Francis Stewart

Epigenetic regulation and genomic engineering

Previous and current research

Epigenetic regulation in chromatin
Although the complete DNA sequence of an organism encodes the primary information, additional information is added by epigenetic regulation. In eukaryotic chromatin, epigenetic regulation is conveyed by covalent modifications of DNA (DNA methylation) and histone tails (acetylation, phosphorylation, methylation, ubiquitinylation). Much attention worldwide is now focused on the histone tails and the proposition that patterns of covalent modifications serve as an epigenetic code. Our approach to unravelling epigenetic mechanisms and hierarchies is based on complementary uses of the yeast, S. cerevisiae and the mouse as experimental systems. We apply advanced reverse genetic strategies, some of which were developed by us, to analyze select classes of epigenetic regulators in both organisms. In yeast, we are using protein-tagging and mass spectrometry to characterize complexes containing epigenetic regulators. Amongst other complexes that we have identified in the proteomic environment of chromatin, we have recently identified a new histone methyltransferase activity for lysine 4 of histone 3.
In mice, we are studying two candidate histone methyltransferases by knock-out and conditional strategies using Cre/lox, as well applying proteomic approaches to characterize the complexes. A future aspect of our mouse work is directed towards use of ES cell differentiation in culture as a model for epigenetic decisions and stem cell manipulations.

Genomic engineering
We have developed several aspects of genetic engineering technology using site specific and homologous recombination. We aim at more fluent manipulation of mammalian cells, particularly ES cells and in mice. Most recent work involves exploration and implementation of a novel homologous recombination system that we discovered in E.coli phages. This permits fluent engineering of BACs in E.coli, and may offer new routes for directly engineering eukaryotic cells.

Future prospects and goals

Further work on epigenetic regulators in eukaryotes will be accompanied by advanced engineering strategies to examine roles of epigenetic regulation in mammalian development, stem cells, ageing and disease.

About

1986: PhD at the University of N.S.W., Australia 1986-1991: Postdoctoral work at the Deutsches Krebsforschungszentrum, Heidelberg 1991-2001: Group Leader at EMBL, Heidelberg since 2001: Professor of Genomics, TU Dresden

Selected publications

Muyrers, JPP, Zhang, Y and Stewart AF (2001): Recombinogenic Engineering: new optionsfor manipulating DNA. Trends in Biochemical Sciences, 26: 325-331.

Schaft, J, Ashery-Padan, R, van der Hoeven, F, Gruss, P and Stewart AF (2001): Efficient FLP recombination in mouse ES cells and oocytes. Genesis, 31: 6-10.

Pijnappel, WWM, Schaft, D, Roguev, A., Tekotte, H, Shevchenko, A, Wilm, M, Rigaut, G, Séraphin, B, Aasland, R, and Stewart, AF (2001): The S. cerevisiae Set3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev., 15: 2991-3004.

Roguev, A, Schaft, D, Shevchenko, A, Pijnappel, WWM, Wilm, M, Aasland, R and Stewart, AF (2001): S. cerevisiae Set1 complex includes an Ash2-like protein and methylates histone 3 lysine 4. EMBO J., 20: (December).

Muyrers, JPP, Zhang, Y, Buchholz, F and Stewart, AF (2000): RecE/RecT and Reda/Redb initiate double stranded break repair by specifically interacting with their respective partners. Genes and Development, 14: 1971-1982.

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