Study shows new RNA letter as regulatory key to control gene expression

DNA, RNA, protein -- the end. Or is it? Until recently, the pattern used to encode genetic information into our cells was considered to be relatively straightforward: four letters (A,G,C,T) for DNA and four (A,G,C,U) for RNA. This equation, however, turned out to be oversimplified -- RNA was holding out.

A new study published in Nature by a team of Tel Aviv University, Sheba Medical Center, and University of Chicago scientists finds that RNA, considered the DNA template for protein translation, often appears with an extra letter -- and this letter is the regulatory key for control of gene expression. The discovery of a novel letter marking thousands of mRNA transcripts will offer insight into different RNA functions in cellular processes and contributions to the development of disease.

"Epigenetics, the regulation of gene expression beyond the primary information encoded by DNA, was thought until recently to be mediated by modifications of proteins and DNA," said Prof. Gidi Rechavi, Djerassi Chair in Oncology at TAU's Sackler Faculty of Medicine and head of the Cancer Research Center at Sheba Medical Center. "The new findings bring RNA to a central position in epigenetics."

The research, led jointly by Prof. Rechavi and Prof. Chuan He, John T. Wilson Distinguished Service Professor in Chemistry and Investigator of the Howard Hughes Medical Institute at the University of Chicago, and conducted by a team of researchers at TAU, Sheba, and Chicago, represents a breakthrough in understanding how RNAs are regulated.

"This discovery further opens the window on a whole new world of biology for us to explore," said Prof. He. "These modifications have a major impact on almost every biological process."

The number of modified nucleotides (letters) in RNA is 10 times larger than that of the letters found in DNA. But what accounts for the evolutionary drive for a large RNA alphabet? RNA molecules have a wide variety of functions, including storage of genetic information as well as catalytic, structural, and regulatory activities. This is in contrast to the important but one-dimensional function of DNA in encoding genetic information.

"The 140 or so different modifications that decorate RNA increase significantly the vocabulary of RNA and enable the various types of RNA, including mRNA, rRNA, tRNA, siRNA, miRNA and, lncRNA, to implement their versatile activities," said Prof. Rechavi.

Prof. Rechavi's group, led by Dan Dominissini and Sharon Moshkovitz, began exploring the landscape of chemical modifications of messenger RNA (mRNA) four years ago through a specific modification: the addition of a methyl group in position 6 of Adenosine (m6A) in mRNA. The research team then showed that this modification is specific to unique regions of the mRNA molecules and that the modification can be "read" by specific proteins. They also showed that this modification is dynamic and responds to environmental stimuli.

These findings complemented the identification by Prof. He's University of Chicago group at the time of an enzyme (FTO) that removes the m6A marks from mRNA. The demonstration of a reversible process that decorates mRNA and affects its stability, translatability, splicing, and localization established a new field of RNA "epigenetics" known as "epitranscriptomics."

In their new study, the researchers unraveled a new dynamic modification of mRNA -- the methylation of position 1 of Adenosine (m1A). Importantly, this modification was shown to be localized in a telltale position near the start of protein translation and linked to increased protein synthesis. Thousands of genes are decorated by this modification, allowing cells to regulate the expression of proteins needed for key biological processes.

"We expect disruption of this new regulatory mechanism to be associated with disease states such as cancer and neurodegenerative disorders," said Prof. Rechavi.

The research groups are currently studying the cellular processes involved in "writing" and "erasing" m1A, as well as the biochemical pathways regulated by this new RNA modification. In the future, they plan to explore the role of m1A methylation in embryonic development and its involvement in cancer and neurodegenerative disorders.