Transposons Jumping Genes and Genome Evolution
Meta commentary - no external expert source; basis: Quantamagazine (2026-09-21). #MetaScience
When Corn Kernels Refused to Follow the Rules
In the 1940s, Barbara McClintock noticed something in corn that should have been impossible. She was studying color variation in corn kernels at the Cold Spring Harbor Laboratory in New York. The strain she worked with typically produced solid purple kernels, but some were speckled — purple pigment spattering a yellow base. McClintock wanted to explain how genes produced this color variation. What she found instead challenged geneticists’ understanding of how the genome works. She discovered genetic elements that could move, excising themselves from one location and inserting themselves into another on the same chromosome or a different one. Sometimes, these genetic acrobats would jump into the middle of a purple pigment gene and interfere with its function, producing a speckled cell. If it jumped out again, the pigment gene would be restored, making a purple cell. McClintock called these mobile genes “controlling elements” for their dominion over the expression of the color-producing genes. Today we call them transposons for their ability to transpose themselves, or change positions, within a genome. Three decades later, in 1983, McClintock was awarded a Nobel Prize for her discovery, which showed that genes are not fixed in place. Since then, researchers have uncovered transposons in organisms across the tree of life and described a whole taxonomy of subtypes that cluster into two main groups. The transposons McClintock discovered are DNA transposons, so called because they travel as a DNA molecule. Transposons in this class jump by means of cut and paste.” Enzymes called transposases bind to the ends of the DNA transposon and splice it free. The liberated bundle then touches down somewhere else in the genome, where native DNA repair processes paste it in. A second class of transposons, known as retrotransposons, is not cut directly out of the genome. Instead, the DNA sequence is copied into RNA, a molecular strand that is flexible and mobile by nature. Liberated from the genome, the sequence in the RNA copy is then reverse-transcribed into DNA at a different location. By copying themselves instead of cutting, retrotransposons can easily flood a genome with many iterations of themselves. Over time, this has led retrotransposons to make up large proportions of a host genome in some cases; for example, nearly half of the human genome consists of retrotransposons. Many retrotransposons are related to viruses, and biologists debate which came first. These viruses, known as retroviruses, insert a DNA copy of their RNA sequence into the host cell’s genome, hijacking the cell’s resources to reproduce themselves. The most widely known example is HIV, which invades the genomes of infection-fighting white blood cells. If they do not kill their host, retroviruses can leave their genetic legacy behind in the host genome, like splinters lodged in a finger. This viral scar tissue can accumulate over millions of years: In humans, these viral ghosts make up an estimated 8% of the total genome. That means humans are, in no small part, made of virus.
The Jump That Crossed Species Lines
The same features that allow DNA transposons and retrotransposons to move within a genome also predispose them to moving between genomes. By hitchhiking on a passing virus, transposons can defy species boundaries and land in a totally new evolutionary setting. “Virtually all of the we know can apparently go from species to species,” said Cedric Feschotte, a geneticist at Cornell University. [1] Initially, these horizontally transferred transposons were thought to be a rare exception to normal biology. By now, thousands of examples have been reported in species that run the gamut from fungal pathogens to snakes to cows. In 2020, researchers described nearly 1,000 independent horizontal transfer events in 307 vertebrate genomes, predominantly in fish. Given their self-replicating, virus-like behavior, transposons might seem to be something between benign bloat and selfish parasite. But researchers are increasingly finding that, as in the case of McClintock’s corn kernels, they can be a source of meaningful evolutionary material. Around 200 years ago, the peppered moths of England were readily identifiable by their black-speckled white wings, which camouflaged well with pale tree bark. After the Industrial Revolution, when pollution from coal-powered factories darkened the trees, black wings came to dominate the population. Evolutionary biologists later explained that in the new, sootier environment, white moths were easily spotted by predatory birds, while black moths blended in with the darkened bark. The white moths had lost their survival advantage, while black moths survived better and reproduced. This story about the dark-winged peppered moths is now considered a textbook example of natural selection. It was not until 2016 that researchers uncovered the genetic mechanism behind the change. By sequencing hundreds of peppered moth genomes, the geneticists found a significant and consistent difference in a gene called cortex involved in wing development. A transposon, absent in the white-winged moths, had been inserted into the beginning of this gene in nearly all the black moths and had led, through a mechanism that remains unknown, to the production of dark-colored wings. The authors estimated that this transposition occurred in 1819 — after the rise in pollution levels had started to alter the moth’s habitat. “This is completely changing how we see rapid adaptation,” said Pierre Baduel, a geneticist at the French National Center for Scientific Research in Paris. [1] Generating new traits is typically thought to take long periods of evolutionary time. In this case, a transposon created a new trait that was immediately selected for. These types of insertions may happen frequently. To be passed on to the next generation, however, they need to occur in the reproductive cells. Any insertions that have large, immediate, and potentially negative effects on an organism are usually rapidly weeded out by natural selection. “The genome is just constantly bombarded by gene insertion, and then most of them are removed,” Baduel said. “If the environment has changed and suddenly they become adaptive, then they stick.”
From Parasite to Partner
Sometimes, instead of changing an existing gene, a transposon in a new context can be co-opted over time to generate something new. For instance, a transposon fused in the right location can, by chance, create a novel protein that goes on to regulate other genes throughout the genome. This process of tweaking genes to establish new traits is thought to have catalyzed evolutionary novelty in animals. Transposable elements are linked to the evolution of animal eyes as well as the adaptive immune system in jawed vertebrates. The domestication of transposons for new purposes has also been implicated in the evolution of the placenta — a defining feature of nearly all mammals. That means a transposon is partly responsible for the months-long process of development in utero that is typical for our lineage, humans included. Even when the effects are more subtle, the relationship between genome and transposon seems to sometimes go deeper than that of a host adapting to an invading, self-interested genetic force. In many cases, it could be considered more of a coevolutionary arrangement. Some products made by transposons may do the same jobs as native proteins, and over time, the host genome may become dependent on the transposon and its products — a situation Feschotte compared to an addiction. This drive for coexistence may undergird fundamental aspects of how genomes regulate themselves. The disruptive nature of transposons may have required organisms to evolve new methods of shutting off their activity. Epigenetic control — the means by which an organism can dial the expression of its genetic repertoire up or down, or shut off the expression of some genes entirely — may have evolved first to bring transposons to heel. “One of the models is that relatively simple organisms evolved epigenetic silencing to silence their transposons,” said Susan Wessler, a geneticist emerita at the University of California, Riverside and vice president of the National Academy of Sciences. [1] Under this theory, organisms figured out how to turn genes off to get these unruly genetic parasites under control. Then evolutionary processes repurposed those controls to turn all sorts of genes off, leading to regulatory processes that, for example, produce dozens of cell types from the same genome. This coevolutionary perspective is a more neutral take on the relationship between transposon and host genome than the view of the recent past, which cast them as selfish, parasitic, or junk DNA. The emerging understanding that transposons are intimately interwoven within the regulatory workings of the host genome is rehabilitating their reputation as critical sources of evolutionary innovation. “We are all influenced by the terms that we use,” Feschotte said. “Transposons are not just passengers. They have been coevolving with organisms from the beginning.”
Sources
Mentioned organisations (context, not sources)
- Cold Spring Harbor Laboratory — Organisation (homepage)
- Cornell University — Organisation (homepage)
- French National Center for Scientific Research — Organisation (homepage)
- University of California, Riverside — Organisation (homepage)