Deep within all of us, at the very core of the human existence, a timeless battle is underway: Within the human genome, jumpers and repressors, are at odds with one another. Sometimes the jumpers develop mutations that allow them to escape the repressors. In turn, the repressors adapt to contain the jumpers. This “arms race,” say researchers at UCSB, reveals a major driving force behind human evolution

“We have basically the same 20,000 protein-coding genes as a frog, yet our genome is much more complicated, with more layers of gene regulation. This study helps explain how that came about,” said Sofie Salama, a research associate at the UC Santa Cruz Genomics Institute who led the study.

Retrotransposons, the “jumping” genes, are believed to be distant remnants of ancient viruses that infected and inserted themselves into the DNA of early animals, well before humans evolved. What’s left of the virus can now only replicate within a genome, which can be bad, neutral or (very rarely) good depending on where the extra copy is inserted within the genome. Since the probability for disease or other ill-effects is so high, evolution favors organisms who can develop methods for containing the retrotransposons.

It’s believed that genes with the propensity to “jump” account for as much as 50% of the human genome, so repressors have their work cut out for them.

“There have been successive waves of retrotransposon activity in primate evolution, when a transposable element changed to become expressed and replicated itself throughout the genome until something turned it off,” Salama said. “We’ve discovered a major mechanism by which the genome is able to shut down these mobile DNA elements.”

The repressor genes are actually protein chains known as “KRAB zinc finger proteins.” The protein group bonds to DNA and represses genetic activity. The human genome has around 400 genes for KRAB zinc finger proteins, and 170 or so are believed to have evolved after humans split from primates. The researchers say this is evidence that they developed in response to waves of retrotransposon activity.

“The way this type of repressor works, part of it binds to a specific DNA sequence and part of it binds other proteins to recruit a whole complex of proteins that creates a repressive landscape in the genome. This affects other nearby genes, so now you have a potential new layer of regulation available for further evolution,” Salama said.