A new discovery by researchers at Weill Cornell Medical College published in the May 17 edition of the journal Cell once again rewrites scientific textbooks. Only 10 years ago, epigenetic researchers had to abandon the long-held belief that DNA consists of just four bases when they discovered that chemically modified bases are, in fact, abundant components of the human genome.

The new discovery, related to RNA, is similar to DNA in carrying genetic information and their method of expression, but researchers have now identified a novel base modification in RNA that will revolutionize our understanding of gene expression.

For a long time, it was believed that messenger RNA (mRNA) were simple blueprints for protein production that were often chemically altered by adding a methyl group to its adenine base. The researchers discovered that contrary to their belief that mRNA contains only four nucleobases; it actually contains a fifth base, namely the N6-methyladenosine (m6A) that pervades the transcriptome. They discovered that up to 20% of human mRNA is routinely methylated, which means that with more than 5,000 different mRNA molecules containing m6A, this modification is likely to have a widespread impact on gene expression.

Senior researcher, Dr. Samie R. Jaffrey, an associate professor of pharmacology at Weill Cornell Medical College declares:

“This finding rewrites fundamental concepts of the composition of mRNA because, for 50 years, no one thought mRNA contained internal modifications that control function. We know that DNA and proteins are routinely modified by chemical switches that have profound effects on their function in both health and disease. But biologists believed mRNA was simply an intermediate between DNA and protein. Now we know mRNA is much more complex, and defects in RNA methylation can lead to disease.”

A part of their study they proved that the obesity risk gene FTO, known as fat mass and obesity-associated protein, encodes an enzyme that is capable of reversing this modification by converting m6A residues in mRNA back to regular adenosine. The researchers uncovered the link that obesity is associated to overactive FTO enzymes in humans with FTO mutations. The overactive FTO results in low levels of m6A, causing abnormalities in food intake and metabolism that ultimately cause obesity. In addition, the team also discovered links between m6A and other diseases.

Dr. Kate Meyer, a postdoctoral researcher in Dr. Jaffrey’s laboratory who led the study says:

“We found that m6A is present in many mRNAs encoded by genes linked to human diseases, including cancer as well as several brain disorders, such as autism, Alzheimer’s disease, and schizophrenia. Methylation in RNA is a reversible modification that appears to be a central step in a wide variety of biological pathways and physiological processes.”

According to Dr. Jaffrey, m6A was, for the first time, detected in mRNA in 1975, yet, back then, scientists were uncertain whether this finding was due to contamination by other RNA molecules. More than 90% of RNAs are cellular ‘workhorses’ that are frequently modified and consist of either transfer RNA (tRNA) or ribosomal RNA (rRNA). Dr. Jaffrey hypothesized that mRNA could be modified, based on the fact that DNA, proteins and other forms of RNA are modified. Together with his team he developed a technique to help reveal methylation in mRNA obtained from mouse as well as human samples.

To isolate the mRNAs that contain m6A, the team used two different antibodies that are able to identify and bind to the mRNAs m6A. They were able to identify the sequence of each individual mRNA they had isolated by subjecting them to next-generation sequencing, and Dr. Christopher Mason and Dr. Olivier Elemento subsequently developed a computational algorithm revealing the identity of each of these methylated mRNAs.

Although the team has no knowledge of the dynamics of the thousands of m6As in humans in terms of how they control the mRNAs function, they have observed that the location of the m6As are near ‘stop codons’ in mRNA sequences, which are areas that signal the end of translation of the mRNA, indicating that m6A may play a role in ribosomal function.

Co-author of the study, Dr. Christopher Mason, assistant professor from the Weill College’s Department of Physiology and Biophysics and Computational Genomics in Computational Biomedicine says:

“But we really don’t know yet. It may allow other proteins to bind to mRNA, or subject these mRNAs to a whole new regulatory pathway. Our bioinformatics analyses are providing several hints about the possible impact of methylation on RNA function.”

The researchers already established that m6A sites often occur in mRNA regions, which are highly conserved across several species of vertebrates.

Dr. Mason explains:

“This shows that m6A sites are not just important for humans, but rather are maintained under selection across hundreds of millions of years of evolution, and thus are likely of critical importance for all animals. This is the first demonstration of an epitranscriptomic modification — alterations in RNA function that are not due to changes in the underlying sequence.”

Dr. Jaffrey adds:

“These findings are very, very exciting, and amazing, really, when you consider that mRNA has been around for so long and that nobody realized, in all this time, that they were being regulated in this way. It was right under our noses.”

The researchers are currently exploring the dynamics of m6As control mechanism of mRNAs within cells, as well as concentrating their efforts on identifying the enzymes and pathways that regulate mRNA methylation. They already provided evidence that FTO has the capacity of reversing adenosine methylation, which indicates that it affects a large percentage of cellular mRNA.

Dr. Meyer comments:

“FTO mutations are estimated to occur in one billion people worldwide and are a leading cause of obesity and type 2 diabetes. Our studies link m6A levels in mRNA to these major health problems and identify for the first time the mRNAs which are potentially targeted by FTO.”

At present, the researchers are focusing on gaining a better insight into the causes of obesity and metabolic disorders by studying the impact of defective m6A regulation in patients with FTO mutations. They are also currently developing tests that allow scientists to rapidly detect the compounds that block overactive FTO activity in humans, which could lead to new treatments for obese individuals and those with diabetes.

Written By Petra Rattue