation and disease mechanisms.

Purpose of the Study:

To develop a novel, rapid, and accurate method for simultaneous detection of multiple RNA modifications.
To introduce MRT-ModSeq, a technique utilizing MarathonRT for high-throughput RNA modification analysis.
To establish a generalizable workflow for identifying diverse RNA modification sites across various RNA targets.

Main Methods:

Development of MRT-ModSeq, a method employing distinct divalent cofactors to generate modification-specific 2-D mutational profiles.
Utilizing MarathonRT for high-throughput sequencing and analysis of RNA modifications.
Implementation of mutation-rate filtering and machine learning algorithms for precise modification site assignment.

Main Results:

MRT-ModSeq successfully detected and mapped multiple RNA modifications, including m1acp3Y, m1A, m3U, m7G, and 2'-OMe, in well-studied rRNAs.
The method demonstrated sensitivity in detecting sparsely modified sites, such as m1A in MALAT1 and PRUNE1 transcripts.
The workflow proved effective for rapid identification of diverse RNA modification subtypes across different RNA targets.

Conclusions:

MRT-ModSeq offers a significant advancement in RNA modification detection, combining speed and accuracy.
The method provides a versatile platform for comprehensive RNA modification profiling.
This technique has the potential to accelerate discoveries in RNA biology and related fields.