The 1% that changes everything

The sequencing of the human and chimpanzee genome enables us to compare their DNAs and understand the genetic foundations of the divergence of these two lines 8 or 10 million years ago. It also gives us the tools to search in our genes for keys to the formidable growth in cognitive capacities which distinguishes our species.

An orang-utan meets children at Basel Zoo (CH). © Michel Vanden Eeckhoudt
An orang-utan meets children at Basel Zoo (CH). © Michel Vanden Eeckhoudt

As a child he dreamed of becoming an archaeologist. He became a biologist instead. But it is the same passion that drives Svanto Pääbo, director of the Max Planck Institute of Evolutionary Anthropology at Leipzig (DE).

He studies DNA in the same way as others excavate archaeological remains: travelling back in time to reconstitute the history of humanity. Pääbo became famous by isolating the DNA of Egyptian mummies, followed by the fossils of Neanderthal Man. His new challenge is to "reconstruct the history of the evolutionary changes that have led to the appearance of the human spirit as we know it today."

Two chromosomes, or one chromosome 2

Between humans and chimpanzees, which separated around 9 million years ago, the difference in genetic heritage is just 1 to 2%. This figure, which has been known for more than 30 years, can be found in any modern textbook.

But the nature of this difference remained an enigma until a first primitive genome of our closest cousin was sequenced in 2005 by an international consortium including researchers from the Max Planck Institute. What did this work teach us? That these 1 to 2% of genetic differences divide into two major categories.

The first consists of occasional substitutions of one nucleotide (those four chemical letters which constitute the alphabet in which DNA is written) by another within genes whose sequence is globally conserved. Between humans and chimpanzee, there are about 35 million such substitutions, out of a total of over 3 billion nucleotides. But their role is difficult to understand, given the large number of variations that also exist within the human species. The second category is made up of local changes in the structure of the genes themselves or of their sequencing, with deletions, duplications or inversions of DNA sequences, which can go as far as the merger of two chimpanzee chromosomes to form the human chromosome 2.

Gene doubling

This latter category of reshuffling is of particular interest to the German, British and Swiss researchers in the PKB 140404 project (Molecular Evolution of Human Cognition) led by Svante Pääbo. Or to be more precise, a subcategory of retrogenes, duplicated by DNA or RNA copying. Molecular geneticists have long suspected these curious biochemical events that end up with the doubling of a gene, of playing a role in the appearance of new animal species. But the question continues to be debated. With the habitual biological role taken by the first copy, the second is certainly capable of evolving more ‘freely'. This can lead to the appearance of new functions for the protein that it codes. But inversely, the second copy can potentially, by integrating randomly into the genome, upset its expression, like a photocopied page of a book upsets the reading of it if inserted at random.

Did these genetic duplication phenomena play a role in the emergence of our species? Yes, says Henrik Kaesmann's team at the University of Lausanne (CH), a partner in the PKB 140404 project, which has identified in the human genome some 60 functional retrogenes, which have appeared at a rate of one per million years in the primate line. What functional role do they play? By studying the organs in which they are expressed, Kaesmann and his team were surprised to observe that most of them are specifically active in the testicles, whereas the genes from which they derive are active in a wide variety of organs. "The retrogenes appear in the testicles, probably because they play a role in spermatogenesis. But thereafter they evolve strongly and are frequently expressed in a diversity of sites", Kaesmann explains.

From GLUD1 to GLUD2

A spectacular example of such diversification is the GLUD2 gene, which appeared by duplication in the common ancestor of humans and primates 18 to 25 million years ago. Its particular interest lies in the fact that it is one of the handful of retrogenes that are expressed in humans not only in the testicles but also in the brain. The protein it codes participates in the regulation of the brain's energy metabolism via the astrocytes, the cells that feed and protect the neurons. More importantly, compared with the ancestor GLUD1 from which it derives, the new gene is better able to feed the neurons with energy in the case of intense electrical activity. This could possibly constitute one of the necessary molecular bases for the growth of brain activity, observed as we approach humans along the line of descent from the primates.

Nobody, however, believes that it is the action of a few dozen recently appearing genes that have produced humankind as we know it. The search for the ‘specifically human' at the genetic level is not limited to the study of the DNA sequence, but also requires us to examine the RNA and proteins that give it its particular function. "We are systematically researching those genes in humans and the great apes which present different levels of genetic expression, because differences in expression can lead to functional modifications," Svante Pääbo explains. With his colleagues he has therefore compared the levels of genetic expression in the prefrontal cortex - the area of the brain most developed in Homo sapiens compared with his ancestors - of humans and of chimpanzees. The big difficulty in this type of analysis lies in interpreting the differences that are observed. Are these simple variations from one individual to another, making two chimpanzees just as different from one another as two human beings? Or are these functional differences which change the way cells or organs function?

Using a new statistical method, Pääbo and his team have identified a sub-group of genes whose expression in RNA in the human brain differs most from that of other primates. Analysis of their function is ongoing and will involve moving from the global analysis of the RNA of the prefrontal cortex to that of the proteins at neuron level. But the preliminary results are already showing that many of these genes play a part in the energy metabolism. These observations make sense if we remember that bipedality allows humans to traverse the same distance with much less energy. These energy savings are then available to feed the brain which alone consumes one-quarter of the energy of the human body.

On the tracks of mental illness

Another comparative approach that targets genetic expression, this time in the context of mental illness, is being undertaken as part of the PKB 140404 project by researchers from the Babraham Institute in Cambridge (UK). By means of the post mortem comparison of genetic expression in brains of schizophrenia or bipolar disorder patients with those of control brains, they are hoping to identify the genes involved in cognition, deficiencies which could be at the root of such disorders.

In the longer term, researchers are planning to introduce the genes, which have been identified for their potential role in cognition, into the mouse genome. "These experiments will serve to test their function by one of our three approaches - using either retrogenes, genes presenting a different expression in the cortex, or genes presenting a malfunction in schizophrenic patients - for their potential role in cognition. In this way we will be comparing the anatomical, biochemical and behavioural consequences of introducing into the mouse a human gene and the equivalent gene from the great apes," Pääbo explains.

Experiments have begun with four genes, the specificities of which in humans could explain the tripling of cerebral volume that marks the passage from great apes to humans. One of these is the ASPM (Abnormal Spindlelike Microcephaly Associate) gene. Its deficiency in humans produces mental retardation associated with a drastic reduction in brain size. Comparison of the accumulation of mutations in this gene in humans and in primates has shown that ASPM has undergone a positive selection in the course of evolution. In humans we also find a greater number of mutations that confer new properties to the gene - which means they could have contributed to increasing brain size - than neutral mutations with no functional consequences.

Other still preliminary results point to the fact that inserting the GLUD2 retrogene found in primates into mice changes the concentration of several neurotransmitters in the latter's cortex... and seems to make it inclined to explore new environments. From there to conclude that it has become as cunning as a monkey is a line that researchers are careful not to cross...

Mikhaïl Stein

  1. The PKB 140404 project (Molecular Evolution of Human Cognition) is part of the European initiative Nest Pathfinder, What it means to be human.