GENOMICS

How a DNA ‘Parasite’ May Have Fragmented Our Genes

By J A K E B U E H L E R

March 30, 2023

A novel type of “jumping gene” may explain why the genomes of complex cells aren’t all equally stuffed with noncoding sequences.

Recent research suggests that many of the noncoding “intron” segments in the genes of complex
organisms may have been inserted there by parasitic mobile genetic elements called introners.

Señor Salme for Quanta Magazine

A
ll animals, plants, fungi and protists — which collectively make up the domain of life called
eukaryotes — have genomes with a peculiar feature that has puzzled researchers for almost
half a century: Their genes are fragmented.

In their DNA, the information about how to make proteins isn’t laid out in long coherent strings of
bases. Instead, genes are split into segments, with intervening sequences, or “introns,” spacing out
the exons that encode bits of the protein. When eukaryotes express their genes, their cells have to
splice out RNA from the introns and stitch together RNA from the exons to reconstruct the recipes for
their proteins.

The mystery of why eukaryotes rely on this baroque system deepened with the discovery that the
different branches of the eukaryotic family tree varied widely in the abundance of their introns. The
genes of yeast, for instance, have very few introns, but those of land plants have many. Introns make
up almost 25% of human DNA. How this tremendous, enigmatic variation in intron frequency evolved
has stirred debate among scientists for decades.

Spliceosomes, like the one modeled here, perform the vital job in complex cells of removing the intron
RNA from genes being transcribed and assembling the other segments into messenger RNA.

Laguna Design/Science Source

Answers may finally be emerging, however, from recent studies of genetic elements called introners
that some scientists regard as a kind of genomic parasite. These pieces of DNA can slip into genomes
and multiply there, leaving profusions of introns behind them. Last November, researchers presented
evidence that introners have been doing this in diverse eukaryotes throughout evolution. Moreover,
they showed that introners could explain why explosive gains in introns seem to have been particularly
common in aquatic forms of life.

Their findings “might explain the vast majority of intron gain,” said Russ Corbett-Detig, senior author
of the new paper and an evolutionary genomics researcher at the University of California, Santa Cruz.

The Puzzle of Eukaryotic Genomes

Because of the introns polka-dotting their DNA, if the genes of eukaryotes were translated directly into
proteins, the resulting molecules would typically be nonfunctional garbage. For that reason, all
eukaryotic cells are equipped with special genetic shears called spliceosomes. These protein complexes
recognize the distinctive sequences that flank intron RNA and remove it from the preliminary RNA
transcripts of active genes. Then they splice together the coding segments from exons to produce
messenger RNA that can be translated into a working protein.

(A few prokaryotes also have introns, but they have ways of working around them that don’t involve
spliceosomes. For example, some of their introns are “self-splicing” and automatically remove
themselves from RNA.)
Merrill Sherman/Quanta Magazine

Why natural selection in eukaryotes favored introns that needed to be removed by spliceosomes is
unknown. But the key might be that such introns allow for alternative splicing, a phenomenon that
dramatically increases the diversity of products that can arise from a single gene. When the intron RNA
is clipped out, the exon RNA sequences can be strung together in a new order to make slightly different
proteins, Corbett-Detig explained.

Despite the influence of introns on the biology and genetic complexity of eukaryotic organisms, their
evolutionary origins have remained murky. Since the discovery of introns in 1977, researchers have
developed numerous theories about where these intrusive sequences came from. Several mechanisms
that could create introns have been identified, and all of them may have contributed some introns to
eukaryotes. But it’s been hard to say which if any of them might explain where the majority of introns
came from.

Moreover, the mystery around the origins of introns only deepens in light of the extreme variation in
where introns tend to show up throughout the eukaryote tree of life. Some lineages are particularly
heavy with them in ways that point to sudden inundations with introns during their evolutionary
history. When you examine the tree of life and how many introns are found on each tip of the tree,
Corbett-Detig said, “you can figure out pretty quickly that there must be certain branches where an
absolute ton of introns evolved all at once.”

One possible explanation for those explosive infusions of introns involves an unusual kind of genetic
element known as an introner. First described in 2009 in the unicellular green algae Micromonas,
introners have subsequently turned up in the genomes of some other algae, some species of fungi, tiny
marine organisms called dinoflagellates and simple invertebrates called tunicates.

The distinctive feature of introners is that they create introns. Introners copy and paste themselves
into stretches of coding DNA that offer an appropriate splicing site. Then they move on, leaving behind
a specific intron sequence flanked by splicing sites, which splits the coding DNA into two exons. This
process can be repeated on a massive scale throughout a genome. In fungi, for example, introners
appear to account for most of the intron gain during at least the last 100,000 years.
For several years, the genetic elements called introners were only known to be in a few organisms, such
as the dinoflagellate Polarella glacialis (left) and the green algae Micromonas.

(from left) Courtesy of Karin Rengefors; courtesy of Elodie Foulon/Roscoff Culture Collection, Sorbonne
Université and CNRS
How introners accomplish this became clearer in 2016, when researchers found that introners in two
species of algae had strong similarities to DNA transposons, members of a larger family of genetic
elements called transposable elements or “jumping genes.” Transposons also insert huge numbers of
copies of themselves into genomes.

The parallels between introners and transposons strongly suggested a possible answer to the mystery
of where most introns came from. Introners could cause introns to burst forth in genomes in great
numbers, which might explain the punctuated pattern of their emergence in various eukaryotes. The
catch was that introners were only known to exist in a few organisms.

“Did anyone look anywhere else?’” asked Landen Gozashti, who was doing research on evolutionary
genomics at Santa Cruz when he read the 2016 algae study. A look at the scientific literature showed
that no groups had published any data about introners elsewhere among the eukaryotes. Gozashti, now
at Harvard University, Corbett-Detig and their colleagues set out to remedy that.

Stealthy, Abundant Invaders

The team systematically scanned more than 3,300 genomes from across the full breadth of eukaryotic
diversity — everything from sheep to sequoias to ciliate protists. They used a series of computational
filters to identify potential introners, looking for introns with very similar sequences and whittling
away false positives. In the end, they found thousands of introns derived from introners in 175 of those
genomes, about 5% of the total, from 48 different species.

Five percent may seem like a small sliver of the eukaryotic pie. But as mutations accumulate in
introners over time, sequence similarities between the copies deteriorate until it’s no longer possible to
tell that they came from the same source. The evolutionary lineages of many species alive today may
have experienced floods of introns, but any influx that occurred more than a few million years ago
would be undetectable. The 5% result therefore hints that introners may be far more ubiquitous.
Merrill Sherman/Quanta Magazine

As genomic parasites, introners may have achieved their success through stealth. A good parasite can’t
draw too much attention to itself. If an introner disrupts the activity of the gene in which it has
embedded itself, it could harm the host organism, and natural selection could remove the genomic
parasite altogether. So these elements are continually evolving to be “as neutral as possible” in their
influence, said Valentina Peona, a comparative genomicist at Uppsala University.

Gozashti, Corbett-Detig and their colleagues found out how adept introners are at slipping under the
radar when they estimated the splicing efficiency of introners, which reflects their ability to avoid
disrupting the function of host genes. “Introners actually are spliced better than other introns,”
Gozashti said. “These things have gotten really good at it.”

An Aquatic Connection

The work by Gozashti and his colleagues proved that introners are not distributed equally among
eukaryotes. For example, introners are more than six times as likely to appear in the genomes of
aquatic organisms as in those of terrestrial organisms. Moreover, nearly three-quarters of the
genomes from aquatic species that contain introners host multiple introner families.
Corbett-Detig, Gozashti and their colleagues think this pattern can be explained by horizontal gene
transfer, the transfer of a genetic sequence from one species to another. These unorthodox gene
transfers tend to happen in aquatic environments or in instances of close interspecies association, such
as between hosts and parasites, explained Saima Shahid, a plant biologist at Oklahoma State
University.

Aquatic environments may encourage horizontal gene transfer because the aqueous medium can
become a soup of the nucleic acids shed by countless species. Single-celled organisms paddle around in
this stew, so it’s easy for them to take up foreign DNA that might be incorporated into their own. But
even much more complex multicellular species lay their eggs or fertilize them in the water, creating
opportunities for DNA to be transferred into their lineages.

When many aquatic species mate, their eggs and sperm could be exposed to horizontal transfers of
mobile genetic elements in the water.

Lauren Ballesta. Creation, a 2021 Grand Title Wildlife Photographer of the Year photo, from the book 700
sharks into the dark, Andromède Editions 2017
Clément Gilbert, an evolutionary genomicist at Paris-Saclay University, thinks the aquatic bias in
introners is an echo of what his group found in horizontal gene transfer events. In 2020, their work
uncovered nearly 1,000 distinct horizontal transfers involving transposons that had occurred in over
300 vertebrate genomes. The vast majority of these transfers happened in teleost fish, Gilbert said.

If introners find their way into hosts primarily through horizontal gene transfers in aquatic
environments, that could explain the irregular patterns of big intron gains in eukaryotes. Terrestrial
organisms aren’t likely to have the same bursts of introns, Corbett-Detig said, since horizontal
transfer occurs far less often among them. The transferred introns could persist in genomes for many
millions of years as permanent souvenirs from an ancestral life in the sea and a fateful brush with a
deft genomic parasite.

Introners acting as foreign, invasive elements in genomes could also be the explanation for why they
would insert introns so suddenly and explosively. Defense mechanisms that a genome might use to
suppress its inherited burden of transposons might not work on an unfamiliar genetic element arriving
by horizontal transfer.

“Now that element can go crazy all over the genome,” Gozashti said. Even if the introners are initially
harmful, the researchers hypothesize that selective pressures could soon tame them by cutting them
out of RNA.

Although horizontal gene transfer and introners share a connection to the aquatic environment, the
findings don’t yet show definitively that this is where introners come from. But the discovery of
introners’ widespread influence does challenge some theories about how genomes — particularly
eukaryotic genomes — have evolved.

Reverberations in the Host

Russell Corbett-Detig, who studies genome evolution at the University of California, Santa Cruz, thinks
that introners could have created most of the introns that various eukaryote lineages have gained.

Shelbi Russell

The pervasiveness of recent intron gain may act as a counterweight to some ideas about the evolution
of genomic complexity. One example involves a theory of intron evolution developed by Michael Lynch
of Arizona State University in 2002. Models suggest that in species with small breeding populations,
natural selection can be less efficient at removing unhelpful genes. Lynch proposed that those species
will therefore tend to build up heaps of nonfunctional genetic junk in their genomes. In contrast,
species with very large breeding populations should not be gaining many introns at all.

But Gozashti, Corbett-Detig and their coauthors found the opposite. Some marine protists with
gargantuan breeding populations had hundreds or thousands of introners. In contrast, introners were
rare in animals and absent in land plants — both groups with much smaller breeding populations.
The evolutionary arms race between invading genetic elements and the host may have a hand in
generating a more complicated genome. The parasitic elements are in “constant conflict” with genetic
elements that belong to the host, Gozashti explained, because they compete for genomic space. “All
these moving pieces are constantly driving each other to evolve,” he said.

That raises the question of what the intron gains meant for the functional biology of the organisms in
which they occurred.

Cedric Feschotte, a molecular biologist at Cornell University, suspects it would be interesting to

compare two closely related species, only one of which has experienced an intron swarm in recent
evolutionary history. The comparison might help to reveal how influxes of introns could promote the
appearance of new genes. “Because we know that bringing in introns can also facilitate the capture of
additional exons — so completely new stuff,” he said.

Similarly, Feschotte thinks that profusions of introns might help drive the evolution of families of
genes that can change rapidly. Stuffed with new introns, those genes could co-opt the new variability
enabled by alternative splicing.

When the researcher Landen Gozashti, now at Harvard University, first heard that introners had been
seen in only a few species, he was inspired to search for the genetic elements more comprehensively in
other organisms.

Courtesy of Landen Gozashti

Such rapidly evolving genes are widespread in nature. Venomous species, for instance, often need to
remix the complex cocktails of peptides in their venoms at the genetic level to adapt to different prey or
predators. The ability of the immune system to generate endlessly diverse molecular receptors also
depends on genes that can rearrange and recombine quickly.

Peona warns, however, that although introners could provide benefits to an organism, they might also
be totally neutral. They should be considered “innocent until proven guilty of function or anything
else.”
“One of the things that’s next is looking at metagenomic data to try to find a case that really is a clear
horizontal transfer with the exact same introners in two different species,” Corbett-Detig said. Finding
this piece of the puzzle would help flesh out the full story of where most of eukaryotes’ introns have
come from.

Irina Arkhipova, a molecular evolutionary geneticist at the University of Chicago Marine Biological
Laboratory, is interested in knowing more about how introners are spreading through the genome at
such large scales. “It just leaves no trace of the enzyme that was responsible for this massive burst of
mobility — that’s a mystery,” she said. “You basically have to catch it in the act while it’s still
moving.”

For Gozashti, the discovery of introners in such a wide range of eukaryotes holds a lesson about how to
approach fundamental questions about the nature of eukaryotic life: Think broadly. Studies often focus
on the sliver of biodiversity represented by animals and land plants. But to understand the important
patterns of genomic information underlying all life, “we need to sequence more eukaryotic diversity,
more of these protist lineages where we don’t know anything about how they evolve,” he said. “Had we
just studied land plants and animals, we never would have found introners.”

Editor’s note: Gozashti is a graduate student in the laboratory of Hopi Hoekstra, who serves on the advisory
board for Quanta.