Last week I wrote about some deviously selfish genetic elements (toxin-antidote systems) and how they evolve. The vast majority of selfish genetic elements, however, are mobile elements we’ll call TEs: tiny modules of DNA that hop around in genomes (including our genomes). These things make up vast tracts of our genomes (more than half, in humans), so it seems that we and our fellow animals are stuck with some kind of truce or coexistence. Animals use elaborate silencing systems to try to control the hordes, which seem bent on reproducing themselves without regard for the damage they cause (that’s selfishness for you). So, I was excited to discover, in a new paper in Nature, one way we are fighting back.
Damage (mutations) from TEs is well known, but there are hints (starting decades ago) that this damage is sometimes removed, not from the genome itself but apparently from the messenger RNA made from the vandalized gene. Here are the authors posing the question:
We wondered whether the excision of TEs from mRNA is an active, host-mediated process that perhaps evolved to protect genes from TE-mediated disruption. Therefore, we set out to explore this possibility.
They discovered an active, targeted (i.e. not haphazard) mechanism by which animal cells remove TEs from messenger RNA, and they named it SOS splicing (in, I think, an homage to the SOS response in bacteria). They explored this new system in nematodes, showing how it finds the TEs in mRNA (it recognizes a specific TE signature, in the form of inverted repeats), and then using a genetic screen to find the machines (proteins) that operate the system. Those proteins exist in human cells, too, and so the authors asked whether there is an SOS splicing system in our cells. Indeed there is, and it is operated by those same components.
There are many very interesting open questions, discussed by the authors, who end with this summary (edited to remove references):
Organisms have sophisticated systems to prevent TE expression and replication. This study, along with other recent studies, show that organisms also have fail-safe systems that enable coexistence with TEs when TE-silencing systems fail and TEs mobilize into genes. Given the diversity and near-ubiquity of TEs in genomes, and across evolutionary time, additional TE-coexistence systems are likely to await discovery.
An RNA splicing system that excises DNA transposons from animal mRNAs
In Nature, 10 December 2025
From the group of Scott Kennedy at Harvard Medical School
Snippet by Stephen Matheson
Image credit: Figure 4a from Zhao et al. cited above (CC BY-NC-ND)