Hidden layer of gene control influences everything from cancer to memory

The idea that chemical tags on genes can affect their expression without altering the DNA sequence, once surprising, is the stuff of textbooks. The phenomenon, epigenetics, has now come to messenger RNA (mRNA), the molecule that carries genetic information from DNA to a cell’s proteinmaking factories. At a conference here last month, researchers discussed evidence that RNA epigenetics is also critical for gene expression and disease, and they described a new chemical modification linked to leukemia.

Research has found that epigenetic marks decorate mRNAs like Christmas lights on a fence. The cell uses the marks “to determine where, when, and how much of the [associated] protein should be generated,” RNA biologist Pedro Batista of the National Cancer Institute (NCI) in Bethesda, Maryland, said at the conference. What’s more, says Michael Kharas of Memorial Sloan Kettering Cancer Center in New York City, mRNA modifications “can affect the viability of cells, whether cells divide, cancer, neurologic diseases.” They are providing promising leads for drug developers. And, he adds, “There’s so many [more] diseases these things could be important in, ones people aren’t even looking at.”

Modified mRNAs had been reported in the 1970s, but by 2008 they were largely forgotten. Then, Chuan He at the University of Chicago, Samie Jaffrey at Weill Cornell Medicine, and Gideon Rechavi at Tel Aviv University in Israel took a fresh look. Their teams focused on one mRNA modification called m6A: a methyl group—a simple chemical unit—attached to some of an RNA molecule’s adenine bases. He’s group showed that a well-known enzyme removes this mRNA modification, indicating that m6A has an important biological role, and Jaffrey’s and Rechavi’s groups developed mapping tools that showed it is widespread. Before the work, researchers knew mRNA epigenetic marks were there, but “they just didn’t know how to actually look for them,” says NCI researcher Shalini Oberdoerffer.

Of at least half a dozen modifications of mRNA, m6A is the best studied. When proteins called readers attach to it, they direct the fate of the marked mRNA—which can vary dramatically.

For example, m6A boosts gene expression needed for embryonic stem cells to properly differentiate into different cell types. But in blood stem cells, m6A restricts differentiation. In leukemia—a disease of blood stem cells gone awry—m6A sustains disease by keeping the cells in a stemlike state. In 2017, three groups, including Kharas’s, independently showed that eliminating the enzyme that places m6A on mRNA kills tumor cells in acute myeloid leukemia. At least three biotech companies are now developing experimental drugs to block such enzymes.

At the meeting, Tony Kouzarides of the University of Cambridge in the United Kingdom reported a new mRNA modification and an associated enzyme that drives leukemia. “I suspect there will be many, many more” links to leukemia, he said.

M6A has also turned out to be critical in the brain. Through its readers, it controls the precise timing of new neuron formation during development in mice and enables axons to regenerate after nerve injury. The modification also enhances memory. When He’s team knocked out the gene for an m6A reader in mice, the otherwise normal animals had memory defects. Injecting a virus carrying the normal reader gene reversed the effect. And when the researchers chemically stimulated the neurons to mimic the addition of a new memory, they saw a burst of protein synthesis that depended on m6A, they reported last year in Nature.

Several years ago, Oberdoerffer followed a hunch that cells might use another simple chemical unit, an acetyl group, on mRNA. Her team reported last year in Cell that many mRNA cytosine bases are acetylated. The change boosts translation by stabilizing the molecules, and perhaps also by helping mRNAs match up with the correct transfer RNAs (tRNAs), the small RNA molecules that read the mRNA and add an amino acid to a growing protein chain. When mRNA and tRNA complement each other, they bind, triggering the addition of the amino acid. But the system isn’t exact—there are many more possible mRNA sequences than there are tRNAs, so tRNAs must somehow find (and bind to) some mRNAs that don’t match.

Oberdoerffer’s team found a clue to the mystery: an acetylated mRNA base often sits where a tRNA must recognize the mRNA despite a mismatch. The RNA modification’s presence dramatically boosts gene translation, the researchers found. Oberdoerffer doesn’t think the modification is necessary for correct mRNA-tRNA recognition, but it may strengthen binding. “I think we will learn that the genetic code as we know it is not a static entity,” she says.

Like other fledgling areas of research, RNA epigenetics (also known as epitranscriptomics) has its skeptics. In 2016, one group reported in Nature it had found a new modification, m1A, at more than 7000 sites across a cell’s complement of mRNAs. But a year later in the same journal, another group claimed that at most 15 mRNA m1A sites exist. “Because of that, everyone in the molecular biology community is a little bit suspicious about the validity of these [mRNA] modifications,” Jaffrey says.

Other disputes rage over the functions of key enzymes and reader proteins. But epitranscriptomics is evolving fast. “We just need … a lot more knowledge about these things,” He says. “We need to stay open minded. The field is still very young.”