Their findings, published in Science magazine, reveal how long strands of DNA code are folded and tightly packed into the nucleus of a human cell.
Unfolded, the cell's genome - those strands of DNA code - would be approximately 2m in length.
The team showed how this is organised into a tight ball to fit inside a nucleus, which is about one hundredth of a millimetre in diameter.
The US-based research team developed improved DNA sequencing and computational methods to build a model of the genome.
 |  This is the first glimpse we're getting of a whole genome in 3D  Job Dekker University of Massachusetts |
Job Dekker, from the University of Massachusetts Medical School, led the research.
He explained to BBC News that, with its new approach, his team had discovered important patterns in the shape of the genome.
"For a given part of the genome, we can determine its neighbours," he said.
"And if you can do that for every gene - if you know which other genes surround it - you can work your way back computationally to calculate the structure.
"This is the first glimpse we're getting of a whole genome in 3D."
Professor Julian Parkhill visits the Wellcome Collection to unravel the science behind the genome
DNA is bundled into chromosomes. The combination of DNA and protein that makes up these chromosomes is called chromatin.
Dr Dekker explained how a 3D view showed how chromatin's complicated folding pattern was important in the regulation of genes.
"We now see that things that are far apart along the linear sequence of the genome are actually next to each other in the folded structure," he said.
"They're close together in the structure, and they're talking to each other."
This constant communication is the basis of the regulation that keeps a cell healthy and functional.
This means that a detailed view of the genome's structure could provide a new window into diseases such as cancer, which is caused by errors in the genetic code.
"Maybe we will be able to predict these [disease-causing] changes better now," said Dr Dekker.
The team also discovered that the human genome is organised into two separate compartments, keeping active genes accessible while keeping inactive DNA in a sort of storage compartment.
The chromosomes snake in and out of the two compartments - separating their active and inactive sections.
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