Chimpanzee study reveals genome variation hotspots

Interesting research coming out of Arizona State University:

Researchers believe that dynamic regions of the human genome -- "hotspots" in terms of duplications and deletions -- are potentially involved in the rapid evolution of morphological and behavioral characteristics that are genetically determined.

Now, an international team of researchers, including a graduate student and an associate professor from Arizona State University, are finding similar hotspots in chimpanzees, which has implications for the understanding of genomic evolution in all species.

"We found that chimpanzees have many copy number variants -- duplications or deletions of large segments of DNA -- in the same regions of the genome as do humans. What this suggests is that some regions of the genomes are inherently unstable in both humans and chimpanzees," says George (P.J.) Perry, a Ph.D. anthropology student working with Anne Stone, an associate professor in ASU's School of Human Evolution and Social Change in the College of Liberal Arts and Sciences.

"This is a relatively new area of research and this is the first time this has been investigated on a genome-wide scale in a population sample of nonhuman primates," Perry says of the findings published May 15 in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS).

Perry, who is the study's lead author, says: "These copy number variants may be very significant from an evolutionary perspective, and they're important to study and understand. We talk about genetic diseases and cures, but first you have to find out that genetic differences such as copy number variants are there. And then you can study what they're involved in and what they mean from a morphological variation and disease standpoint."

Specifically, the study of the processes that lead to variations and mutations within a species can help researchers understand the evolution of copy number differences between species, Perry explains.

"Ultimately, we can use information about within-a-species variation to identify unusual patterns between species," he says. "This may highlight copy number differences between humans and chimpanzees that were somehow involved in the evolution of human-specific traits."

"This study is an important first step, not the ultimate answer, but an exciting first step in studying the evolution of copy number variant regions and their downstream implications for disease and phenotypic variation," Perry says.

In the study, researchers looked at the structural genomic variation in DNA samples of 20 wild-born male chimpanzees.

"We identified 355 copy number variants among the genomes of these 20 unrelated chimpanzees and found that the overall chimpanzee genetic diversity may be more extensive than was previously thought," Perry says.

"This research not only illustrates the importance of studying the genetic variation in other primates to understand our own genome better, but it can also shed light on the diversity and adaptations of our nearest relatives," says Stone, who is one of the study's senior co-authors, along with Charles Lee, an assistant professor in the Department of Pathology at Brigham and Women's Hospital, a teaching affiliate of Harvard Medical School.

The PNAS paper is: George H. Perry, Joelle Tchinda, Sean D. McGrath, Junjun Zhang, Simon R. Picker, Angela M. Cáceres, A. John Iafrate, Chris Tyler-Smith, Stephen W. Scherer, Evan E. Eichler, Anne C. Stone, and Charles Lee (2006) "Hotspots for copy number variation in chimpanzees and humans" PNAS published May 15, 2006, 10.1073/pnas.0602318103