A research team led by Director KIM V. Narry at the Center for RNA Research within the Institute for Basic Science (IBS) has discovered compact viral RNA elements that can make mRNA more stable and increase protein production. These elements could provide a simple way to develop longer-lasting and more efficient mRNA technologies for vaccines and other RNA-based therapeutics. The study also uncovered an unexpected mechanism by which viruses recruit cellular enzymes to protect their RNA from degradation.

Messenger RNA (mRNA) carries genetic instructions that cells use to produce proteins. By synthesizing mRNA containing instructions for a desired protein and delivering it into cells, researchers can temporarily turn the cells into protein-producing factories. This principle enabled the development of COVID-19 mRNA vaccines and holds promise for a much wider range of applications, including cancer immunotherapy and treatments that replace proteins missing or insufficient in the body.

One major limitation, however, is that mRNA is inherently short-lived. Conventional mRNA is rapidly degraded inside cells, often limiting protein production to a relatively short period. A major factor determining its stability is the poly(A) tail, a stretch of adenine nucleotides at the end of the molecule. As this protective tail becomes shorter, the mRNA becomes increasingly vulnerable to degradation.

Viruses face a similar problem. To successfully reproduce inside host cells, they must keep their RNA intact long enough to produce the proteins they need. Over millions of years of evolution, viruses have developed diverse strategies to protect their RNA from degradation. These viral survival mechanisms therefore represent a potentially rich source of naturally evolved tools for stabilizing therapeutic mRNA.

Mining Viruses for RNA-Stabilizing Elements

The researchers divided genomes from 337 vertebrate-infecting viruses into nearly 200,000 short segments and tested how each affected mRNA abundance, translation, and protein production. The screen revealed hundreds of viral RNA segments capable of enhancing gene expression.

Many of these elements relied on a cellular enzyme called terminal nucleotidyltransferase 4 (TENT4). TENT4 can protect mRNA by extending its poly(A) tail through a process known as mixed tailing, slowing the degradation of the RNA. The researchers identified 23 TENT4-dependent elements distributed across 19 viral genera and classified them into six distinct types based on their sequences, structures, and use of cellular cofactors.

The diversity of these elements suggests that different viruses independently evolved multiple ways to exploit the same host RNA-stabilizing machinery. The team collectively named viral RNA elements that promote poly(A)-tail extension “tailons”.

The researchers also discovered elements that function independently of TENT4. Among the most potent was Pt1, an RNA element derived from Potamipivirus. Pt1 stabilized mRNA through an entirely different mechanism, directly recruiting the cellular enzymes poly(A) polymerase gamma (PAPγ) and poly(A) polymerase alpha (PAPα).

These enzymes are best known for adding poly(A) tails to newly produced pre-mRNAs during RNA processing in the nucleus. However, the researchers found that a portion of PAPγ and PAPα is also present in the cytoplasm. There, Pt1 directly recruits the enzymes to extend the poly(A) tail after transcription, revealing an unexpected cytoplasmic function for conventional poly(A) polymerases.

Making Linear mRNA Last Longer

Circular RNA has attracted attention as a way to overcome the instability of conventional linear mRNA. Because its two ends are joined together, circular RNA is more resistant to degradation and can remain inside cells longer. However, it can produce proteins less efficiently than linear mRNA and is more complex to manufacture.

Notably, adding Pt1 allowed linear mRNA to achieve stability comparable to that of circular RNA. In cultured cells, conventional linear mRNA had a half-life of approximately 7.6 hours, while linear mRNA containing Pt1 had a half-life of 23.1 hours, comparable to the 24.9-hour half-life of circular RNA.

Tailons therefore offer another approach to improving mRNA stability while retaining the advantages of linear mRNA. In a previous study published in Nature Biotechnology, the researchers demonstrated the therapeutic potential of tailons. Linear mRNAs containing tailons such as Pt1 and A7 achieved stability comparable to circular RNA while producing approximately nine times more protein overall.

The researchers further demonstrated that tailons such as A7 remain effective when used together with N1-methylpseudouridine, a modified nucleotide widely used in therapeutic mRNAs. When administered to mice, tailon-containing linear mRNA produced more protein than circular RNA, with detectable protein-production signals persisting for up to two weeks. By comparison, signals from conventional linear and circular mRNAs disappeared within one to three days.

Toward Longer-Lasting mRNA Therapeutics

These properties could help address several limitations of current mRNA therapeutics. Extending the lifetime of mRNA while increasing protein production could potentially reduce the amount of mRNA required for treatment and thereby lower the risk of dose-related side effects. Because tailons are short RNA sequences that can simply be incorporated into existing mRNA designs, they could also be readily compatible with established mRNA manufacturing processes.

The technology could ultimately broaden the use of mRNA beyond vaccines to applications such as cancer and immune therapies and protein replacement treatments. At the same time, the findings demonstrate that viruses can serve not only as subjects of infectious disease research but also as biological resources containing molecular tools refined through evolution.

The study builds on more than a decade of research at the IBS Center for RNA Research into the mechanisms that control RNA stability. This body of work was recently recognized with the HFSP Nakasone Award for Director KIM V. Narry for her discovery of the “non-canonical RNA tailing” pathway, through which cells regulate gene expression by modifying the ends of RNA molecules.

“This study shows that viruses have evolved highly efficient and diverse ways to protect their RNA,” said Director Kim. “By systematically identifying these survival strategies, we have laid the groundwork for developing stronger and longer-lasting mRNA technologies.”

The study was published in Cell.