Researchers create software-based 3-D genome map

You might think Chia Pets are terra cotta heads with sprouted seeds as hair. But ChIA-PET (chromatin interaction analysis using paired end tag) sequencing is a lot more high-tech than that--it's a technique for understanding 3-D interactions of genetic material in the nucleus that, with the ChIA-PET Tool software, has allowed scientists from the Genome Institute of Singapore to create a 3-D map of the human genome.

The software automatically processes, analyzes, visualizes and manages the ChIA-PET data, including identifying the sites in the DNA where proteins bind and strands of DNA interact together, and then displays the genome in 3-D on a graphical genome browser.

"Dr. Yijun Ruan and his team at Genome Institute of Singapore ... address the fundamental question of how communication occurs between genes and their on and off switches in the human genome," said Dr. Edward Rubin, director of the Joint Genome Institute in the U.S. "The study reveals in three-dimensional space that genes separated linearly by enormous distances in the human genome can come to lie next to each other in the cell when it is time for them to become active."

Knowing where genes are in three-dimensional space, and how they interact and communicate with each other will help researchers to understand how genes are expressed and how they work together in health and disease. This will provide more information about the basic tenets of biology, as well as support the development of new therapeutics that interact with DNA.

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