Transposons make up a large proportion of most genomes and can move from one place to another, driving evolution and creating genome instability. Jumping genes have also given rise to new, useful cell functions e.g. V(D)J recombination and the adaptation process of CRISPR-Cas adaptive immunity. Eukaryotic DNA transposons (including Sleeping Beauty) are also useful tools for genomic manipulations.
At the mechanistic level, DNA transposition is related to HIV-1 integration and V(D)J recombination. To establish in molecular detail how DNA transposons move, we have determined structures of nucleoprotein complexes that form along the transposition pathway of the mariner transposon Mos1. They reveal how the transposon is cut from host DNA, and how the ends are held together and then inserted at a new genomic location. These findings have implications for our understanding of DNA rearrangements more broadly and will advance biotechnology applications of transposons.
Topoisomerases relax supercoiled DNA, allowing transcription/replication machinery access to the DNA in order to copy or replicate it. They do this by forming a transient 3' phosphotyrosine complex, which breaks a DNA strand and allows unwinding. Usually the broken DNA strand is repaired, but, if the Topo-DNA complex is stalled, potentially toxic double strand breaks can form. Anti-cancer therapies, such as camptothecin, exploit this by preventing repair of such Topoisomerase-induced DNA damage.
The DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) is the cell's back up plan: it can process stalled Topo-DNA complexes by hydrolysing the phosphotyrosine bond between Topo IB and a 3’ DNA phosphate. In collaboration with Dr Heidrun Interthal, we are using structural and genetic approaches to understand in molecular detail how human Tdp1 recognises and processes its physiological Topo IB-DNA substrates.
Regulation of DNA methylation
The de novo DNA methyltransferases (DNMT3A and DNMT3B) establish cytosine methylation at CpG sites; an epigenetic modification that is essential for mammalian development. Mis-regulation of DNA methylation can lead to disease, in particular carcinogenesis. DNA methyltransferases require access to DNA to make covalent modifications to its structure, and genetic information packaged into chromatin must be opened up before these enzymes can do their job. This is achieved by chromatin remodellers, which can reposition nucleosomes to allow access to genetic material.
The putative chromatin remodeller lymphoid-specific helicase (LSH) regulates de novo DNA methylation and is required for normal levels of DNA methylation in mammals. LSH may regulate DNA methylation via its interactions with nucleosomes and/or with the de novo DNA methyltransferase DNMT3B. In collaboration with Dr Irina Stancheva's lab, we are using structural and biochemical methods to establish how LSH interacts with and remodels nucleosomes and how it cooperates with DNMT3B.