Sequencing of multiple RNA base modifications if

image: Principle of operation of quantum sequencing of a single molecule to determine base sequences and identify chemically modified base molecules.
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Credit: Takahito Ohshiro et al.

Osaka, Japan – Once a gene is transcribed into RNA, changes can occur in the subunits or “bases” that make up the RNA molecule, which can affect its structure and function. The study of these changes is known as “epitranscriptomics”. These basic changes can occur in most types of RNA molecules, including microRNAs.

Today, a research group from Osaka University, led by Prof. Masateru Taniguchi and Prof. Hideshi Ishii, sequenced a microRNA that is a marker for “refractory” gastrointestinal cancer, which does not respond to cancer. processing. They were able to directly detect two types of chemical base changes simultaneously using a single-molecule quantum sequencer.

MicroRNAs are small, non-coding RNA molecules that play a regulatory role by interfering with and suppressing the expression of a gene. Basic changes in microRNAs can affect the way they are processed and the efficiency with which they can suppress their targets, altering their function. These modifications are therefore important for understanding the functions of RNAs but have previously proved difficult to detect.

The Osaka University team isolated microRNAs from colorectal cancer cells and sequenced single RNA molecules. The quantum sequencer uses electricity to distinguish bases based on their unique electrical conductance values, which measure the ability of molecules to conduct electric current. Since chemical changes alter the electrical conductance of bases, this method could potentially be used to identify any type of nucleotide change. Here, the researchers focused on two common modifications, m6A and 5mC, involving the addition of a methyl group to an adenosine nucleotide (A) and to a cytidine nucleotide (C), respectively.

Using the single-molecule quantum sequencer, the team observed change ratios comparable to those calculated using other methods that are only able to detect one type of change at a time. Not only that, but the results they observed suggest that the two types of modification may have influenced each other. The presence of the m6A modification appeared to facilitate the 5mC modification. “The methylation level of 5mC is generally affected by the activities of methylation and demethylation enzymes, and our results therefore imply that the activities of these enzymes may be promoted or deactivated by m6A modifications,” explains Takahito Ohshiro, senior author of the article.

This work provides a robust new tool for sequencing various types of RNA base modifications. “Our method can be used for a comprehensive analysis and detection of methylation sites in the epitranscriptome,” explains corresponding author Masateru Taniguchi, “which will allow a better understanding of these methylation events and their mechanisms, changing the landscape of RNA biology and ushering in a new era. “


The article “Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC” was published in Scientific reports at DOI:

About Osaka University

Osaka University was founded in 1931 as one of the Seven Imperial Universities of Japan and today is one of the leading comprehensive universities in Japan with a broad disciplinary spectrum. This strength is coupled with a desire for singular innovation that extends throughout the scientific process, from fundamental research to the creation of applied technologies with positive economic impacts. Its commitment to innovation has been recognized in Japan and around the world, being named the most innovative university in Japan in 2015 (Reuters 2015 Top 100) and one of the most innovative institutions in the world in 2017. (Innovative Universities and Nature Index Innovation 2017). Today, Osaka University is leveraging its role as a designated national academic society selected by the Ministry of Education, Culture, Sports, Science and Technology to contribute to innovation for the human well-being, the sustainable development of society and social transformation.


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