Cells pack DNA in the nucleus in two different ways

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One study suggests that there are only a limited number of ways to cram DNA into a cell’s nucleus.

A cell’s complete genetic blueprint, or genome, is densely packaged in chromosomes, condensing meters of DNA into a tiny cell vessel just a few microns wide (NS: 08/24/15). But how chromosomes fold to fit inside the nuclei of various species is unclear.

There appear to be two methods of cramming all that DNA, researchers report on May 28. Science. Cells can even change their arrangement by inactivating a molecule called condensin II, the team found.

If chromosomes were pieces of paper, some, like those in humans, would look like a crumpled ball inside the nucleus, explains Claire Hoencamp, molecular biologist at the Dutch Cancer Institute in Amsterdam (SN: 08/10/09). Others, like those of fruit flies (Drosophila melanogaster), look like flat sheets of stacked paper.

In the new study, Hoencamp and his colleagues created heat maps that analyzed how chromosomes in the nuclei of 24 animal, plant and fungal species interacted inside their respective cells. The maps show the average number of connections between chromosomes in a cell’s nucleus – revealing how genetic molecules fold up – “on the scale from white to red,” says Olga Dudchenko, genomics at Baylor College of Medicine in Houston . “The more red there is, the more interactions there are. The less red there is, the less interaction there is.

Throughout evolutionary history, tree of life organisms have switched between different packaging methods, the researchers found. “We worked with a species zoo, and [at first] it looked like a zoo of folding genome models, ”says Dudchenko. “Some cards would look like a checkerboard pattern. Others would look like a mattress with weird x’s on it. Over time, it became clear that many of the same features of chromosome folding appeared over and over again in different species.

Three types of interactions result in stacked sheets of chromosomes, giving heat maps the appearance of a checkerboard or mattress. In one interaction, seen in the ground peanut (Arachis hypogeum) for example, the ends of different chromosomes tend to touch each other. In another, the chromosomes of organisms like fruit flies touch each other in the middle. And in an interaction observed in soft wheat (Triticum aestivum), the arms of different chromosomes fold over each other.

Crumpled ball chromosomes, like those of the red piranha (Pygocentrus nattereri), display a fourth type of interaction. In these structures, one chromosome folds back on itself in an entanglement rather than touching other chromosomes, resulting in large red squares on heat maps.

Breaking down parts of condensin II – a complex of proteins that helps assemble chromosomes as cells divide – can change the organization of a nucleus. Modifications to Condensin II can make a crumpled human nucleus look like a bent fly nucleus, the team found. But some organisms have stacked leaves despite intact condensin II. This means that there may be other factors the researchers have yet to find that cause cells to cram chromosomes into the nucleus in a specific way, says Hoencamp.


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