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Cells clump DNA into the nucleus in two different ways

One study suggests that there are only so many ways to put DNA into the nucleus of a cell.

The genetic plan or complete genome of a cell is densely packed into chromosomes, condensing meters of DNA into a tiny cell vessel only micrometers wide (SN: 8/24/15). But it is not clear how chromosomes bend to fit within the nuclei of various species.

There seem to be two methods for putting all that DNA in, researchers report in the May 28 issue of the journal Science. The team found that cells can even flip the arrangement they have by inactivating a molecule called condensin II.

If the chromosomes were scraps of paper, some, like those of humans, would look like a wrinkled ball inside the nucleus, says Claire Hoencamp, a molecular biologist at the Netherlands Cancer Institute in Amsterdam (SN: 8/10/09). Others, such as those of fruit flies (Drosophila melanogaster), look like flat sheets of stacked paper.

In the new study, Hoencamp and colleagues created heat maps that analyzed how the chromosomes in the nuclei of 24 animal, plant, and fungal species interacted within their respective cells. The maps show the average number of connections between chromosomes in a cell's nucleus – revealing how genetic molecules fold – "on a white-to-red scale," says Olga Dudchenko, a genomic at Baylor College of Medicine in Houston. “The more red, the more interactions. The less red, the less interactions. "

Throughout evolutionary history, life-tree organisms have switched between different packaging methods, the researchers found. “We worked with a zoo of species and (at first) it looked like a zoo of genome folding patterns,” Dudchenko says. “Some maps would look like a chess pattern. Others would look like a strange x-mattress. ”Over time, it became clear that many of the same folding features of chromosomes appeared again and again in different species.

Three types of interactions result in stacked chromosome sheets, giving rise to heat maps that appear on chess or mattress. In an interaction, seen in ground peanuts (Arachis hypogaea), for example, the ends of different chromosomes tend to touch. In another, the chromosomes of organisms such as fruit flies touch in the middle. And in an interaction observed in bread wheat (Triticum aestivum), the arms of different chromosomes folded on top of each other.

Chromosomes in the form of wrinkled balls, such as those of the red piranha (Pygocentrus nattereri), have a fourth type of interaction. In these structures, a chromosome folded over itself in a tangle instead of touching other chromosomes, resulting in large red squares on heat maps.

The rupture of parts of condensin II, a protein complex that helps assemble chromosomes as cells divide, can change which organization has a nucleus. Adjustments to condensin II can make a wrinkled human core look like the core of a folded fly, the team found. But some organisms have leaves stacked despite having condensin II intact. That means there may be other factors that researchers have yet to discover that push cells to put chromosomes in the nucleus in a specific way, Hoencamp says.

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