When a cell gets ready to divide, it shuts down its gene-reading machinery almost entirely.

"As cells prepare to divide, they rapidly shut down most gene reading, or transcription," says Claudio R. Alarcón, PhD, associate professor of pharmacology at Yale School of Medicine. "At that point, the cell needs to focus on dividing."

For decades, the mechanism behind that shutdown was only partially understood. A new study co-led by Alarcón and Lilian Kabeche, PhD, associate professor of molecular biophysics and biochemistry at Yale School of Medicine, identifies a missing piece: an enzyme best known for tagging RNA molecules that turns out to be wired into the cell division machinery itself. The findings, recently published in Molecular Cell, may point toward new cancer therapies.

The enzyme at the center of the study is METTL3, which modifies RNA by attaching a small chemical tag. Scientists have long known these tags help determine whether messenger RNA (mRNA) molecules are stabilized, transported, or broken down. Alarcón's lab previously discovered that METTL3 not only affects the fate of mRNA molecules but also regulates how mRNA molecules are produced. It does this by tagging a small RNA called 7SK.

"7SK is a scaffolding nuclear RNA that is very important to regulate transcription,” says Alarcón, a member of Yale Cancer Biology Institute and Yale Cancer Center. “You can think of 7SK as a little sponge that sequesters transcription-elongating factors—traps them—so they can't promote transcription.”

Growth-stimulating factors activate METTL3 to tag 7SK, which opens the trap. A protein complex is released, and the cell's gene-reading machine gets the signal to promote mRNA transcription. The newly generated mRNA molecules will then be translated into the proteins required for cell growth.

The new paper shows this same chain reaction is triggered the moment a cell commits to division. An enzyme called CDK1 activates METTL3, which sets off the same cascade of events. However, in this case, the goal is to complete transcription and clear mRNA molecules from DNA, rather than making new proteins.

"What the work is showing is that you need to activate METTL3 to get the RNA off the chromosomes to be able to really condense that DNA and segregate faithfully," says Kabeche, also a member of Yale Cancer Biology Institute and Yale Cancer Center. "It's connecting an interphase process with the mitotic process. The mechanisms by which those two things were really connected weren't understood."

The window for all of this is narrow. "Mitosis only lasts about an hour," Kabeche says. Cells have to condense their chromosomes, segregate them, and complete the whole process within a short period of time. “So it has to be very tightly controlled and very quick."

Kabeche describes CDK1 as operating like a light switch: "When you have high enough CDK1 activity, it turns off METTL3. Then, CDK1 activity drops at the end of mitosis, and the switch goes the other way. Everything has to work exactly perfectly for it to look the way it's supposed to."

So what happened when the researchers used the gene-editing tool CRISPR to prevent METTL3 from being activated by CDK1, or prevent 7SK from being modified by METTL3?

“You start making mistakes,” Alarcón says. “Chromosomes don't segregate properly. You have lagging chromosomes. You can generate mutations. You can have all sorts of problems."

A chromosome in the wrong cell creates what's called aneuploidy, or a cell with too many or too few chromosomes. Kabeche, whose lab focuses on chromosomal instability in cancer, says aneuploidy is one of the defining features of tumors.

"In cancer cells, aneuploidy is highly correlated with poor patient prognosis, increased metastasis, and increased drug resistance," she says.

Chromosomal instability is present in over 90% of solid tumors. METTL3 inhibitors already exist, and Kabeche sees potential in combining them with other drugs to overwhelm cancer cells. "You can think of it like heat," she says. "You can tolerate a little, but if it's 110 degrees in the desert, those cells are not going to survive. The goal is to push them past that point."

Researchers studying METTL3's role in cancer, neurodegeneration, and stem cell biology have historically explained its effects through post-transcriptional mechanisms, or changes to mRNA stability or splicing. Those explanations may have overlooked METTL3's transcriptional mechanism, which was unknown until now.

Alarcón frames the paper as the start of a broader collaboration among cancer researchers. And Kabeche agrees.

"Because we're in the Yale Cancer Biology Institute where all of the scientists work on different aspects of cancer, we can come together," Kabeche says. "If we weren't next to each other, I don't think it would have been as fruitful."