Mechanism, regulation, and application of mobile DNA
Figure 1: The structure of the IS608 transpososome, modelled based on a series of crystal structures
Figure 2: Crystal structure of the primary piRNA biogenesis factor Zucchini reveals its endonuclease function
The Barabas group uses structural and molecular biology approaches to investigate how DNA rearrangements are carried out and regulated, with the ultimate goal of developing genetic engineering tools for research and therapy.
Previous and current research
Our research focuses on transposons, a class of mobile genetic elements that can autonomously move from one location to another in the genome. They drive genetic diversity and evolution and constitute about half of the human genome. However, the physiological roles of transposons are just starting to be unravelled. Recent studies show that they have key functions in gene regulation, development, immunity, and neurogenesis (Beck et al., 2011). In addition, these ‘jumping’ DNA elements offer attractive tools for genetics and human gene therapy.
To better understand transposition and facilitate the development of transposon-based genetic tools, we investigate the molecular mechanisms of their movement and regulation using structural biology (mainly X-ray crystallography), molecular biology, biochemistry, biophysics, microbiology, and cell biology approaches. We strive to understand the structure of functional transposition complexes, the chemistry they use to cut and paste DNA, their target-site selection and their regulation in the cell.
Sleeping Beauty: This resurrected transposon provides a prime tool in vertebrate genetics with applications spanning from forward mutagenesis screens to chromosomal engineering and gene therapy (Ivics et al., 2009). We study the structure and mechanisms of this transposon and, in collaboration with the Gavin and Beck groups, we also investigate how it interacts with other components of the human host cells.
Target site-specific transposons: One of the main obstacles in gene therapy is integration of the therapeutic gene at unwanted locations. We seek tools that integrate to specific genomic sequences. Our mechanistic work revealed that the IS608 transposon uses a short sequence in the transposon DNA to guide its integration to a specific sequence via base pairing (Barabas et al., 2008). The site of insertion can also be altered by making point mutations in the transposon (Guynet et al., 2009). We are now testing if this target recognition can be extended to select unique genomic sites.
Antibiotic resistance carrying elements: The spread of antibiotic resistance is one of today’s biggest public health concerns. Conjugative transposons provide a major mechanism to transfer resistance between bacteria. To shed light on their mechanism of transfer, we study two conjugative transposons from Helicobacter and Enterococcus, respectively.
Transposon regulation: To avoid deleterious outcomes, cells must keep their transposons under control. One major control mechanism is provided by small RNAs. In collaboration with the Carlomagno and Pillai groups, we investigate these processes in prokaryotes and eukaryotes. Our recent work on the eukaryotic piRNA pathway has revealed the structure and function of a novel component, a piRNA biogenesis factor called Zucchini.
Future Projects and Goals
- Develop novel genetic engineering tools and explore their applications in transgenesis and synthetic biology.
- Study the mechanism and regulation of a class of ‘beneficial’ transposons that are involved in the development of ciliated protists.
- Explore the movement of retrotransposons.