Researchers decipher 3-D structure of human genome

October 13, 2009 - 0:0

WASHINGTON (AFP) -– Scientists have decoded the three dimensional structure of the human genonome, opening the way for new insights into its functioning and structures.

“By breaking the genome into millions of pieces, we created a spatial map showing how close different parts are to one another,” said Nynke van Berkum, one of two main authors of the study, which appears in the journal Science.
“We made a fantastic three-dimensional jigsaw puzzle and then, with a computer, solved the puzzle,” said Berkum, a postdoctoral researcher at University of Massachussets Medical School.
To do it, scientists used a new technology called 'Hi-C' that allowed them to solve previously unanswered questions about how each human cell could contain some three million pairs of base DNA and still be able to access functionally crucial segments.
“We've long known that on a small scale, DNA is a double helix. But if the double helix didn't fold further, the genome in each cell would be two meters long,” said Erez Lieberman-Aiden, a graduate student in the Harvard-MIT Division of Health Science and Technology and a researcher at Harvard and the Broad Institute.
“Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter. This new approach enabled us to probe exactly that question,” said Lieberman-Aiden, the study's other main author.
The researchers found that the human genome is organized in two distinct compartments that keep active genes accessible to proteins and separate from densely packed stocks of inactive DNA.
Chromosomes snake from one compartment to another as their DNA alternates between active and inactive stretches of the genome.
The research also revealed how the genome employs an unusual form of organization known in mathematics as a “fractal” that enables the cell to pack DNA into its nucleus at a density three trillion times greater than a computer chip.
It manages that while avoiding knots and tangles that might interfere with the cell's ability to read its own genome, while allowing the DNA to easily unfold and refold during gene activation, gene repression, and cell replication.
“Nature's devised a stunningly elegant solution to storing information -- a super-dense, knot-free structure,” says senior author Eric Lander, director of the Broad Institute.