Stem cells' rapid response due to short-lived RNA messages

Stem cells stay developmentally nimble by actively targeting key RNA messages for destruction. Researchers say this 'anti-epigenetics' works to ensure the transience of genetic information.

- By Krista Conger

Howard Chang and his colleagues have learned that embryonic stem cells in mice and humans chemically tag RNA messages encoding key stem-cell genes.
Norbert von der Groeben

Many stem cells live a life of monotony, biding their time until they’re needed to repair tissue damage or propel the growth of a developing embryo. But when the time is right, they must spring into action without hesitation. Like Clark Kent in a phone booth, they fling aside their former identity to become skin, muscle, bone or other cell types. 

Now researchers at Stanford, Harvard and UCLA have learned that embryonic stem cells in mice and humans chemically tag RNA messages encoding key stem-cell genes. The tags tell the cell not to let the messages linger — to degrade them quickly. Getting rid of those messages allows the cells to respond more nimbly to their new marching orders.

“Until now, we’ve not fully understood how RNA messages within the cell dissipate,” said Howard Chang, MD, PhD, professor of dermatology at the Stanford School of Medicine. “In many cases, it was thought to be somewhat random. This research shows that embryonic stem cells actively tag RNA messages that they may later need to forget. In the absence of this mechanism, the stem cells are never able to forget they are stem cells. They are stuck and cannot become brain, heart or gut, for example.”

Chang, who is a Howard Hughes Medical Institute scientist and a member of the Stanford Cancer Institute, is a co-senior author of a paper describing the research, which was published on Oct. 16 in Cell Stem Cell. He shares senior authorship with Yi Xing, PhD, associate professor of microbiology, immunology and molecular genetics at UCLA, and Cosmas Giallourakis, MD, assistant professor of medicine at Harvard. Lead authorship is shared by postdoctoral scholars Pedro Batista, PhD, of Stanford, and Jinkai Wang, PhD, of UCLA; and by senior research fellow Benoit Molinie, PhD, of Harvard.

Following instructions

Messenger RNAs are used to convey information from the genes in a cell’s nucleus to protein-making factories in the cytoplasm. They carry the instructions necessary to assemble the hundreds of thousands of individual proteins that do the work of the cell. When, where and how long each protein is made is a carefully orchestrated process that controls the fate of the cell. For example, embryonic stem cells, which can become any cell in the body, maintain their “stemness” through the ongoing production of proteins known to confer pluripotency, a term used to describe how these cells can become any cell in the body.

The researchers, who knew that cells sometimes mark their RNA messages with chemical tags called methyl groups, were particularly interested in one type of methyl tag called m6A. Although the process of tagging the RNA is somewhat similar to how DNA is modified to control gene expression, it has not been clear exactly how these RNA tags function in development. On DNA, the chemical tags serve to help a cell remember which genes to express at particular times — signaling a skin cell to preferentially make collagen and keratin, for example, rather than digestive enzymes or hormones. The study of these tags on DNA is called epigenetics.

When the researchers compared m6A patterns among thousands of RNA molecules in mouse and human embryonic stem cells, they found striking similarities between the organisms. Often key pluripotency genes were methylated at particular points along their length; these messages were degraded more quickly than unmethylated RNA molecules. Blocking the methylation mechanism in the embryonic stem cells, the researchers found, not only protected the pluripotency messages from degradation, but it also made it more difficult for the cells to respond appropriately to external cues and significantly slowed their ability to differentiate into other cell types.

An ‘anti-epigenetic’ mechanism

The researchers concluded that it’s necessary for the cells to be able to quickly degrade those key RNA messages. If no differentiation is necessary, the cells simply replenish the messages by repeatedly copying them from the DNA. However, if a change in fate is needed, the cell can quickly shut down RNA production and any remaining messages will rapidly dissipate.  

“This research is conceptually groundbreaking because it reveals an ‘anti-epigenetic’ mechanism that works to keep genetic messages transient,” Chang said. “In contrast to epigenetic mechanisms that provide cellular memory of gene expression states, m6A helps the cells to forget the past and embrace the future.”

Other Stanford co-authors are Marius Wernig, MD, associate professor of pathology; Donna Bouley, PhD, DVM, professor of comparative medicine; bioinformaticians Kun Qu, PhD, and Jiajing Zhang, PhD; postdoctoral scholar Lingjie Li, PhD;  research assistant Bahareh Haddad; and graduate students Ava Carter, Ryan Flynn and Ernesto Lujan.

The research was supported by the California Institute for Regenerative Medicine, the National Institutes of Health, Massachusetts General Hospital, the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, the Damon Runyon Cancer Research Foundation, the Alfred Sloan Foundation and the Howard Hughes Medical Institute.

Stanford’s Department of Dermatology also supported the work.

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2023 ISSUE 3

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