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3D map of human genome shows DNA 'loops'

15 December 2014

By Simon Hazelwood-Smith

Appeared in BioNews 784

A study into the 3D structure of the human genome has revealed the locations of DNA 'loops' at an unprecedented resolution.

The work will help scientists better understand how genes are regulated, the study authors say.

'Our maps of looping revealed thousands of hidden switches that scientists didn't know about before. In the case of genes that can cause cancer or other diseases, knowing where these switches are is vital,' said study author Miriam Huntley from Harvard University.

There are around two metres of DNA in each human cell, which is compacted in a complex looping system to fit into the cell's nucleus. This brings together regions of DNA that can interact with each other, meaning the function of genes can be regulated, switching them 'on' or 'off'.

The research, led by Dr Erez Lieberman Aiden at the Baylor College of Medicine, used a technique called in situ Hi-C to create a 3D map of the structure of DNA. 'For over a century, scientists have known that DNA forms loops inside of cells, and that knowing where the loops are is incredibly important,' said Dr Suhas Rao, who worked on the study.

The research shows that there are around 10,000 loops in the human genome, which is significantly lower than expected. 'The genome project revealed far fewer genes than everyone was expecting; the fact that there are so few loops is a similar surprise,' said Dr Aiden.

Many of the largest loops were found only on the second X chromosome in women, indicating that loops play a major role in switching it off. 'The copy of the X chromosome that is off in females contains gigantic loops that are up to 30 times the size of anything we see in males,' said Huntley.

The work also highlighted differences and similarities in loop structures between eight different cell types, including human cancer and mouse cell lines. Many of the looping patterns were conserved between cell lines, suggesting that many of these structures have been maintained through evolution.

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