The fact that humans have bigger brains than their closest cousin, the chimpanzee, may have more to do with which genes are turned off than which are turned on.

According to a new study, one of the most rapidly evolving segments of the human genome occurs in a DNA region that doesn’t actually code for proteins (often called “junk DNA”), but seems to be expressed during the early stage of brain development.

In research published in the Aug. 17 issue of Nature, a team of scientists from the U.S., Belgium, and France, sought to identify genetic sequences important in human evolution by comparing the genomes of humans, chimps, and 12 other species. They looked for stretches of DNA that remained relatively unchanged during the hundreds of thousands of years that separated the emergence of the chicken and the chimp, but then changed rapidly between chimps and humans.

This method allowed them to identify 49 Human Accelerated Regions (HARs), or segments of DNA that changed primarily in humans. The one that changed the most between humans and chimpanzees was named HAR1. 

Humans and chimps share 96 percent of their DNA. But, since the completion of the human genome map in 2003, scientists have been scouring its 3 million base pairs, looking for genes and mutations that are uniquely ours.

The 118-base pair HAR1 segment developed changes in just two base pairs during the 310 million years that separated the divergence of chickens and chimpanzees. But 18 base pair changes happened during the 5 million years between the divergence of chimps and humans.

“It’s so extreme,” said Katherine Pollard, a geneticist at the University of California, Davis, and the study’s lead author. “It’s been a major acceleration. It’s just totally unexpected.”

The rapid rate of change suggests that changes within that sequence may have given humans a significant adaptive advantage.

HAR1 is one of 47 HARs the researchers found that do not code for proteins. The segment is actually part of two overlapping RNA genes—called HAR1F and HAR1R—which are transcribed from DNA, but whose function is then unknown.

Pollard and other scientists believe that such genes can be as important as those that govern the creation of proteins.

For instance, the scientists discovered that HAR1F is expressed in embryonic brain cells during a crucial point in brain development. Between week 7 and 19 of gestation, RNA from the gene can be found in cells involved in the formation of the brain’s cortex, or outer layer. The finding suggests that HAR1F could play a unique role in the evolution of the human brain, Pollard said.

“It’s at the right place at the right time,” he said. “We still don’t know what it actually does, but it could play a role in the development of the cortex, which is particularly well developed in humans.”

Andrew Clark, a geneticist at Cornell University, has identified significant changes on the human-chimp branch, including large numbers of substitutions along genes for the senses of smell and hearing. Although Pollard has discovered an RNA gene at work, Clark said it’s hard to examine what function a gene serves when it doesn’t make a protein.

“The difficulty is that you can’t tell,” he said. “You can’t classify these genes into functional categories.”

Originally published August 29, 2006


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