How Cells Pack Tangled DNA Into Neat Chromosomes

A human cell carries in its nucleus two meters of spiraling DNA, split up among the 46 slender, double-helical molecules that are its chromosomes. Most of the time, that DNA looks like a tangled ball of yarn — diffuse, disordered, chaotic. But that messiness poses a problem during mitosis, when the cell has to make a copy of its genetic material and divide in two. In preparation, it tidies up by packing the DNA into dense, sausagelike rods, the chromosomes’ most familiar form. Scientists have watched that process through a microscope for decades: The DNA condenses and organizes into discrete units that gradually shorten and widen. But how the genome gets folded inside that structure — it’s clear that it doesn’t simply contract — has remained a mystery. “It’s really at the heart of genetics,” said Job Dekker, a biochemist at the University of Massachusetts Medical School, “a fundamental aspect of heredity that’s always been such a great puzzle.”

To solve that puzzle, Dekker teamed up with Leonid Mirny, a biophysicist at the Massachusetts Institute of Technology, and William Earnshaw, a biologist at the University of Edinburgh in Scotland. They and their colleagues used a combination of imaging, modeling and genomic techniques to understand how the condensed chromosome forms during cell division. Their results, published recently in Science and confirmed in part by experimental evidence reported by a European team in today’s issue of the journal, paint a picture in which two protein complexes sequentially organize the DNA into tight arrays of loops along a helical spine.

The researchers collected minute-by-minute data on chromosomes — using a microscope to see how they changed, as well as a technology called Hi-C, which provides a map of how frequently pairs of sequences in the genome interact with one another. They then generated sophisticated computer simulations to match that data, allowing them to calculate the three-dimensional path the chromosomes traced as they condensed.

Their models determined that in the lead-up to mitosis, a ring-shaped protein molecule called condensin II, composed of two connected motors, lands on the DNA. Each of its motors move in opposite directions along the strand while remaining attached to one another, causing a loop to form; as the motors continue to move, that loop gets larger and larger. (Mirny demonstrated the process for me by clasping a piece of his computer’s power cord with both hands, held knuckles to knuckles, through which he then proceeded to push a loop of cord.) As tens of thousands of these protein molecules do their work, a series of loops emerges. The ringlike proteins, positioned at the base of each loop, create a central scaffolding from which the loops emanate, and the entire chromosome becomes shorter and stiffer.

Those results lent support to the idea of loop extrusion, a prior proposal about how DNA is packaged. (Loop extrusion is also responsible for preventing duplicated chromosomes from becoming knotted and entangled, according to Mirny. The mechanics of the looped structure cause sister chromatids to repel each other.) But what the scientists observed next came as more of a surprise and allowed them to build further detail into the loop extrusion hypothesis.

After about 10 minutes, the nuclear envelope keeping the chromosomes together broke down, giving a second ring-shaped motor protein, condensin I, access to the DNA. Those molecules performed loop extrusion on the loops that had already formed, splitting each into around five smaller loops on average. Nesting loops in this way enabled the chromosome to become narrower and prevented the initial loops from growing large enough to mix or interact.

After approximately 15 minutes, as these loops were forming, the Hi-C data showed something that the researchers found even more unexpected. Typically, sequences located close together along the string of DNA were most likely to interact, while those farther apart were less likely to do so. But the team’s measurements showed that “things [then] kind of came back again in a circle,” Mirny said. That is, once the distance between sequences had grown even further, they again had a higher probability of interacting. “It was obvious from the first glance at this data that we’d never seen something like this before,” he said. His model suggested that condensin II molecules assembled into a helical scaffold, as in the famous Leonardo staircase found in the Chambord Castle in France. The nested loops of DNA radiated out like steps from that spiraling scaffold, packing snuggly into the cylindrical configuration that characterizes the chromosome.

“So this single process immediately solves three problems,” Mirny said. “It creates a scaffold. It linearly orders the chromosome. And it compacts it in such a way that it becomes an elongated object.”

“That was really surprising to us,” Dekker said — not only because they’d never observed the rotation of loops along a helical axis, but because the finding taps into a more fundamental debate. Namely, are chromosomes just a series of loops, or do they spiral? And if they do spiral, is it that the entire chromosome twists into a coil, or that only the internal scaffolding does? (The new study points to the latter; the researchers attribute the former helix-related hypothesis to experimental artifacts, the result of isolating chromosomes in a way that promoted excessive spiraling.) “Our work unifies many, many observations that people have collected over the years,” Dekker said.

“This [analysis] provides a revolutionary degree of clarity,” said Nancy Kleckner, a molecular biologist at Harvard University. “It takes us into another era of understanding how chromosomes are organized at these late stages.”