Budding yeast colonies show

DNA has been repaired by

transcript RNA within the cells

Credit: Georgia Tech/Rob Felt

Scientists have shown that RNA produced within yeast cells can serve as a template for repairing the most devastating DNA damage—a break in both strands of a DNA helix.

The group believes their study is the first to show that a cell’s own RNA can be used for DNA recombination and repair.

If the phenomenon extends to human cells, it could potentially lead to new therapeutic or preventative strategies for genetic diseases.

The scientists described the phenomenon in Nature.

“We have found that genetic information can flow from RNA to DNA in a homology-driven manner, from cellular RNA to a homologous DNA sequence,” said study author Francesca Storici, PhD, of the Georgia Institute of Technology in Atlanta.

“This process is moving the genetic information in the opposite direction from which it normally flows. We have shown that when an endogenous RNA molecule can anneal to broken homologous DNA without being removed, the RNA can repair the damaged DNA. This finding reveals the existence of a novel mechanism of genetic recombination.”

Dr Storici’s team previously showed that synthetic RNA introduced into cells—including human cells—could repair DNA damage. But the process was inefficient, and there were questions about whether it could occur naturally.

To find out whether cells could use endogenous RNA transcripts to repair DNA damage, she and her colleagues devised experiments using the yeast Saccharomyces cerevisiae.

The team developed a strategy for distinguishing repair by endogenous RNA from repair by the normal DNA-based mechanisms in the budding yeast cells, including using mutants that lacked the ability to convert the RNA into a DNA copy.

They then induced a DNA double-strand break in the yeast genome and observed whether the organism could survive and grow by repairing the damage using only transcript RNA within the cells.

The DNA region that generates the transcript was constructed to contain a marker gene interrupted by an intron. Following intron removal during transcription, the transcript RNA sequence has no intron, while the DNA region that generates the transcript retains the intron.

Only the repair templated by the transcript devoid of the intron can restore the function of a homologous marker gene in which the DNA double-strand break is induced.

Dr Storici and her colleagues measured success by counting the number of yeast colonies growing on a Petri dish, indicating that the repair had been made by endogenous RNA.

They conducted testing on two types of breaks, one in the DNA from which the RNA transcript had been made, and the other in a homologous sequence from a different location in the DNA.

The team found that proximity of the RNA to the broken DNA increased the efficiency of the repair, and the repair occurred via a homologous recombination process. Dr Storici believes the repair mechanism may operate in cells beyond yeast, and many types of RNA can be used.

“We are showing that the flow of genetic information from RNA to DNA is not restricted to retro-elements and telomeres but occurs with a generic cellular transcript, making it more of a general phenomenon than had been anticipated,” she explained. “Potentially, any RNA in the cell could have this function.”

For the future, Dr Storici hopes to learn more about the mechanism, including what regulates it. She also wants to determine whether it takes place in human cells. If so, that could have implications for treating or preventing diseases caused by genetic damage.

“Cells synthesize lots of RNA transcripts during their life spans,” Dr Storici said. “Therefore, RNA may have an unanticipated impact on genomic stability and plasticity. We need to understand in which situations cells would activate RNA-DNA recombination. Better understanding this molecular process could also help us manipulate mechanisms for therapy, allowing us to treat a disease or prevent it altogether.”

Cellular RNA can template DNA repair in yeast