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The Human Genome in 3-D

New technology reveals how DNA molecules pack themselves inside a cell nucleus.
October 8, 2009

Unfurled, the human genome would contain approximately six feet of DNA. Amazingly, all of that length is packed into a cell nucleus about three micrometers in diameter–roughly one-tenth the width of a human hair.

Fractal genome: Researchers theorize that DNA molecules inside the cell nucleus are packed into a compact, unknotted structure called a fractal globule (shown above), making it easy to pack and unpack. Adjacent regions in the linear chain of DNA are indicated using similar colors.

New technology that makes it possible to assess the three-dimensional interactions among different parts of the genome has revealed how these molecules are packed into such a tiny space. The findings could also yield new clues to genome regulation–how specific genes are turned on and off.

While scientists have previously been able to resolve the three-dimensional structure of parts of the genome, a new study is the first to do so on a genome-wide scale. “Our technology is kind of like MRI for genomes,” says Erez Lieberman-Aiden, a researcher in the Harvard-MIT Division of Health Sciences and Technology and one of the authors of a new paper detailing the work. (Lieberman was named to Technology Review’s TR35 list young innovators this year).

DNA has multiple levels of organization–the linear sequence of bases, its famous helical structure, and higher-order formations that wrap it around proteins and coil it to form chromosomes. But identifying how DNA is organized at these higher levels across the genome has been difficult. “We have the entire linear sequence of the genome, but no one knows even the principles of how DNA is organized in higher-order space,” says Tom Misteli, a scientist at the National Cancer Institute, in Bethesda, MD, who was not involved in the study.

A growing pool of research also shows that this organization is crucial for regulating gene activity. For example, genes must be unwound before they can be transcribed into proteins. And some genes are turned on only when bound to DNA sequences on entirely different chromosomes, says Misteli. “That means they have to come together in three-dimensional space.”

In a new method, dubbed Hi-C, scientists first use a preservative such as formaldehyde to fix the three-dimensional structure of a folded DNA molecule in place. This way, gene sequences that are close together in the three-dimensional structure but not necessarily adjacent in the linear sequence become bonded together. The fixed genome is then broken into a million pieces using a DNA-cutting enzyme. But the DNA segments that were stuck together during the fixation process remain bonded together.

Researchers then add a marker called biotin to the ends of the bonded genome fragments and use another enzyme to glue the ends of each fragment together, making a circle of DNA. The biotin-marked pieces are then sequenced, revealing which pieces of DNA were physically close together in the three-dimensional conformation.

While scientists have been working on some aspects of the Hi-C technology for several years, the rapidly declining cost of gene sequencing has just recently made it possible to tackle the whole genome. “Only now, with the development of novel sequencing technologies, can we pull this off,” says Job Dekker, a biologist at the University of Massachusetts Medical School, in Amherst, and senior author of the paper. The findings are published today in the journal Science.

DNA origami: The linear sequence of a segment of chromosome 14 has been folded in a fractal folding pattern using origami, the Japanese art of paper folding. Researchers believe that DNA employs a three-dimensional fractal folding pattern inside the cell nucleus.

Using this new technology, the researchers identified two organizing principles in DNA. Chromosomes appear to be folded in such a way that active genes–those that are being made into proteins–are close together, and inactive genes are also close together, properties that had previously only been observed on a smaller scale. “The active stuff tends to be in one compartment that is not so densely packed,” says Lieberman. “The second compartment is like a storage compartment–it’s a bit denser and holds most of the genome.” Adds Dekker: “We think this is an efficient way for cells to organize chromatin within the nucleus.”

The researchers also developed a model for how they think DNA is organized within these active and inactive compartments. DNA molecules appear to form a polymer structure known as a fractal globule, in which segments that are close to each other in the linear sequence are also close in the three-dimensional globule. Lieberman likens the structure to a fresh packet of ramen noodles, before they are stirred into a tangled glob. “It suggests there is a kind of beautiful un-entangled structure that the genome folds into,” says Lieberman. “It has no knots, and a very simple physical process can be used to pull out a piece of fractal globule and then put it back.”

The technology makes it possible to tackle a number of questions, such as how the three-dimensional structure of the genome varies among cell types, among organisms, and between normal and cancerous cells. “Maybe this could help explain why cancer genomes are so misregulated,” says Dekker.

But it’s not yet clear how quickly the technology will catch on. While fast, cheap sequencing has made such experiments possible, “it is still a major undertaking,” says Misteli. That may change as prices continue to fall.

The researchers now hope to improve the resolution of the technology. Currently, they can examine the three-dimensional structure of the genome on a megabase scale–in units of a million DNA letters–but they are ultimately aiming for a kilobase resolution. “I think there are more structural features we haven’t discovered,” says Dekker. Increasing the resolution by a factor of 10 will require a hundredfold more sequencing, he says.

Scientists also want to explore exactly how the three-dimensional structure of the genome affects regulation. “What happens when you move a gene artificially from an inactive to an active area?” asks Dekker. “People have started to develop methods to move genes around in the nucleus, but the results are generally mixed.”

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