Genome Engineering

Researchers at the University of California have created the first three-dimensional map of the human genome. The team at USC describes the genomic DNA strand as being ‘so long that if a nucleus were the size of a soccer ball, the strand of DNA inside it could be unraveled to stretch more than 30 miles long.’ The research was published online in Nature on Christmas Day.

Inside the nucleus, DNA forms hundreds of millions of contacts with itself. Using a new technique for genome-wide mapping of chromatin interactions, known as tethered conformation capture (TCC), USC researchers plotted out the location of each of those DNA-on-DNA contacts and used sophisticated computer algorithms to model the results in 3D.

By analyzing the differences and similarities in genome structure between various cells, the scientists were able to discern what basic principles of 3D organization are. In addition, this technique will allow scientists to see where each gene is located relative to any other gene, and how this arrangement is important to cellular functions.

By carrying out a statistical analysis of many genomes, they were able to determine “preferred positions” for the majority of interchromosomal interactions, providing an idea of how the DNA strand is most likely to appear.

“It provides you with a completely new prospective in the genome,” Lin Chen, professor of molecular biology at the USC Dornsife College of Letters, Arts and Sciences said. The study will appear on the Nature Biotechnology website on December 25 ahead of its publication in the print edition.

This map could be used to identify potentially cancerous cells based on structural defects in the cell’s genome.

Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2011). Genome architectures revealed by tethered chromosome conformation capture and population-based modeling Nature Biotechnology DOI: 10.1038/nbt.2057