How to Engineer Sustainable Chromosome Changes in Mice

Evolutionary chromosomal changes may take a million years in nature, but researchers are now reporting a novel technique enabling programmable chromosome fusion that has successfully produced mice with genetic changes that occur on a million-year evolutionary scale in the laboratory. The result may provide critical insights into how rearrangements of chromosomes—the tidy packages of organized genes, provided in equal number from each parent, which align and trade or blend traits to produce offspring—influence evolution.

In results published today in Science, the researchers reveal that chromosome-level engineering can be achieved in mammals, and they successfully derived a laboratory house mouse with novel and sustainable karyotype, providing critical insight into how  may influence evolution.

The laboratory house mouse has maintained a standard 40-chromosome karyotype—or the full picture of an organism’s chromosomes—after more than 100 years of artificial breeding,” said co-first author Li Zhikun, researcher in the Chinese Academy of Sciences (CAS) Institute of Zoology and the State Key Laboratory of Stem Cell and Reproductive Biology. “Over longer time scales, however, karyotype changes caused by chromosome rearrangements are common. Rodents have 3.2 to 3.5 rearrangements per million years, whereas primates have 1.6.”

Such small changes may have big impacts, according to Li. In primates, the 1.6 changes are the difference between humans and gorillas. Gorillas have two separate chromosomes whereas in humans they are fused, and a translocation between ancestor human chromosomes produced two different chromosomes in gorillas. At an individual level, fusions or translocations can lead to missing or extra chromosomes or even to such diseases as childhood leukemia.

How To Protect Cells From Premature Aging

Molecules that accumulate at the tip of chromosomes are known to play a key role in preventing damage to our DNA. Now, researchers at EPFL (Ecole Polytechnique Fédérale de Lausanne in Switzerland) have unraveled how these molecules home in on specific sections of chromosomes—a finding that could help to better understand the processes that regulate cell survival in aging and cancer.

Much like an aglet of a shoelace prevents the end of the lace from fraying, stretches of DNA called telomeres form protective caps at the ends of chromosomes. But as cells divide, telomeres become shorter, making the protective cap less effective. Once telomeres get too short, the cell stops dividing. Telomere shortening and malfunction have been linked to cell aging and age-related diseases, including cancer.

A new study by EPFL researchers shows how RNA species called TERRA muster at the tip of chromosomes, where they help to prevent telomere shortening and premature cell aging

Scientists have known that RNA species called TERRA help to regulate the length and function of telomeres. Discovered in 2007 by postdoc Claus Azzalin in the team of EPFL Professor Joachim Lingner, TERRA belongs to a class of molecules called noncoding RNAs, which are not translated into proteins but function as structural components of chromosomes. TERRA accumulates at chromosome ends, signaling that telomeres should be elongated or repaired.

However, it was unclear how TERRA got to the tip of chromosomes and remained there. “The telomere makes up only a tiny bit of the total chromosomal DNA, so the question is ‘how does this RNA find its home?’”, Lingner says. To address this question, postdoc Marianna Feretzaki and others in the teams of Joachim Lingner at EPFL and Lumir Krejci at Masaryk University set out to analyze the mechanism through which TERRA accumulates at telomeres, as well as the proteins involved in this process. The findings are published in Nature.

By visualizing TERRA molecules under a microscope, the researchers found that a short stretch of the RNA is crucial to bring it to telomeres. Further experiments showed that once TERRA reaches the tip of chromosomes, several proteins regulate its association with telomeres. Among these proteins, one called RAD51 plays a particularly important role, Lingner says.

RAD51 is a well-known enzyme that is involved in the repair of broken DNA molecules. The protein also seems to help TERRA stick to telomeric DNA to form a so-called “RNA-DNA hybrid molecule”. Scientists thought this type of reaction, which leads to the formation of a three-stranded nucleic acid structure, mainly happened during DNA repair. The new study shows that it can also happen at chromosome ends when TERRA binds to telomeres. “This is paradigm-shifting,” Lingner says.

The researchers also found that short telomeres recruit TERRA much more efficiently than long telomeres. Although the mechanism behind this phenomenon is unclear, the researchers hypothesize that when telomeres get too short, either due to DNA damage or because the cell has divided too many times, they recruit TERRA molecules. This recruitment is mediated by RAD51, which also promotes the elongation and repair of telomeres. “TERRA and RAD51 help to prevent accidental loss or shortening of telomeres,” Lingner says. “That’s an important function.”


How To Reverse Cellular Aging Process

Central to a lot of scientific research into aging are tiny caps on the ends of our chromosomes called telomeres. These protective sequences of DNA grow a little shorter each time a cell divides, but by intervening in this process, researchers hope to one day regulate the process of aging and the ill health effects it can bring. A Harvard team is now offering an exciting pathway forward, discovering a set of small molecules capable of restoring telomere length in mice. Telomeres can be thought of like the plastic tips on the end of our shoelaces, preventing the fraying of the DNA code of the genome and playing an important part in a healthy aging process. But each time a cell divides, they grow a little shorter. This sequence repeats over and over until the cell can no longer divide and dies.

This process is linked to aging and disease, including a rare genetic disease called dyskeratosis congenita (DC). This is caused by the premature aging of cells and is where the team focused its attention, hoping to offer alternatives to the current treatment that involves high-risk bone marrow transplants and which offers limited benefits.

One of the ways dyskeratosis congenita comes about is through genetic mutations that disrupt an enzyme called telomerase, which is key to maintaining the structural integrity of the telomere caps. For this reason, researchers have been working to target telomerase for decades, in hopes of finding ways to slow or even reverse the effects of aging and diseases like dyskeratosis congenita.

Once human telomerase was identified, there were lots of biotech startups, lots of investment,” says Boston Children’s Hospital’s Suneet Agarwal, senior investigator on the new study. “But it didn’t pan out. There are no drugs on the market, and companies have come and gone.


Gene-Editing: From Pigs To Humans

If any swine is fit to be an organ donor for people, then the dozens of pigs snuffling around Qihan Bio’s facility in Hangzhou, China, may be the best candidates so far. The Chinese company and its U.S. collaborators reported today that they have used the genome editor CRISPR to create the most extensively genetically engineered pigs to date—animals whose tissues, the researchers say, finally combine all the features necessary for a safe and successful transplant into humans.

This is the first prototype,” says Luhan Yang, a geneticist at Qihan Bio. In a preprint published today on bioRxiv, Qihan researchers and collaborators, including Cambridge, Massachusetts–based eGenesis—which Yang co-founded with Harvard University geneticist George Church—described the new generation of animals and various tests on their cells; the researchers have already begun to transplant the pigs’ organs into nonhuman primates, a key step toward human trials.

Qihan and eGenesis aren’t alone in their quest. Several academic and commercial research groups are racing to make up a shortage of life-saving human organs with the comparably sized hearts, kidneys, and livers of pigs. For these cross-species transplants, also known as xenotransplants, the pig’s genome must be re-engineered so that its organs will get along with the new host body. Pigs produce species-specific molecules that set off the human immune system, prompting rejection. Their tissue can also cause abnormal clotting and bleeding when it interacts with human blood. And the pig genome is littered with DNA sequences from viruses that infected the animals long ago and slipped genes into their chromosomes. These sequences, known as porcine endogenous retroviruses (PERVs), have been shown to produce potentially infectious viral particles, though their risk to humans is unclear.