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RNA Biology Section

About Our Research

RNA-guided Genome Protection: Small non-coding RNAs play vital roles in development and disease by regulating gene expression, defending against viruses, and silencing mobile genetic elements (transposons). Our research focuses on PIWI-interacting RNAs (piRNAs), which safeguard genome integrity and are essential for germ cell health and fertility.

To unravel the molecular mechanisms of this RNA-based immune system, we take an interdisciplinary approach that integrates genetics, genomics, and biochemistry. Results from our studies have deepened the understanding of the fundamental processes protecting genome integrity in animals and humans, and hold promise for uncovering molecular strategies for technological and therapeutic advancements.

Research Images

Chart showing the protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA cluster builder.
Protocol for Assembling, Prioritizing, and Characterizing piRNA Clusters Using the piRNA Cluster Builder (PICB) (Ahrend et al., and Haase, STAR Protocols, in press, 2025)
A chart of the comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals.
A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals (Konstantinidou*, Loubalova*, Ahrend*, Friman*, et al., and Haase, Cell Reports, 2024)
Chart explaining PIWI-interacting RNAs.
PIWI-interacting RNAs: who, what, when, where, why, and how (Haase*, Ketting*, Lai*, van Rij*, Siomi*, Svoboda*, van Wolfswinkel*, Wu*, EMBO J., 2024)
An oversimplified depiction of the three major small RNA pathways in animals
An oversimplified depiction of the three major small RNA pathways in animals.’ (Review, RNA Biology 2023)
PiRNA biogenesis in flies and mice
PiRNA biogenesis in flies and mice.’ (Review, RNA Biology 2023)
Hierarchical length and sequence preferences.
Hierarchical length and sequence preferences establish a single major piRNA 3′-end’ (Stoyko et al., iScience 2022)
Functional editing of endogenous genes through rapid selection of cell pools.
Functional editing of endogenous genes through rapid selection of cell pools’ (Meng*, Stoyko*, Marlin Andrews*, et al., NAR 2022; and Stoyko et al., Curr Protoc. 2022)
Graph of cellular abundance.
Cellular abundance shapes function in piRNA-guided genome defense’ (Genzor*, Konstantinidou*, Stoyko*, et al., Genome Research 2021)
Aberrant expression of select piRNA-pathway genes.
Aberrant expression of select piRNA-pathway genes does not reactivate piRNA silencing in cancer cells’ (Genzor et al., PNAS 2019)
Model for the establishment of a 1U-bias.
PiRNAs like to be with 'U': The 1U-bias is established by differential gating against all nucleotides but Uridine (U) (from: Stein*, Genzor*, Mitra*, Elchert* et al., Nat Commun. 2019)
Simplified model of mammalian piRNA pathways.
Mammalian piRNA pathways (from: Genzor et al., PNAS 2019).
Mouse homolog of Drosophila zucchini (zuc), mmZuc/PLD6.
The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis (adapted from: Ipsaro*, Haase* et al., Nature 2012).
Last Reviewed March 2025