DNA Repair Gone Wrong Leads to Cascade of Chromosome Rearrangements

Homologous Recombination Can Cause More Breaks As It Fixes Them

The traditional view of cancer is that a cell has to sustain a series of hits to its DNA before its defenses break down enough for it to turn cancerous. But cancer researchers have also found that cells can experience very rapid and widespread DNA damage that could quickly lead to cancer or developmental defects.

Now researchers at the University of California, Davis, have found that these complex chromosomal rearrangements can be triggered in a single event when a process used to repair DNA breaks, homologous recombination, goes wrong. The work is published Aug. 10 in the journal Cell.

“Homologous recombination is a Dr. Jekyll and Mr. Hyde phenomenon, and this is definitely the Mr. Hyde side,” said Wolf-Dietrich Heyer, professor of microbiology and molecular genetics at UC Davis and senior author on the paper.

Repairing Double Strand Breaks

Our DNA is subject to damage all the time, from external sources such as radiation or chemicals, as well as from the by-products of routine processes inside the cell. Keeping DNA intact and fully functional is a constant task for our cells.

Chromosomes rearranged during DNA repair

Repairing a double-strand break in DNA by homologous recombination involves stripping back one strand to leave one exposed. If this strand (AB) matches with two pieces of DNA (A and B) at the same time, it results in a piece of DNA being moved around in the genome. This can lead to genome instability and cancer.

DNA is made of two strands curled around each other in the famous double helix. A break across both strands is a serious matter. These double-stranded breaks can be fixed by a process called homologous recombination. In this process one strand is stripped away leaving a single bare strand near the break site. This single strand goes looking for its complementary matching strand elsewhere in the genome. Because most animals and plants have at least two copies of each chromosome, there will be at least one match. The probing single strand lines up with its match, and homologous recombination uses it as a template to repair the original break.

So far, so good. But during that probing, single strand DNA has to search through a lot of DNA very quickly to find its match. In addition, genomes contain many repeated sequences, making it more difficult to find the correct target.

“The homology search has to be incredibly fast,” said Heyer. “It’s like finding a key on an old mechanical typewriter – sometimes you would hit two keys at once and it would get tangled.
What happens if you hit two homologies at the same time?”

William Wright, a postdoctoral fellow Heyer’s lab and an author on the paper, realized that such double hits were happening during in vitro reactions with purified DNAs and recombination proteins. He called these double hits “multiple invasions.” But would this happen in cells? And with what consequences for genome integrity?

Multiple Invasions and Cascading Breaks

Aurèle Piazza, a postdoctoral researcher in Heyer’s lab and lead author on the study set out to answer these questions. Using the genetically tractable model organism baker’s yeast, which has chromosomes that are organized, copied and repaired in essentially the same ways as ours, he found that such “multiple invasions” do indeed form in cells.

Importantly, resolving these multiple invasions causes chunks of DNA to be swapped around in the genome, a process geneticists call “rearrangement.” Most of the time, that’s a bad thing, a step towards cancer or developmental problems in an embryo or fetus.

The rearrangements caused by multiple invasions can occur as frequently as once in two hundred recombination events in normal cells, despite the presence of a number of proteins working to safeguard against such rearrangements.

Piazza and Heyer also found an additional problem: resolving one multiple invasion causes at least two additional double-stranded DNA breaks, which in turn cause more rearrangements. This cascade of breaks and attempted repairs may underlie the sudden complex rearrangements observed in certain human cancers, a phenomenon known as “chromothripsis,” Greek for chromosome shattering.

“We can now explain how this cascade of disastrous events occurs,” Heyer said.

There is one time when chromosomal rearrangements are useful, even encouraged, although under tight control: to shuffle parental DNA during meiosis, when sperm and egg cells are formed. Better understanding these events can explain how chromosomes are shuffled over the course of evolution, Heyer said.

Heyer also holds an appointment at the UC Davis Comprehensive Cancer Center. The work was supported by grants from the NIH and fellowships from the French Cancer Fund, the European Molecular Biology Organization and the European Union.

More information

“Chromosome shattering” seen in plants, cancer

Heyer Lab web page

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