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Mapping Recombination Hotspots

Chromosomes (green) and their genetic recombination hotspots (red).Fatima Smagulova, Ph.D., USU, and Kevin Brick, Ph.D., NIDDK, NIH.

Researchers have zoomed in on mouse chromosomes to map hotspots of genetic recombination — sites where DNA breaks and reforms to shuffle genes. The findings move scientists one step closer to understanding how mammals evolve and respond to their environments.

Genetic rearrangements in the cells that form sperm and eggs ensure that the set of genes passed on to every sperm and egg cell is unique. However, abnormalities brought on by this process are the leading known cause of miscarriages, congenital birth defects and mental retardation nationwide.

Recombination is known to occur at discrete regions of the genome called hotspots. Researchers have recently identified recombination hotspots in humans. But these hotspots were mapped from a large pool of people with different genetic backgrounds and at a resolution that didn’t allow for fine analysis.

In a new study, scientists set out to develop a technique to generate a more detailed map. They used precursors of mouse sperm cells for their study because they needed a population with a specific and identical genetic background. The research team was led by Dr. R. Daniel Camerini-Otero at NIH’s �����鶹��Ƶ Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and Dr. Galina Petukhova at the Uniformed Services University of Health Sciences. NIH’s �����鶹��Ƶ Institute of General Medical Sciences (NIGMS) also helped fund the study. The results appeared online on April 3, 2011, in Nature.

The researchers isolated and sequenced sites that were bound by a protein known to be involved in recombination. This provided a snapshot of all the pieces of DNA taking part in recombination. Computational techniques allowed the scientists to use this set of short DNA pieces to make a map of where chromosomes have an increased potential to be broken and to come back together in new ways. This map, of about 10,000 hotspots, shows where diversity can arise in the genome and where the process can go awry.

Camerini-Otero compared the map’s new level of precision to the difference between being able to zoom in to see a city block to being able to zoom in to see each building on that block. “What we were looking for was resolution that was much higher than ever seen before,” says Camerini-Otero. “Now that we can actually see these individual events, we can begin to understand their molecular structure.”

The researchers plan to use this map to further understand evolution as well as chromosomal abnormalities brought on by recombination. With this initial study a success, they also hope to apply the same techniques to study recombination in people in the near future.

“Now that we have mapped recombination hotspots genome-wide, we can actually carry out studies on the whole mouse genome. This will be very beneficial in extending our knowledge to organisms as complex as humans,” Petukhova says. “Faulty recombination can lead to infertility or birth defects, and this work brings us closer to our ultimate goal of helping to prevent these health issues.”