Related Experiment Video

Updated: May 6, 2026

A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
08:56

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

Published on: December 5, 2016

12.0K

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

Nian Liu, Marc Parisien, Qing Dai

    RNA (New York, N.Y.)
    |October 22, 2013
    PubMed

    Insights

    We developed SCARLET, a new method to precisely map N(6)-methyladenosine (m(6)A) RNA modifications. This technique reveals dynamic m(6)A patterns and uncovers an RNA structural motif.

    Area of Science:

    • Biochemistry
    • Molecular Biology
    • Epigenetics

    Background:

    • N(6)-methyladenosine (m(6)A) is the most prevalent epitranscriptomic mark on mammalian RNA.
    • m(6)A modifications are dynamic and play crucial biological roles, similar to DNA methylation.
    • Previous studies lacked methods for single-nucleotide resolution m(6)A identification.

    Purpose of the Study:

    • To develop a novel method for accurate, site-specific m(6)A detection in mRNA and lncRNA.
    • To quantify the m(6)A modification fraction at specific RNA sites.
    • To investigate m(6)A patterns in human mRNAs and lncRNAs.

    Main Methods:

    • Developed site-specific cleavage and radioactive-labeling followed by ligation-assisted extraction and thin-layer chromatography (SCARLET).
    • Applied SCARLET to determine m(6)A status and modification fraction at single-nucleotide resolution.
    • Analyzed m(6)A status in human lncRNAs and mRNAs.

    Main Results:

    • SCARLET accurately determines m(6)A location and modification fraction.
    • m(6)A fractions varied significantly (6-80%) across different sites in human RNAs.
    • Identified previously unknown m(6)A-containing RNA structural motifs in lncRNAs.
    • Revealed that many putative m(6)A sites are not actually modified.

    Conclusions:

    • SCARLET is a powerful tool for studying dynamic m(6)A modifications.
    • Provides crucial insights into the biological roles and regulation of m(6)A.
    • Enables the discovery of RNA structural motifs associated with m(6)A modification.
    Keywords:
    N6-methyladenosineRNA modificationsingle nucleotide resolution

    More Related Videos

    Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis08:50

    Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis

    Published on: May 14, 2020

    6.8K
    Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry08:45

    Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry

    Published on: April 21, 2022

    3.4K

    Related Concept Videos

    RNA Stability01:53

    RNA Stability

    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...
    31.7K
    RNA Editing02:23

    RNA Editing

    RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
    8.3K
    Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

    Pre-mRNA Processing: Modification of pre-mRNA Ends

    In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
    Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
    14.3K
    Ribosome Profiling02:24

    Ribosome Profiling

    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...
    3.2K
    pre-mRNA Processing02:01

    pre-mRNA Processing

    In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
    Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...
    49.1K
    RNA-seq03:21

    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...
    9.5K