Related Experiment Video
Updated: Jan 5, 2026
08:56
A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
Published on: December 5, 2016
11.3K
Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution
Daniel A Lorenz1,2,3, Shashank Sathe1,2,3, Jaclyn M Einstein1,2
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.
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.
Related Concept Videos
03:21RNA-seq
11.6K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.6K
02:24Ribosome Profiling
4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K
01:53RNA Stability
35.5K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
35.5K
02:35RACE - Rapid Amplification of cDNA Ends
7.1K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.1K