How a complex, multicellular organism develops from a single fertilised egg is among the most intriguing concepts in biology. This phenomenon is further augmented by the fact that metazoan organisms consist of many distinct cell types that largely differ in their morphology, function and gene expression patterns, yet contain identical genomic DNA. Nowadays, we know that such a vast variety of cell types is generated and maintained by mechanisms that in most cases do not involve alterations in the primary DNA sequence. Such epigenetic mechanisms include (but are not limited to): DNA methylation, post-translational modifications of histone tails, long non-coding RNA and nucleosome positioning. The development of massively parallel DNA sequencing technologies has facilitated the generation of precise epigenome maps corresponding to myriad cell-lines, tissues and disease samples with the aim of deciphering the epigenomic component of diverse cellular forms and functions.
The research in our lab aims to understand the contributions of the epigenome to embryonic development, cell differentiation and disease. We are particularly interested in how DNA methylation patterns are established, maintained and altered during those processes. Our interest in DNA methylation stems from the fact that this epigenetic mark can be stably propagated through cell division and that the presence or absence of DNA methylation correlates well with the activity of regulatory regions. Finally, a vast wealth of studies has demonstrated strong links between DNA methylation and various disease phenotypes suggestive of its potential applicability as a biomarker.
1.Roles of embryonic promoter DNA methylation in tissue differentiation and cancer
A surprisingly small number of genes becomes silenced by promoter DNA hypermethyation during vertebrate embryogenesis. In many cases, these genes are essential regulators of germline development that are frequently found altered in multiple adult cancers. Through a combination of biochemical and zebrafish transgenesis approaches we are trying to understand the mechanisms of this targeting specificity as well as the roles of these genes in cancer formation in vivo.
2.Functional characterization of DNA demethylation pathways during embryogenesis
We have recently described a highly conserved, active DNA demethylation event that takes place in vertebrate embryos during body plan formation and predominantly targets transcriptional enhancers. While we know that this wave of demethylation largely depends on the Tet proteins, there is currently a lack of understanding as to how this process is triggered and which molecular components are playing a role in it. By using latest genome editing technologies (CRISPR/Cas9) in combination with high-throughput DNA sequencing, we aim to answer those important questions and provide a deeper understanding of epigenetic mechanisms required for vertebrate body plan formation and cellular differentiation.
3. Evolution of the DNA methylome
The levels of DNA methylation can vary greatly between and within animal phyla. For example, in insects, genomic DNA methylation levels can range from 0% to 14%. Invertebrates, on an average, display lower global methylation levels than vertebrates, with the majority of 5mC localised to gene bodies of active genes. Such intragenic 5mC has also been observed in highly transcribed genes in mouse ESCs where it is thought to prevent spurious transcription initiation. Unlike invertebrates, vertebrate genomes are characterised by genomic DNA methylation that often reaches 70–80% in the CpG context. We are studying the function, readout, and genomic distribution of DNA methylation in diverse vertebrate and invertebrate species to be able to better understand the function of DNA methylation in human embryonic development and disease.