Humans are clearly different from chimpanzees. The question is, why? According to researchers at the Stanford University School of Medicine, it may boil down in part to what we don't have, rather than what we do. The loss of snippets of regulatory DNA, the scientists found, could be the reason why, for example, humans lack the penile spines found in many other mammals, and also why specific regions of our brains are larger than those of our closest relatives.
Understanding these and other differences may help us learn what it means to be human. But it took the recent advent of whole-genome sequencing of several species and an open-minded, combined computational and experimental approach to reveal the particular two-steps-forward, one-step-back evolutionary dance that set us apart from other primates millions of years ago.
"Rather than looking for species-specific differences in specific genes or genomic regions that exist in humans, we asked, 'Are there functional, highly conserved genetic elements in the chimpanzee genome that are completely missing in humans?'" said Gill Bejerano, PhD, assistant professor of developmental biology and of computer science. "We found several hundred locations that, as far as we could see, are absent in our species alone." Until now, many evolutionary geneticists focused on differences among genes, rather than the regulatory regions outside the genes.
Losing small pieces of regulatory DNA, rather than the genes they control, means that the related changes are likely to be subtle: Although the location or the timing of the expression of the gene within the body may change, the gene product itself remains functional. The distinction leads to viable differences among individuals that can eventually lead to the development of new traits and species.
"It's not only unusual, but also particularly interesting, to find these sequences missing in humans," said David Kingsley, PhD, professor of developmental biology. "These are the same type of molecular events that have been shown to produce evolutionary differences among other organisms."
Other organisms like the three-spined stickleback fish, for instance. Kingsley's previous research focused on understanding how similar genetic changes over time have led to body modifications in the small fish that allow it to live in many very different environments.
"In fish, we find that the loss of regulatory DNA has produced key evolutionary differences in body structures," Kingsley said. "The current study not only identifies an intriguing list of deletions in humans, but also links particular deletions with specific anatomical changes that are unique to the human lineage."
Bejerano and Kingsley are co-senior authors of the research, which will be published March 10 in Nature. Three scientists share first authorship of the article: Cory McLean, a graduate student in Bejerano's laboratory; Alex Pollen, a graduate student in Kingsley's laboratory; and Philip Reno, PhD, a former postdoctoral scholar in Kingsley's laboratory now starting his own lab at Pennsylvania State University.
The researchers compared the genomes of several species to identify 510 regions that are highly conserved among chimpanzees and other mammals but are missing in humans. (Only one of the regions contained a coding region of a gene, or the portion that is turned into proteins to do the cell's work.) They then used a software program developed in Bejerano's laboratory called GREAT (for genomic regions of enrichment of annotations tool) to see whether these regions preferentially occurred near certain types of genes. (GREAT is publicly available to researchers around the world at http://great.stanford.edu
"We basically asked where evolution favored tweaking gene expression to get human-specific traits," said Bejerano. "We found two main categories of enrichment: genes involved in receptor signaling for steroid hormones like testosterone, and genes involved in neural development in the brain."
"Most, but not all, of these regions are also missing in the Neanderthal genome," said Kingsley, "which indicates the deletion took place more than 500,000 years ago."
The researchers found that one of the missing regions normally drives the expression of the androgen receptor in sensory whiskers and genitalia. Androgen is a sex hormone responsible for growth of sensory hairs, or vibrissae, and surface spines found on the penises of many mammals. The loss of these structures in humans decreases tactile sensitivity and increases the duration of intercourse in humans relative to other species.
Another region was adjacent to a tumor suppressor gene that suppresses neural growth in a particular part of the brain. Loss of expression of this inhibitory gene could thus contribute to an expansion of neural production in humans and a larger brain.
The resulting changes may have paved the way for monogamous pair-bonding and the complex social structure necessary to raise our species' relatively helpless infants, the scientists speculate.
There are still many other human-specific deletions to investigate, say the scientists, who are encouraging their lab members to study the functions of other interesting regions.
"Finding these sorts of human-specific changes is also a good motivator to look at other genomic events," said Bejerano. "Previous work in my lab has shown that many thousands of DNA regions are highly conserved among mammals, and almost never lost during evolution. Much of my lab is devoted to understanding what these regions do. Now we are starting to learn what can happen when they are lost."