Complex organisms have complex genomes. While bacteria and archaea keep all of their genes on a single loop of DNA, humans scatter them across 23 large DNA molecules called chromosomes; chromosome counts range from a single chromosome in males of an ant species to more than 400 in a butterfly.

There have been indications that chromosomes matter for an organism's underlying biology. Specialized structures within them influence the activity of nearby genes. And studies show that areas on different chromosomes will consistently be found next to each other in the cell, suggesting their interactions are significant.

So how do we square these two facts? Chromosome counts vary wildly and sometimes differ between closely related species, suggesting the actual number of chromosomes doesn't matter much. Yet the chromosomes themselves seem to be critical for an organism's genome to function as expected. To explore this issue, two different groups tried an audacious experiment: using genome editing, they gradually merged a yeast's 16 chromosomes down to just one giant molecule. And, unexpectedly, the yeast were mostly fine.

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Combining the yeast's 16 chromosomes involved repeated applications of the same process. Chromosomes are simply big DNA molecules, and they have two structures that have to be managed. The first is at each of their two ends, where there's a structure called a telomere. The chromosome's loose ends are difficult to make copies of when a cell divides, are susceptible to damage, and could trigger the cell's response to dangerous damage to its DNA. The telomere handles all of that, protecting the ends and providing a mechanism for their duplication.

The other issue is something called a centromere. This can reside anywhere in the chromosome and plays a critical role when cells divide. It keeps both copies of the chromosome linked together and is then the site of where fibers are attached that pull the two chromosomes apart, one into each daughter cell. Having two centromeres on a single chromosome is a problem, because fibers could attach in a way that pulled a single chromosome toward both of the daughter cells, causing it to break apart.

So, to combine two chromosomes, you have to chop off two of the telomeres, fuse the new ends to form a single chromosome, and chop out one of the centromeres.

Chopping things up is exactly what CRISPR DNA editing technology is good at. In designing their editing system, the researchers guided the CRISPR proteins to specific sites near telomeres, where they cut the chromosomes. Additional DNA molecules they put into these cells favored a repair of the cuts that fused the cut ends of the chromosomes. Additional CRISPR targeting would cut out one of the centromeres. Fusing pairs of chromosomes cut the 16 chromosomes down to eight. Further fusions could continue to reduce the total count.

In one case, the researchers continued this process down to a single giant chromosome. But the second group got stuck at two; attempting to combine them kept killing the cells. The researchers think they know why this happened, and we'll get back to that in a moment.

Remarkably healthy

The resulting strains of yeast (with only one or two chromosomes, depending on the lab) were... remarkably normal. They grew more slowly than a normal strain but still grew under a variety of conditions. They were more sensitive to how they obtained critical building blocks, like nitrogen and carbon, but could still survive no matter how they were fed. And tests of their gene activity showed very minimal changes compared to a wild-type strain—only 28 genes out of more than 5,800. The normally structured arrangement of DNA inside the cell was completely disrupted, but this didn't seem to affect the yeast's health.

The big problems came with mating (yes, yeast have sex). Yeast's default state is carrying a single set of chromosomes. When they mate, two yeast fuse, creating a single yeast with two sets of chromosomes. This can divide and maintain itself in this two-chromosome-set state, or it can form spores, each of which has a single set of chromosomes. Tests showed that, while cells with a single-chromosome genome could mate and form spores, the viability of these spores was lower than in a normal strain.

Attempting to mate normal strains with those carrying fewer chromosomes led to very low fertility, since the chromosomes would have difficulty lining up to be distributed to daughter cells normally. The researchers suggested this could be useful; doing genetic engineering on cells with fewer chromosomes would mean that the engineered genes wouldn't end up mixing with the yeast population if it were to escape into the wild (or a bakery).

So, why do these yeast have problems? One indication is that the single enormous chromosome makes copying DNA and separating DNA during cell division more difficult. While very few genes saw altered activity, a number of the ones that were changed are involved in stress responses.

A second problem comes from changing the number of telomeres at ends of chromosomes. Normally, genes near telomeres have their activity lowered or shut down; yeast tend to have genes near there that are only needed under specific environmental conditions. A number of these genes ended up in the middle of the giant chromosome as a result of all the DNA editing and so may not be regulated properly. In addition, the fact that there were only two telomeres means that the proteins that normally shut nearby genes were present in excess, allowing the gene-shutdown effect to spread further from the two telomeres that remained. In other words, some genes that would normally be far enough away from the telomeres may have found themselves shut down on the giant chromosome.

All of which may explain the yeast's lower growth rate and difficulty with some specific environmental conditions. It may also explain why some specific combinations of chromosome fusions failed, leaving one research group stuck at two. The nice thing, however, is that these problems should be subject to evolutionary changes. By growing the single-chromosome-carrying yeast for many generations in culture, we should see them adapt to their odd genome. And those changes might give us some indications of what aspects of chromosome biology are critical to normal genome activity, and which ones are just historical accidents.

Nature, 2017. DOI: 10.1038/s41586-018-0382-x, 10.1038/s41586-018-0374-x (About DOIs).