News item

How cells make piRNAs: from a peculiar observation to mechanistic insights

Dominik Handler, a VBC PhD student, is a co-first author in a paper just published in Science. A project that started like a hobby to Dominik, turned out to be a rewarding experience, which made fundamental contributions to the field. In this paper Dominik, together with a postdoc, Fabio Mohn, and with their supervisor Julius Brennecke (all from IMBA) uncover the mechanism that cells use to generate piRNAs, a germline specific class of small regulatory RNAs.

Dominik Handler

The Brennecke lab studies the piRNA pathway, a small RNA-based silencing process that ensures that transposable elements are efficiently repressed in the animal germline.  The piRNA pathway is conserved from sponges to humans; but the molecular mechanisms that underlie it are only poorly understood. In a recent project led by the postdoc Fabio Mohn, the Brennecke lab identified a master regulator of piRNA precursor transcription: the Rhino-Deadlock-Cutoff protein complex. During that project Fabio made a peculiar observation: when cells were depleted for Rhino, transposon derived piRNAs collapsed, but there was an increase in piRNAs derived from cellular mRNAs.

Dominik Handler decided to investigate further these mRNA-derived piRNAs and ran a first genome wide analysis. From this he realized that the possibility to map these RNAs to unique sites in the genome allows the detection of intriguing patterns. Dominik, Fabio and Julius set out to systematically uncover how piRNAs are being made in ovaries of Drosophila melanogaster.

“It was a lot of fun, each of us would analyze a different data set but we ended up sitting together, almost every day, discussing and comparing each others results.” Dominik Handler

In the course of this project, Fabio and Dominik sequenced nearly one billion small RNAs. Like many other students and postdocs, they quickly faced the fact that they need to learn programming to be able to analyze their data. And so the project was a primer for Dominik to acquire programming and bioinformatics skills. 

“I did a course on campus, but I basically learnt bioinformatics during this project. The way to learn it is to just do it! You start by asking a few scripts from more experienced colleagues, and then you try it on your own!” Dominik Handler

In their report in Science the group formulates a coherent model for piRNA biogenesis: piRNA-guided RNA cleavage forces the generation of a ping-pong partner piRNA but then also triggers 3' directed and phased piRNA biogenesis on the remaining target RNA. Phasing in piRNA biogenesis is a consequence of the action of Zucchini, an endonuclease that is anchored in the outer mitochondrial membrane. This publication unites several previously unexplained observations in the field and also demonstrates that a very similar biogenesis process occurs during spermatogenesis of mice. 

Congratulations to Dominik and his colleagues on yet another beautiful story!

Dominik started his PhD at IMBA in 2010 and defended his PhD Thesis last December. This is Dominik’s third publication as a first author, resulting from his PhD work.


Mohn F, Handler D and Brennecke J (2015) piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science 348: 812-817 DOI:10.1126/science.aaa1039