Epigenetic information is for example stored in the form of modified bases in the genome. The positions and the kind of the base modifications is one factor that determines the identity of the corresponding cell. Setting and erasing of epigenetic imprints is one factor that controls the development process from a zygote over an omnipotent stem cells to finally an adult specialized cell. The underlying biochemical mechanism are largely unknown. I am going to discuss results related to the function and distribution of the new epigenetic bases 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), 5-carboxycytosine (caC), and 5-hydroxymethyluracil.[1] These nucleobases seem to control epigenetic programming of cells. Synthetic routes to these new bases and isotope derivatives will be discussed that enable the preparation of oligonucleotides and allow high end mass spectrometry studies to decipher the biological functions of the new bases.[2] In particular, results from quantitative mass spectrometry, new covalent-capture proteomics mass spectrometry and isotope tracing techniques will be reported.[3] Finally I am dicussing potential präbiotic origins of modified bases[4].

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BRA-STRAP is performing targeted-sequencing of 24 genes commonly included on panel tests for breast cancer predisposition in 30,000 Australian women of all ages across the cancer risk spectrum, affected and unaffected with breast cancer, and their families. Contributing to BRA-STRAP are i) large research cohorts of aging populations and of women above population risk, and ii) the clinical genetics community and women found negative for BRCA1 and BRCA2 mutations following testing in a Familial Cancer Centre over the last 2 decades. BRA-STRAP is also engaged with the broader translational research community and other similarly designed studies set outside of Australia (e.g. BRIDGES and CARRIERS). 

Data on this scale represents the spectrum of genetic variation observed in these genes and exemplifies the opportunities and challenges for realizing precision medicine and precision public health for breast cancer.

Dr Tu Nguyen-Dumont is a cancer geneticist and a bioinformatician. She is a Senior Research Fellow at Monash University, Australia. She obtained her PhD from Claude Bernard University, Lyon, France in 2010. During her undergrad and PhD studies, she trained at the International Agency for Research on Cancer (Lyon). In 2011, she was awarded a Komen Foundation Postdoctoral Fellowship, which allowed her to gain international research experience and move to Melbourne. In 2017, Tu was awarded a Career Development Fellowship by the National Breast Cancer Foundation.

Her research work is directed towards the identification and characterization of cancer susceptibility genes. Her primary area of interest is breast cancer, although she is also involved in the investigation of prostate and childhood cancers susceptibility. Tu applies cutting-edge technologies and computational approaches to conduct advanced genomics research. She has a strong commitment to translation of research and is currently leading research programs aiming at making fundamental -and much required- changes to breast cancer clinical genetics practice, for the benefit of all Australian women at genetic risk of breast cancer.

R-loop structures form co-transcriptionally upon re-invasion of the duplex DNA by the nascent RNA. This causes the formation of an extended RNA:DNA hybrid on the template strand and the looping out of the non-template strand. R-loop structures are the most abundant non-B DNA structures in eukaryotic genomes and have been associated with physiological as well as pathological roles in the context of human disorders. Here, I will provide an update on global R-loop mapping strategies, present a novel single-molecule R-loop footprinting technique and present new mathematical models of R-loop formation that revealed a key role for DNA topology in driving R-loop formation. Ultimately, R-loops are prevalent genomic structures that make important contributions to genome dynamics including by allowing rapid relief from superhelical stress.

The genomes of higher organisms are annotated by chromosomal proteins and histone modifications, which delineate active genes, regulatory elements, and silent regions. This annotation is critical for proper cell type specification, and an ongoing challenge is to decipher the rules that establish and maintain chromatin organization. Our studies of the highly conserved Polycomb group (PcG) epigenetic regulators in Drosophila has led my lab to propose a model in which the Polycomb Repressive Complex 1 (PRC1) and classical co-activators form ‘bivalent’ protein complexes on transcriptionally poised developmental genes.  We speculate that these function as ‘master switches’ that are responsive to the amount of local acetylation or deacetylation activities recruited by cell type-specific DNA binding factors, leading to stable but reversible activation or repression, respectively.  Our model is based on chromatin crosslinking, affinity purification, and mass spectrometry experiments, in which Drosophila PRC1 strongly interacts with classical co-activators, dBRD4 and dMOZ.  We are currently exploring potential parallels in mammalian development.

Biochemical and mechanistic understanding of the H3.3-specific histone chaperone DAXX 

Selected Publications

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Extracellular vesicles (EVs) have emerged as important mediators of intercellular communication due to their ability to transfer bioactive lipids, proteins and different species of RNA into cells. Thus, EVs hold therapeutic potential in their own right and can additionally be harnessed for the delivery of macromolecular drugs.  This presentation will cover the developments in producing, purifying and characterizing EVs. It will also cover the different strategies to engineer producer cells in order to generate EVs harboring selected RNAs or proteins for treatment of inflammatory diseases.

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An important goal in biology is to understand how organs robustly operate as a single system that integrates variable environmental information. I am interested in the gut epithelia as this tissue integrates and transduces information from changing environments such as diet and metabolites from bacteria. While increasing examples show that gut bacteria alter diverse body functions, there is currently a lack of mechanistic understanding of these interactions. Primarily because it has been challenging to identify both the individual bacterial metabolites that drive key phenotypes in the host, and the appropriate experimental systems for testing activity of these molecules.

I am using the nematode C. elegans as a system to identify bacterial pathways driving ecologically and biologically relevant phenotypes that connect metabolites to host physiology. The genetic tractability of C. elegans bacterial diets will allow to experimentally link individual metabolic pathways to modulation of the molecular and cell biology of host tissues, a challenging task in mammalian systems.

In this talk I will present the technical advantages we developed to study these problems. First, a biologically and ecologically relevant phenotype where bacterial metabolites induce altered germline stem cell divisions and sterility in the host. Second, a high-throughput method we adapted based on translating-ribosome affinity purification to profile the effect of a given diet on gene expression in specific tissues, such as the gut or the nervous system. In the long run we want to understand how microbial metabolism influences cell proliferation and neuronal physiology through host signaling pathways.

Neuroblast development usually involves asymmetric cell division and migration, and defects of these processes are implicated in neuronal disorders. My lab studies neuroblast migration and asymmetric division with modern imaging, genetic, and biochemical approaches using the C. elegans Q neuroblast lineage. My talk will address (1) how polarized distribution of  myosin II-based contractility and Arp2/3-dependent actin polymerization on the cell cortex contributes to the asymmetry of daughter cell sizes and fates; and (2) how the MIG-13/LRP12 signaling pathway guides cell migration along the anterior-posterior body axis.