How Cells Pack Tangled DNA Into Neat Chromosomes


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A human cell carries in its nucleus two meters of spiraling DNA, break up up among the many 46 slender, double-helical molecules which are its chromosomes. More often than not, that DNA appears to be like like a tangled ball of yarn—diffuse, disordered, chaotic. However that messiness poses an issue throughout mitosis, when the cell has to make a duplicate of its genetic materials and divide in two. In preparation, it tidies up by packing the DNA into dense, sausagelike rods, the chromosomes’ most acquainted type. Scientists have watched that course of via a microscope for many years: The DNA condenses and organizes into discrete models that steadily shorten and widen. However how the genome will get folded inside that construction—it’s clear that it doesn’t merely contract—has remained a thriller. “It’s actually on the coronary heart of genetics,” mentioned Job Dekker, a biochemist on the College of Massachusetts Medical Faculty, “a basic facet of heredity that’s all the time been such an incredible puzzle.”

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Authentic story reprinted with permission from Quanta Journal, an editorially unbiased publication of the Simons Basis whose mission is to boost public understanding of science by overlaying analysis developments and tendencies in arithmetic and the bodily and life sciences.

To unravel that puzzle, Dekker teamed up with Leonid Mirny, a biophysicist on the Massachusetts Institute of Expertise, and William Earnshaw, a biologist on the College of Edinburgh in Scotland. They and their colleagues used a mix of imaging, modeling and genomic methods to grasp how the condensed chromosome types throughout cell division. Their outcomes, printed lately in *Science and confirmed partially by experimental proof reported by a European group on this week’s problem of the journal, paint an image through which two protein complexes sequentially manage the DNA into tight arrays of loops alongside a helical backbone.

The researchers collected minute-by-minute knowledge on chromosomes—utilizing a microscope to see how they modified, in addition to a expertise referred to as Hello-C, which gives a map of how incessantly pairs of sequences within the genome work together with each other. They then generated subtle pc simulations to match that knowledge, permitting them to calculate the three-dimensional path the chromosomes traced as they condensed.

Their fashions decided that within the lead-up to mitosis, a ring-shaped protein molecule referred to as condensin II, composed of two linked motors, lands on the DNA. Every of its motors transfer in reverse instructions alongside the strand whereas remaining hooked up to at least one one other, inflicting a loop to type; because the motors proceed to maneuver, that loop will get bigger and bigger. (Mirny demonstrated the method for me by clasping a bit of his pc’s energy twine with each fingers, held knuckles to knuckles, via which he then proceeded to push a loop of twine.) As tens of hundreds of those protein molecules do their work, a collection of loops emerges. The ringlike proteins, positioned on the base of every loop, create a central scaffolding from which the loops emanate, and your entire chromosome turns into shorter and stiffer.

These outcomes lent assist to the thought of loop extrusion, a previous proposal about how DNA is packaged. (Loop extrusion can be chargeable for stopping duplicated chromosomes from changing into knotted and entangled, in accordance with Mirny. The mechanics of the looped construction trigger sister chromatids to repel one another.) However what the scientists noticed subsequent got here as extra of a shock and allowed them to construct additional element into the loop extrusion speculation.

After about 10 minutes, the nuclear envelope protecting the chromosomes collectively broke down, giving a second ring-shaped motor protein, condensin I, entry to the DNA. These molecules carried out loop extrusion on the loops that had already shaped, splitting every into round 5 smaller loops on common. Nesting loops on this approach enabled the chromosome to turn into narrower and prevented the preliminary loops from rising giant sufficient to combine or work together.

Based on the researchers’ fashions, one main facet of the chromosome’s folding course of is the formation of nested loops. First, a ring-shaped motor protein (crimson) lands on DNA and extrudes a loop. Later, a second protein (blue) extrudes loops on prime of that one. When many such molecules throughout your entire size of the DNA do that, the chromosome compacts.

Dr. Anton Goloborodko

After roughly 15 minutes, as these loops have been forming, the Hello-C knowledge confirmed one thing that the researchers discovered much more surprising. Usually, sequences positioned shut collectively alongside the string of DNA have been most certainly to work together, whereas these farther aside have been much less seemingly to take action. However the group’s measurements confirmed that “issues [then] type of got here again once more in a circle,” Mirny mentioned. That’s, as soon as the space between sequences had grown even additional, they once more had the next likelihood of interacting. “It was apparent from the primary look at this knowledge that we’d by no means seen one thing like this earlier than,” he mentioned. His mannequin urged that condensin II molecules assembled right into a helical scaffold, as within the well-known Leonardo staircase discovered within the Chambord Citadel 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 course of instantly solves three issues,” Mirny mentioned. “It creates a scaffold. It linearly orders the chromosome. And it compacts it in such a approach that it turns into an elongated object.”

“That was actually stunning to us,” Dekker mentioned—not solely as a result of they’d by no means noticed the rotation of loops alongside a helical axis, however as a result of the discovering faucets right into a extra basic debate. Particularly, are chromosomes only a collection of loops, or do they spiral? And in the event that they do spiral, is it that your entire chromosome twists right into a coil, or that solely the inner scaffolding does? (The brand new research factors to the latter; the researchers attribute the previous helix-related speculation to experimental artifacts, the results of isolating chromosomes in a approach that promoted extreme spiraling.) “Our work unifies many, many observations that individuals have collected through the years,” Dekker mentioned.

“This [analysis] gives a revolutionary diploma of readability,” mentioned Nancy Kleckner, a molecular biologist at Harvard College. “It takes us into one other period of understanding how chromosomes are organized at these late levels.”

This collection of pictures illustrates how a compacted chromosome takes form. Ring-shaped motor proteins (crimson) type a helical scaffold. Folded loops of DNA emanate from that spiraling axis in order that they are often packed tightly right into a cylindrical rod.

Dr. Anton Goloborodko

Different consultants within the subject discovered these outcomes much less stunning, as a substitute deeming the research extra noteworthy for the small print it offered. Hints of the overall chromosomal meeting the researchers described have been already “within the air,” in accordance with Julien Mozziconacci, a biophysicist at Sorbonne College in France. The extra novel points of the work, he mentioned, lay within the researchers’ assortment of Hello-C knowledge as a operate of time, which allowed them to pinpoint particular constraints, such because the sizes of the loops and helical turns. “I believe it is a technical tour de drive that permits us to see for the primary time what individuals have been pondering,” he mentioned.

Nonetheless, Dekker cautioned that, though it’s been recognized for a while that condensins are concerned on this course of—and even though his group has now recognized extra particular roles for these “molecular fingers that cells use to fold chromosomes”—scientists nonetheless don’t perceive precisely how they do it.

“If condensin is organizing mitotic chromosomes on this method, how does it achieve this?” mentioned Kim Nasmyth, a biochemist on the College of Oxford and a pioneer of the loop extrusion speculation. “Till we all know the molecular mechanism, we are able to’t say for certain whether or not condensin is certainly the one driving all this.”

That’s the place Christian Häring, a biochemist on the European Molecular Biology Laboratory in Germany, and Cees Dekker, a biophysicist (unrelated to Job Dekker) at Delft College of Expertise within the Netherlands, enter the image. Final yr, they and their colleagues instantly demonstrated for the primary time that condensin does transfer alongside DNA in a check tube—a prerequisite for loop extrusion to be true. And on this week’s problem of Science, they reported witnessing an remoted condensin molecule extruding a loop of DNA in yeast, in actual time. “We lastly have visible proof of this taking place,” Häring mentioned.

And it occurred nearly precisely as Mirny and his group predicted it might for the formation of their bigger loops—besides that within the in vitro experiment, the loops shaped asymmetrically: The condensin landed on the DNA and reeled it in from just one aspect, somewhat than in each instructions as Mirny initially assumed. (Because the experiments concerned condensin from yeast, and solely examined a single molecule at a time, they might neither affirm nor refute the opposite points of Mirny’s fashions, specifically the nested loops and helical scaffold.)

As soon as researchers have utterly unpacked that biochemistry—and performed comparable research on how chromosomes unwind themselves—Job Dekker and Mirny assume their work can lend itself to a spread of sensible and theoretical functions. For one, the analysis may inform potential most cancers therapies. Most cancers cells divide rapidly and incessantly, “so something we find out about that course of can assist particularly goal these sorts of cells,” Dekker mentioned.

It may additionally present a window into what goes on within the chromosomes of cells that aren’t dividing. “It has wider implications for, I imagine, every other factor the cell does with chromosomes,” Job Dekker mentioned. The condensins he and his colleagues are finding out have shut kinfolk, referred to as cohesins, that assist with organizing the genome and creating loops even when the DNA isn’t getting compacted. That folding course of may have an effect on gene expression. Loop extrusion principally brings pairs of loci collectively, nevertheless briefly, on the base of the rising or shrinking loop—one thing that might very nicely be taking place throughout gene regulation, when a gene must be in bodily contact with a regulatory component that could be positioned fairly a distance away alongside the chromosome. “We now have such a strong system to review this course of,” Dekker mentioned.

“I believe there’s an unimaginable quantity of synergy between the issues we are able to study at completely different components of the cell cycle,” added Geoff Fudenberg, a postdoctoral researcher on the College of California, San Francisco, who beforehand labored in Mirny’s lab. Understanding how chromosomes endure such a “dramatic transition” throughout mitosis, he mentioned, may additionally reveal so much about what they’re doing “beneath the floor” when cells usually are not dividing and sure actions and behaviors are much less clear.

Mirny factors out that any such folding may additionally present insights into different processes in cells that contain energetic adjustments in form or construction. Proteins get folded largely by interactions, whereas motor processes create the cytoskeleton within the cytoplasm. “Now we got here to comprehend that chromosomes could also be one thing in between,” Mirny mentioned. “We have to acquire a greater understanding of how these kind of energetic methods self-organize to create advanced patterns and important constructions.”

Earlier than that’s attainable, the researchers should affirm and flesh out the answer they’ve proposed to what Job Dekker referred to as a “nice puzzle.” Kleckner has excessive hopes as nicely. “This work units the inspiration for an entire new mind-set about what is perhaps occurring,” she mentioned.

Authentic story reprinted with permission from Quanta Journal, an editorially unbiased publication of the Simons Basis whose mission is to boost public understanding of science by overlaying analysis developments and tendencies in arithmetic and the bodily and life sciences.

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