Transposons—sometimes called “jumping genes”—are mobile genetic elements that can jump and copy themselves within an organism’s genome. Making up almost half of the human genome, transposons play an important role in driving genetic diversity and evolution, but their movement can also cause harmful mutations affecting genes or regulatory regions. To mitigate this risk, cells have evolved sophisticated defense systems to keep transposons in check and preserve genome integrity.
One of these defenses is the PIWI–piRNA pathway. PIWI proteins, working together with small RNAs called PIWI-interacting RNAs (piRNAs), act like a genome surveillance system in animals. They identify transposon sequences and activate a powerful gene silencing response, which involves recruiting different effector proteins. This mechanism is active in reproductive cells, where safeguarding the genome is critical to ensure that genetic information can be faithfully passed on to the next generation.
To silence transposons, PIWI proteins act in two different compartments of the cell. In the cytosol, they cut transposon RNAs transcripts into little fragments that are then used to build new piRNAs. In the nucleus, PIWI proteins direct chemical modifications that compact transposon-containing chromatin regions, locking them down to stop transposon expression. In both cases, PIWI proteins must bind to other proteins to perform these functions—yet the identity of these factors and the molecular mechanisms that restrict their interactions to target-engaged PIWI proteins had remained out of reach due to technical limitations.
Now, a collaborative project between the labs of Julius Brennecke at the Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences and Clemens Plaschka at the Research Institute of Molecular Pathology (IMP) closes this long-standing gap. The team combined AlphaFold-based modelling of protein-protein interactions with genetics, biochemistry and cell biology to identify the first steps of silencing that occur once a PIWI protein engaged with a piRNA-complementary target RNA . The findings, published in Molecular Cell on September 4th, showcase the enormous potential of AI-based protein structure prediction to understand how context-specific protein-protein and protein-RNA interactions direct dynamic molecular processes.
Combining genetics with AI: cracking the PIWI code
Using the fruit fly Drosophila melanogaster as a model system, the team first identified hundreds of proteins that could bind to the nuclear Piwi protein. They then applied the AI-based tool AlphaFold to narrow this list down to likely direct interactors. The power of these predictions, however, does not only lie in the identification of partner proteins, but in providing molecular details of how the different proteins interact with Piwi. The team could use genetics in cells and flies to validate these structural models. These combined experiments showed that only upon recognizing a transposon sequence, Piwi binds to two other proteins, Maelstrom and Asterix, a protein from the GTSF family. Together, the three proteins form an activated protein-RNA complex, dubbed Piwi*, which is essential for keeping transposons in check.
However, the Piwi* complex itself is not capable of repressing transposons. Remarkably, AlphaFold also provided a structural model of how Piwi* specifically recruits the downstream chromatin silencing effectors through interactions that would not be possible to Piwi, Maelstrom, or Asterix alone.
In an eye-opening moment, the team then realized that cytoplasmic PIWI proteins also team up with Maelstrom and GTSF proteins to form similar PIWI* complexes. But instead of recruiting the heterochromatin-inducing machinery, cytosolic PIWI* complexes recruit a different effector, the RNA helicase Spindle-E, which was previously shown to be required for piRNA biogenesis once a cytosolic PIWI protein cleaved its target RNA.
Notably, the molecular interactions that underlie the formation of PIWI* complexes are conserved from sponge to human, indicating an ancient mechanism that enables PIWI proteins to protect genome integrity in animals.
Bridging expertise to solve a 20-year puzzle.
The discovery of PIWI* complexes results from a tight collaboration between two labs with different expertise but working in close proximity within the Vienna BioCenter.
“This project is a great example of the collaborative spirit that makes the Vienna BioCenter such a special place to do science,” said co-corresponding author Julius Brennecke. The project was led by Júlia Portell i de Montserrat, a shared PhD student of the Brennecke and Plaschka labs. “The shared supervision as well as Júlia’s broad skillset and her passion were essential to bridge the gap between the two teams. Combining our expertise in Drosophila models of transposon silencing with Clemens Plaschka’s knowledge of protein-RNA structure, we were finally able to answer a question we had been chasing for nearly twenty years.”
“The world-class Mass Spectrometry Core Facility at the Vienna BioCenter was another essential component for this discovery,” adds Plaschka. “Combined with the power of AlphaFold, we were able to identify and study a protein-RNA complex for which an experimental structure is not available. We believe that this approach will also allow us to tackle the next big questions in piRNA biology and beyond."
Publication: Portell-Montserrat J., Tirian L., Yu C., Silvestri G., Hohmann U., Handler D,m Duchek P., Fin L., Plaschka C., Brennecke J., Target RNA recognition drives PIWI* complex assembly for transposon silencing. Molecular Cell, September 4th, 2025. DOI:10.1016/j.molcel.2025.08.007
About IMBA
The Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences is one of Europe’s leading research institutes in the field of molecular biology. With over 200 scientists from more than 40 nations, IMBA is committed to excellent fundamental research. At IMBA, scientists seek to gain insight into human health, including inborn diseases of the heart and brain, degenerative diseases and regenerative strategies. Research topics pursued at IMBA include chromosome biology, RNA biology, cell and developmental biology, stem cell biology, neuroscience, and organoid research.
About the IMP
The Research Institute of Molecular Pathology (IMP) in Vienna is a basic life science research institute largely sponsored by Boehringer Ingelheim. With over 220 scientists from 40 countries, the IMP is committed to scientific discovery of fundamental molecular and cellular mechanisms underlying complex biological phenomena.
About the Vienna BioCenter
The Vienna BioCenter, one of Europe’s most dynamic life science hubs with 2,800 people from over 80 countries in six research institutions, and 40+ biotech companies.
Further reading
Lab of Clemens Plaschka