Flatworm DNA methylation: deciphering the mark and characterising the machinery

DNA methylation, catalysed by DNA methyltransferases (Dnmts), is an epigenetic process that regulates metazoan gene expression, repetitive element silencing, allelic exclusion and development. However, within the economically and biomedically important Platyhelminthes (flatworms), virtually nothing is known about the role of this regulatory mediator. Studies of flatworm DNA methylation systems will, therefore, be essential to our understanding of how epigenetic processes have evolved and how DNA methylation specifically contributes to platyhelminth lifecycle diversity, host interactions and disease pathogenesis. Our laboratory is using complementary techniques to identify and characterise flatworm DNA methylation systems. Through RNAi and drug inhibition studies, we have demonstrated that Schistosoma mansoni (a parasitic flatworm) contains a Dnmt (SmDnmt2) responsible for DNA methylation and oviposition. Follow-up investigations now show that DNA methylation is not restricted to schistosomes, but is also present in the two other parasitic platyhelminth classes. To further understand the significance of a representative platyhelminth DNA methylation system, this proposal aims to fully characterise schistosome SmDnmt2 and identify genome-wide DNA methylation patterns in schistosome larvae and adults. We will first identify sub-cellular localisations, interacting partners, additional enzymatic activities and DNA binding loci of SmDnmt2 using cell transfections, yeast 2 hybrid screens, recombinant protein expression/RNA methyltransferase activities and CHiP assays. Secondly, we will utilise 2-D proteomics to identify the schistosome gene products affected by SmDnmt2 inhibition or knockdown. These collective studies will fully define the schistosome DNA methylation mediator. Finally, using newly generated Illumina sequence data obtained from WGBS or MeDIP libraries, we will thoroughly characterise the DNA methylome of schistosome larvae and adults.

We are all familiar with the subject of genetics, which describes how the fundamental unit of inheritance (the gene) is passed on from parent to offspring. Changes in the underlying DNA sequence that make up our inherited genes help explain why differences (eye colour, eye shape, chin size, etc.) in our outward appearance (phenotype) occur. However, genetics cannot fully explain the wide-ranging phenotypic diversity exhibited by all organisms on this planet. To do so in a systematic manner, we also have to consider another type of inheritance system called epigenetics. Epigenetics is the study of inherited changes in gene function (leading to different phenotypes) that cannot be explained by changes in the underlying DNA sequence of the gene. In other words, epigenetics attempts to explain everything that genetics cannot. One particular type of epigenetic process responsible for inherited changes in phenotype is facilitated by DNA methylation. Loss of DNA methylation regulation has been extensively studied in humans and is associated with cancer, obesity, immunodeficiencies and intellectual disabilities. Recent studies have additionally demonstrated that heritable DNA methylation patterns are influenced by our interaction with environmental (chemicals, drugs, etc.) factors. However, very little is known about DNA methylation or the processes that regulate it in other animal systems, especially invertebrates. Flatworms are a tremendously important invertebrate group (within the phylum Platyhelminthes) responsible for many economically- and biomedically-relevant parasitic diseases. These parasitic invertebrates undergo extensive developmental changes throughout their complicated lifecycles, which often involves interaction with more than one host or environment. Does environmentally influenced DNA methylation contribute to the success of parasites like these? If so, how does this occur and what genes are targeted by this epigenetic mechanism? Working in Aberystwyth, we will apply state of the art molecular biology tools to try and understand how DNA methylation regulates flatworm development. We have already found that DNA methylation is present in all three classes (Trematoda, Cestoda and Monogenea) of parasitic platyhelminth and that the enzymes responsible for these genome modifications are highly conserved. Using a model platyhelminth (Schistosoma mansoni), our project aims to further characterise the enzyme responsible for flatworm DNA methylation and to identify the genes specifically targeted by the DNA methylation machinery. By doing so in a synergistic manner, we expect to discover new roles for this epigenetic process during animal evolution. This information may eventually lead to novel ways to combat parasitic diseases.