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Related Experiment Video

Updated: Jan 5, 2026

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

Published on: December 5, 2016

Direct RNA sequencing enables m⁶A detection in endogenous transcript isoforms at base-specific resolution.

Daniel A Lorenz^1,2,3, Shashank Sathe^1,2,3, Jaclyn M Einstein^1,2

¹Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA.

RNA (New York, N.Y.)

|October 19, 2019

Summary

Direct RNA sequencing now identifies RNA modifications like N6-methyladenosine (m6A) with single-coordinate resolution. Our MINES software accurately maps thousands of new m6A sites in human cells.

Keywords:

RNA modifications m6A nanopore

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A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues

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Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis

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Published on: May 14, 2020

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Direct RNA sequencing offers potential for novel RNA modification discovery.
Interpreting direct RNA sequencing data to identify modified bases is challenging.

Purpose of the Study:

To develop a computational tool for identifying N6-methyladenosine (m6A) modifications using direct RNA sequencing.
To annotate m6A sites at single-coordinate resolution in human transcripts.

Main Methods:

Developed a random forest classifier using experimentally detected m6A sites.
Trained the classifier on N6-methyladenosine (m6A) sites within DRACH motifs.
Utilized Oxford Nanopore's direct RNA sequencing technology.

Main Results:

The MINES software identified over 13,000 unannotated DRACH sites in HEK293T cells.
Identified over 40,000 m6A sites with isoform-level resolution in human mammary epithelial cells.
Observed sensitivity of identified sites to METTL3 (writer) and ALKBH5 (eraser).

Conclusions:

MINES enables accurate m6A annotation at single-coordinate resolution from direct RNA nanopore sequencing data.
Facilitates the discovery of novel RNA modification sites and their regulatory dynamics.