Keeping Telomeres in Their Places

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A day in the life of DNA can be rough. It gets yanked across a dividing cell, zapped by radiation, and assaulted by chemicals. Luckily, cells have developed a complex set of repair mechanisms to protect vulnerable DNA and fix damage so that the cell’s genomic instruction manual remains intact. Cells use homologous recombination to stitch double-stranded breaks (DSB) back together and the enzyme telomerase to cap exposed ends of a DNA strand with a repetitive DNA sequence called a telomere. 

However, if cells use the wrong repair mechanism for a given situation, it can be disastrous. For example, if telomerase tries to seal up a DSB, it can sever the chromosome, causing the cell to lose key genes. “The whole system falls apart,” said Titia de Lange, a cell biologist at Rockefeller University. 

Scientists have observed that this can happen in yeast and corn, but whether it occurred in humans remained a mystery until now.1,2 de Lange’s team has finally figured out just how rare this catastrophic event is in humans and how cells keep it in check. In a study published in Science, they revealed that while telomerase occasionally acts at DSB, the ataxia telangiectasia and Rad3-related (ATR) protein typically runs interference to give the cell a chance to repair these breaks.3 The findings shed light on how this type of genomic instability could play a role in diseases such as cancer.

If telomeres formed at DSB, de Lange suspected that it would be infrequent, given how few telomerases there are in any cell and how much damage it would cause. “We expected that this would be instantly repressed,” de Lange said. “Cells would not tolerate this.”

Starting with immortalized HeLa cells with artificially high levels of telomerase, the researchers cut the cells’ DNA with Cas9 enzyme to create DSB. They carefully designed the system to target positions in the DNA that telomerase gravitates towards but that are not fatal to the cell when broken. As de Lange expected, telomerase added telomeres at the DSB, but this was very rare; telomerase only created approximately four new telomeres per 1,000 genomes.

“I don’t know if it’s surprising that it occurs, or if it’s surprising that it doesn’t occur more often,” said Nausica Arnoult, a cell biologist at the University of Colorado Boulder who was not involved in this study. “It’s really well controlled.”

To figure out how the cells blocked telomerase from acting at DSB, de Lange’s team genetically inactivated many different enzymes and repair pathways to see if any of them repressed telomere formation. Eventually, they discovered the genomic guardian: ATR, a protein that senses DNA damage and triggers homologous recombination. When they inhibited ATR, the number of new telomeres nearly tripled. 

In the process of pinpointing ATR’s role, the researchers stumbled upon other cellular surprises. For example, they knew that certain proteins were required for telomerase to interact with DNA, but reducing those proteins’ levels didn’t seem to block telomere formation at Cas9-induced DSB. They quickly realized that telomerase could act directly on the type of DNA cuts that Cas9 makes, which creates “a little wrinkle in the use of CRISPR,” de Lange said. 

Arnoult agreed. “Especially if you consider the therapeutic use of CRISPR-Cas9, we really need to understand if there are some contexts where that misguided action of telomerase is going to be more frequent,” she said.

Much remains for de Lange and her team to reveal about ATR. Although they found that ATR represses telomerase, they don’t know how this happens. Arnoult said that she wonders whether there are other redundant pathways that can also influence telomere formation at DSB in other contexts. She pointed to other species where telomeres that form at DSB are a normal part of development.4,5 “Studying those species may give us clues of how they can do that very efficiently and why it’s prevented in humans,” Arnoult said.

de Lange is also thinking about how this process could be involved in cancer. Cancer cells’ genomes are plagued by DNA breaks, but their survival and proliferation depends on them finding a way to stabilize that damaged DNA; inappropriate telomerase activity may be one tool at their disposal. de Lange’s team is creating cells with abnormal chromosomes similar to those in cancer to see if telomerase helps these cells survive.

References

1. Kramer KM, Haber JE. New telomeres in yeast are initiated with a highly selected subset of TG1-3 repeatsGenes Dev. 1993;7(12A):2345-56. 
2. McClintock B. The stability of broken ends of chromosomes in Zea MaysGenetics. 1941;26(2):234-82.
3. Kinzig CG, et al. ATR blocks telomerase from converting DNA breaks into telomeresScience. 2024;383(6684):763-770.
4. Yu G, Blackburn EH. Developmentally programmed healing of chromosomes by telomerase in tetrahymenaCell. 1991;67(4):823-32.
5. Müller F, et al. New telomere formation after developmentally regulated chromosomal breakage during the process of chromatin diminution in ascaris lumbricoides. Cell. 1991;67(4):815-22.

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